Diff of the two buildlogs: -- --- b1/build.log 2024-02-01 11:03:15.569043545 +0000 +++ b2/build.log 2024-02-01 11:18:33.289559314 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Mar 5 05:06:07 -12 2025 -I: pbuilder-time-stamp: 1741194367 +I: Current time: Thu Mar 6 07:26:24 +14 2025 +I: pbuilder-time-stamp: 1741195584 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -57,49 +57,81 @@ dpkg-source: info: applying 0028-libtbx-update-test-for-Python-3.11.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2841186/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1270917/tmp/hooks/D01_modify_environment starting +debug: Running on codethink01-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 Mar 5 17:26 /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/1270917/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1270917/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]="2" [2]="15" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.15(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='bookworm' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='a2e389cb0e5541349145514f8a65c096' - 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='2841186' - PS1='# ' - PS2='> ' + INVOCATION_ID=2d59307e1d73416f84fbf320c5cb9008 + 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=1270917 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.bIcwvilM/pbuilderrc_JTCU --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.bIcwvilM/b1 --logfile b1/build.log cctbx_2022.9+ds2+~3.11.2+ds1-6.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.104:3128' + 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.bIcwvilM/pbuilderrc_OuXC --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.bIcwvilM/b2 --logfile b2/build.log cctbx_2022.9+ds2+~3.11.2+ds1-6.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.104:3128 I: uname -a - Linux codethink03-arm64 6.1.0-17-cloud-arm64 #1 SMP Debian 6.1.69-1 (2023-12-30) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-17-cloud-arm64 #1 SMP Debian 6.1.69-1 (2023-12-30) aarch64 GNU/Linux I: ls -l /bin total 7104 -rwxr-xr-x 1 root root 1346480 Apr 23 2023 bash @@ -159,7 +191,7 @@ -rwxr-xr-x 1 root root 68480 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 68392 Jul 28 2023 run-parts -rwxr-xr-x 1 root root 134536 Jan 5 2023 sed - lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash + lrwxrwxrwx 1 root root 9 Mar 5 17:26 sh -> /bin/bash -rwxr-xr-x 1 root root 68432 Sep 20 2022 sleep -rwxr-xr-x 1 root root 134088 Sep 20 2022 stty -rwsr-xr-x 1 root root 133312 Mar 23 2023 su @@ -185,7 +217,7 @@ -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew -I: user script /srv/workspace/pbuilder/2841186/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/1270917/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -767,7 +799,7 @@ Get: 451 http://deb.debian.org/debian bookworm/main arm64 python3-tqdm all 4.64.1-1 [97.7 kB] Get: 452 http://deb.debian.org/debian bookworm/main arm64 python3-wxgtk4.0 arm64 4.2.0+dfsg-3 [6930 kB] Get: 453 http://deb.debian.org/debian bookworm/main arm64 scons all 4.4.0+dfsg-1 [663 kB] -Fetched 259 MB in 4s (59.2 MB/s) +Fetched 259 MB in 1s (219 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libargon2-1: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 ... 18171 files and directories currently installed.) @@ -2215,8 +2247,8 @@ Setting up tzdata (2023c-5+deb12u1) ... Current default time zone: 'Etc/UTC' -Local time is now: Wed Mar 5 17:08:09 UTC 2025. -Universal Time is now: Wed Mar 5 17:08:09 UTC 2025. +Local time is now: Wed Mar 5 17:27:19 UTC 2025. +Universal Time is now: Wed Mar 5 17:27:19 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libdconf1:arm64 (0.40.0-4) ... @@ -2639,7 +2671,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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_2022.9+ds2+~3.11.2+ds1-6_source.changes +I: user script /srv/workspace/pbuilder/1270917/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for bookworm +I: user script /srv/workspace/pbuilder/1270917/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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_2022.9+ds2+~3.11.2+ds1-6_source.changes dpkg-buildpackage: info: source package cctbx dpkg-buildpackage: info: source version 2022.9+ds2+~3.11.2+ds1-6 dpkg-buildpackage: info: source distribution unstable @@ -2815,8 +2851,8 @@ Building wheels for collected packages: dxtbx Building editable for dxtbx (pyproject.toml): started Building editable for dxtbx (pyproject.toml): finished with status 'done' - Created wheel for dxtbx: filename=dxtbx-3.11.2-0.editable-py3-none-any.whl size=6141 sha256=6555d02bbda2b4fb537cdaec689fb789ebcefcac239a33a1797ed2d8fb84a8e9 - Stored in directory: /tmp/pip-ephem-wheel-cache-h8f0nk0j/wheels/c9/65/9f/2b98990eed63492b01400828d96e4dbc5e74502aed74937ddf + Created wheel for dxtbx: filename=dxtbx-3.11.2-0.editable-py3-none-any.whl size=6141 sha256=779a73fad60be6e8404d9cb2710c389422a92d3af5c7c495cc122465af3a8539 + Stored in directory: /tmp/pip-ephem-wheel-cache-0_kplryl/wheels/c9/65/9f/2b98990eed63492b01400828d96e4dbc5e74502aed74937ddf Successfully built dxtbx Installing collected packages: dxtbx Successfully installed dxtbx-3.11.2 @@ -6785,9 +6821,6 @@ g++ -o cctbx/eltbx/xray_scattering/it1992.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/eltbx/xray_scattering/it1992.cpp g++ -o cctbx/eltbx/xray_scattering/wk1995.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/eltbx/xray_scattering/wk1995.cpp g++ -o cctbx/eltbx/xray_scattering/n_gaussian_raw.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/eltbx/xray_scattering/n_gaussian_raw.cpp -g++ -o cctbx/eltbx/xray_scattering/n_gaussian.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/eltbx/xray_scattering/n_gaussian.cpp -g++ -o cctbx/eltbx/fp_fdp.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/eltbx/fp_fdp.cpp -g++ -o cctbx/eltbx/henke.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include cctbx/eltbx/henke.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -6803,14 +6836,17 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +g++ -o cctbx/eltbx/xray_scattering/n_gaussian.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/eltbx/xray_scattering/n_gaussian.cpp +g++ -o cctbx/eltbx/fp_fdp.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/eltbx/fp_fdp.cpp +g++ -o cctbx/eltbx/henke.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include cctbx/eltbx/henke.cpp g++ -o cctbx/eltbx/henke_tables_01_12.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include cctbx/eltbx/henke_tables_01_12.cpp -g++ -o cctbx/eltbx/henke_tables_13_24.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include cctbx/eltbx/henke_tables_13_24.cpp -g++ -o cctbx/eltbx/henke_tables_25_36.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include cctbx/eltbx/henke_tables_25_36.cpp 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++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lm -g++ -o cctbx/eltbx/henke_tables_37_48.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include cctbx/eltbx/henke_tables_37_48.cpp 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-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include cctbx/eltbx/henke_tables_13_24.cpp +g++ -o cctbx/eltbx/henke_tables_25_36.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include cctbx/eltbx/henke_tables_25_36.cpp +g++ -o cctbx/eltbx/henke_tables_37_48.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include cctbx/eltbx/henke_tables_37_48.cpp g++ -o cctbx/eltbx/henke_tables_49_60.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include cctbx/eltbx/henke_tables_49_60.cpp g++ -o cctbx/eltbx/henke_tables_61_72.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include cctbx/eltbx/henke_tables_61_72.cpp g++ -o cctbx/eltbx/henke_tables_73_84.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include cctbx/eltbx/henke_tables_73_84.cpp @@ -6871,12 +6907,12 @@ g++ -o cctbx/uctbx/spoil_optimization.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/uctbx/spoil_optimization.cpp g++ -o cctbx/uctbx/crystal_orientation.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/uctbx/crystal_orientation.cpp g++ -o omptbx/stubs.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/omptbx/stubs.cpp +g++ -o boost_adaptbx/graph/breadth_first_search_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/boost_adaptbx/graph/breadth_first_search_ext.cpp g++ -o lib/libomptbx.so.0.0.1 -shared -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lboost_thread -lboost_system +g++ -o boost_adaptbx/graph/clustering_algorithm_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/boost_adaptbx/graph/clustering_algorithm_ext.cpp 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-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/boost_adaptbx/graph/breadth_first_search_ext.cpp -g++ -o boost_adaptbx/graph/clustering_algorithm_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/boost_adaptbx/graph/clustering_algorithm_ext.cpp g++ -o boost_adaptbx/graph/connected_component_algorithm_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/boost_adaptbx/graph/connected_component_algorithm_ext.cpp g++ -o boost_adaptbx/graph/graph_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/boost_adaptbx/graph/graph_ext.cpp g++ -o boost_adaptbx/graph/graph_structure_comparison_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/boost_adaptbx/graph/graph_structure_comparison_ext.cpp @@ -6904,13 +6940,10 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/object.hpp:9, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/boost_adaptbx/graph/graph_type.hpp:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/boost_adaptbx/graph/graph_ext.cpp:1: + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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( | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -6941,7 +6974,7 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/object.hpp:9, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/boost_adaptbx/graph/graph_type.hpp:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/boost_adaptbx/graph/connected_component_algorithm_ext.cpp:1: + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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( | ^~~~~~~~~~~~~~~~~~~~ @@ -6958,10 +6991,13 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/object.hpp:9, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/boost_adaptbx/graph/graph_type.hpp:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/boost_adaptbx/graph/breadth_first_search_ext.cpp:1: + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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( | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -6975,7 +7011,7 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/object.hpp:9, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/boost_adaptbx/graph/graph_type.hpp:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/boost_adaptbx/graph/maximum_clique_ext.cpp:1: + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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( | ^~~~~~~~~~~~~~~~~~~~ @@ -6992,7 +7028,7 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/object.hpp:9, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/boost_adaptbx/graph/graph_type.hpp:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/boost_adaptbx/graph/metric_ext.cpp:1: + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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( | ^~~~~~~~~~~~~~~~~~~~ @@ -7009,7 +7045,7 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/object.hpp:9, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/boost_adaptbx/graph/graph_type.hpp:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/boost_adaptbx/graph/graph_structure_comparison_ext.cpp:1: + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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( | ^~~~~~~~~~~~~~~~~~~~ @@ -7026,7 +7062,7 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/object.hpp:9, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/boost_adaptbx/graph/graph_type.hpp:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/boost_adaptbx/graph/utility_ext.cpp:1: + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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( | ^~~~~~~~~~~~~~~~~~~~ @@ -7043,7 +7079,7 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/object.hpp:9, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/boost_adaptbx/graph/graph_type.hpp:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/boost_adaptbx/graph/min_cut_max_flow_ext.cpp:1: + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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( | ^~~~~~~~~~~~~~~~~~~~ @@ -7052,6 +7088,7 @@ g++ -o boost_adaptbx/tests/boost_thread_test.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/boost_adaptbx/tests/boost_thread_test.cpp g++ -o boost_adaptbx/tests/python_streambuf_test_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/boost_adaptbx/tests/python_streambuf_test_ext.cpp g++ -o boost_adaptbx/tests/tst_optional_copy.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/boost_adaptbx/tests/tst_optional_copy.cpp +g++ -o boost_adaptbx/tests/tst_optional_copy -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lboost_thread -lboost_system g++ -o boost_adaptbx/tuple_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/boost_adaptbx/tuple_ext.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, @@ -7069,7 +7106,6 @@ /usr/include/boost/timer.hpp:21:1: note: ‘#pragma message: This header is deprecated. Use the facilities in instead.’ 21 | BOOST_HEADER_DEPRECATED( "the facilities in " ) | ^~~~~~~~~~~~~~~~~~~~~~~ -g++ -o boost_adaptbx/tests/tst_optional_copy -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DSWIG_PYTHON_STRICT_BYTE_CHAR -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include/hdf5/serial -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/base/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/cbflib -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cbflib_adaptbx -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cbflib_adaptbx/detectors/boost_python/cbflib_ext.cpp g++ -o cbflib_adaptbx/detectors/buffer_based_service.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include/hdf5/serial -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/base/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/cbflib -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cbflib_adaptbx /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cbflib_adaptbx/detectors/buffer_based_service.cpp g++ -o cbflib_adaptbx/detectors/cbf_adaptor.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include/hdf5/serial -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/base/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/cbflib -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cbflib_adaptbx /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cbflib_adaptbx/detectors/cbf_adaptor.cpp @@ -7104,6 +7140,9 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +g++ -o cctbx/adp_restraints/isotropic_adp_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/adp_restraints/isotropic_adp_bpl.cpp +g++ -o cctbx/adp_restraints/rigid_bond_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/adp_restraints/rigid_bond_bpl.cpp +g++ -o cctbx/adp_restraints/rigu_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/adp_restraints/rigu_bpl.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -7124,9 +7163,6 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -g++ -o cctbx/adp_restraints/isotropic_adp_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/adp_restraints/isotropic_adp_bpl.cpp -g++ -o cctbx/adp_restraints/rigid_bond_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/adp_restraints/rigid_bond_bpl.cpp -g++ -o cctbx/adp_restraints/rigu_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/adp_restraints/rigu_bpl.cpp g++ -o cctbx/adptbx/boost_python/adptbx_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/adptbx/boost_python/adptbx_ext.cpp g++ -o cctbx/adptbx/boost_python/anharmonic_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/adptbx/boost_python/anharmonic_ext.cpp g++ -o cctbx/adptbx/boost_python/hirshfeld.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/adptbx/boost_python/hirshfeld.cpp @@ -7135,12 +7171,8 @@ g++ -o cctbx/array_family/boost_python/flex_miller_index.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/array_family/boost_python/flex_miller_index.cpp g++ -o cctbx/array_family/boost_python/flex_xray_scatterer.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/array_family/boost_python/flex_xray_scatterer.cpp g++ -o cctbx/boost_python/emma_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/boost_python/emma_ext.cpp -g++ -o cctbx/boost_python/french_wilson_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/boost_python/french_wilson_ext.cpp 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++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lm -g++ -o cctbx/boost_python/orientation_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/boost_python/orientation_ext.cpp -g++ -o cctbx/boost_python/statistics_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/boost_python/statistics_ext.cpp -g++ -o cctbx/covariance/boost_python/covariance_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/covariance/boost_python/covariance_ext.cpp -g++ -o cctbx/crystal/asu_clusters_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/crystal/asu_clusters_bpl.cpp +g++ -o cctbx/boost_python/french_wilson_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/boost_python/french_wilson_ext.cpp 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' @@ -7149,6 +7181,10 @@ '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++11 -pthread cctbx/maptbx/blobs_cmd.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lasymmetric_map -liotbx_xplor -lcctbx_sgtbx_asu -lcctbx -lomptbx -lm +g++ -o cctbx/boost_python/orientation_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/boost_python/orientation_ext.cpp +g++ -o cctbx/boost_python/statistics_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/boost_python/statistics_ext.cpp +g++ -o cctbx/covariance/boost_python/covariance_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/covariance/boost_python/covariance_ext.cpp +g++ -o cctbx/crystal/asu_clusters_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/crystal/asu_clusters_bpl.cpp g++ -o cctbx/crystal/close_packing_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/crystal/close_packing_bpl.cpp g++ -o cctbx/crystal/coordination_sequences_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/crystal/coordination_sequences_bpl.cpp g++ -o cctbx/crystal/crystal_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/crystal/crystal_ext.cpp @@ -7157,7 +7193,6 @@ g++ -o cctbx/crystal/neighbors_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/crystal/neighbors_bpl.cpp g++ -o cctbx/crystal/pair_tables_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/crystal/pair_tables_bpl.cpp g++ -o cctbx/crystal/site_cluster_analysis_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/crystal/site_cluster_analysis_bpl.cpp -g++ -o cctbx/crystal/symmetry_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/crystal/symmetry_bpl.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -7178,9 +7213,7 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -g++ -o cctbx/dmtbx/boost_python/dmtbx_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/dmtbx/boost_python/dmtbx_ext.cpp -g++ -o cctbx/dmtbx/boost_python/triplet_generator.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/dmtbx/boost_python/triplet_generator.cpp -g++ -o cctbx/dmtbx/boost_python/triplet_phase_relation.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/dmtbx/boost_python/triplet_phase_relation.cpp +g++ -o cctbx/crystal/symmetry_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/crystal/symmetry_bpl.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -7201,6 +7234,9 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +g++ -o cctbx/dmtbx/boost_python/dmtbx_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/dmtbx/boost_python/dmtbx_ext.cpp +g++ -o cctbx/dmtbx/boost_python/triplet_generator.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/dmtbx/boost_python/triplet_generator.cpp +g++ -o cctbx/dmtbx/boost_python/triplet_phase_relation.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/dmtbx/boost_python/triplet_phase_relation.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -7224,6 +7260,8 @@ g++ -o cctbx/eltbx/boost_python/attenuation_coefficient_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/eltbx/boost_python/attenuation_coefficient_ext.cpp g++ -o cctbx/eltbx/boost_python/chemical_elements_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/eltbx/boost_python/chemical_elements_ext.cpp g++ -o cctbx/eltbx/boost_python/covalent_radii_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/eltbx/boost_python/covalent_radii_ext.cpp +g++ -o cctbx/eltbx/boost_python/fp_fdp_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/eltbx/boost_python/fp_fdp_ext.cpp +g++ -o cctbx/eltbx/boost_python/henke_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/eltbx/boost_python/henke_ext.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -7244,8 +7282,6 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -g++ -o cctbx/eltbx/boost_python/fp_fdp_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/eltbx/boost_python/fp_fdp_ext.cpp -g++ -o cctbx/eltbx/boost_python/henke_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/eltbx/boost_python/henke_ext.cpp g++ -o cctbx/eltbx/boost_python/icsd_radii_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/eltbx/boost_python/icsd_radii_ext.cpp g++ -o cctbx/eltbx/boost_python/neutron_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/eltbx/boost_python/neutron_ext.cpp g++ -o cctbx/eltbx/boost_python/sasaki_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/eltbx/boost_python/sasaki_ext.cpp @@ -7273,17 +7309,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/site_symmetry.h:203:75: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/site_symmetry.h:214:75: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -7295,16 +7320,42 @@ 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/tuple.hpp:10, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/shared_wrapper_pickle.hpp:6, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/bond_bpl.cpp:2: + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/bond_sorted_bpl.cpp:3: /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/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/scatterer.h:5, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/restraints.h:6, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/bond_similarity.h:6, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/bond_similarity_bpl.cpp:12: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/site_symmetry.h:203:75: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/site_symmetry.h:214:75: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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, scitbx::af::trivial_accessor>&, const cctbx::geometry_restraints::bond_similarity_proxy&)’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/bond_similarity.h:108:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] + 108 | for(int i=0;i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] - 100 | for (int i=0; i, scitbx::af::trivial_accessor>&, const cctbx::geometry_restraints::bond_similarity_proxy&)’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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, scitbx::af::trivial_accessor>&, const cctbx::geometry_restraints::bond_similarity_proxy&)’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/bond_similarity.h:108:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] - 108 | 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-2022.9+ds2+~3.11.2+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]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/site_symmetry.h:203:75: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/site_symmetry.h:214:75: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] +In file included from /usr/include/boost/assert.hpp:58, + 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:53, + from /usr/include/boost/optional.hpp:15, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/ref_reductions.h:8, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny.h:5, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/shared_plain.h:31, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/shared.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/shared_wrapper.h:12, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/bond_similarity_bpl.cpp:9: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/bond_similarity_bpl.cpp:55:44: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/wyckoff.h:4, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/sym_equiv_sites.h:5, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/crystal/direct_space_asu.h:4, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/asu_cache.h:4, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/bond.h:5, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/bond_misc.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/bond_bpl.cpp:14: + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/bond_sorted.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/bond_sorted_bpl.cpp:9: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = scitbx::af::tiny, 2>; GetitemReturnValuePolicy = boost::python::return_value_policy; std::string = std::__cxx11::basic_string]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/bond_similarity_bpl.cpp:79:54: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] +In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/site_symmetry.h:6: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/site_symmetry.h:203:75: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/site_symmetry.h:214:75: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -7370,15 +7443,53 @@ 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/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/bond_sorted_bpl.cpp:3: + from /usr/include/boost/python/object.hpp:9, + from /usr/include/boost/python/tuple.hpp:10, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/shared_wrapper_pickle.hpp:6, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/bond_bpl.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/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +g++ -o cctbx/geometry_restraints/geometry_restraints_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/geometry_restraints_ext.cpp +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/crystal/direct_space_asu.h: In instantiation of ‘int cctbx::crystal::direct_space_asu::asu_mappings::find_i_sym(unsigned int, const cctbx::sgtbx::rt_mx&) const [with FloatType = double; IntShiftType = int]’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/crystal/pair_tables.h:643:46: required from ‘bool cctbx::crystal::pair_asu_table::process_pair(unsigned int, unsigned int, const cctbx::sgtbx::rt_mx&) [with FloatType = double; IntShiftType = int]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/crystal/pair_tables.h:543:35: required from ‘cctbx::crystal::pair_asu_table& cctbx::crystal::pair_asu_table::add_pair(const scitbx::af::tiny&) [with FloatType = double; IntShiftType = int]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/bond_sorted.h:16:30: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/crystal/direct_space_asu.h:859:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] + 859 | for(int i_sym=0; i_sym, 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::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-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/dihedral_bpl.cpp:110:17: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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()) { + | ~~~~~~~~~~^~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/site_symmetry.h:6: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ @@ -7401,6 +7512,14 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]’ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/site_symmetry.h:214:75: required from here /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] +In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/scatterer.h:5, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/restraints.h:6, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/chirality.h:5, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/chirality_bpl.cpp:13: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy; PyObject = _object]’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/bond_similarity_bpl.cpp:55:44: required from here + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/dihedral_bpl.cpp:11: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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::dihedral_proxy; GetitemReturnValuePolicy = boost::python::return_internal_reference<>; std::string = std::__cxx11::basic_string]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/dihedral_bpl.cpp:84:65: required from here /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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, 2> >; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy; PyObject = _object]’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = scitbx::af::tiny, 2>; GetitemReturnValuePolicy = boost::python::return_value_policy; std::string = std::__cxx11::basic_string]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/bond_similarity_bpl.cpp:79:54: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] In file included from /usr/include/boost/assert.hpp:58, from /usr/include/boost/move/detail/type_traits.hpp:33, from /usr/include/boost/move/traits.hpp:31, @@ -7436,25 +7550,14 @@ from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/shared_plain.h:31, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/shared.h:4, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/shared_wrapper.h:12, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/chirality_bpl.cpp:11: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/chirality_bpl.cpp:75:60: required from here + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/bond_bpl.cpp:10: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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 = std::map; GetitemReturnValuePolicy = boost::python::return_internal_reference<>; std::string = std::__cxx11::basic_string]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/bond_bpl.cpp:129:23: required from here /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/wyckoff.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/sym_equiv_sites.h:5, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/crystal/direct_space_asu.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/asu_cache.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/bond.h:5, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/bond_sorted.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/bond_sorted_bpl.cpp:9: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ @@ -7466,27 +7569,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]’ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/site_symmetry.h:214:75: required from here /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] -g++ -o cctbx/geometry_restraints/geometry_restraints_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/geometry_restraints_ext.cpp -g++ -o cctbx/geometry_restraints/motif_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/motif_bpl.cpp -In file included from /usr/include/boost/assert.hpp:58, - 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:53, - from /usr/include/boost/optional.hpp:15, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/ref_reductions.h:8, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny.h:5, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/shared_plain.h:31, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/shared.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/shared_wrapper.h:12, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/bond_bpl.cpp:10: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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 = std::map; GetitemReturnValuePolicy = boost::python::return_internal_reference<>; std::string = std::__cxx11::basic_string]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/bond_bpl.cpp:129:23: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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_simple_proxy; GetitemReturnValuePolicy = boost::python::return_internal_reference<>; std::string = std::__cxx11::basic_string]’ @@ -7497,53 +7579,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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_asu_proxy; GetitemReturnValuePolicy = boost::python::return_internal_reference<>; std::string = std::__cxx11::basic_string]’ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/bond_bpl.cpp:340:25: required from here /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] -In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/site_symmetry.h:6: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/site_symmetry.h:203:75: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/site_symmetry.h:214:75: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/crystal/direct_space_asu.h: In instantiation of ‘int cctbx::crystal::direct_space_asu::asu_mappings::find_i_sym(unsigned int, const cctbx::sgtbx::rt_mx&) const [with FloatType = double; IntShiftType = int]’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/crystal/pair_tables.h:643:46: required from ‘bool cctbx::crystal::pair_asu_table::process_pair(unsigned int, unsigned int, const cctbx::sgtbx::rt_mx&) [with FloatType = double; IntShiftType = int]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/crystal/pair_tables.h:543:35: required from ‘cctbx::crystal::pair_asu_table& cctbx::crystal::pair_asu_table::add_pair(const scitbx::af::tiny&) [with FloatType = double; IntShiftType = int]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/bond_sorted.h:16:30: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/crystal/direct_space_asu.h:859:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] - 859 | for(int i_sym=0; i_sym, 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-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/dihedral_bpl.cpp:110:17: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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()) { - | ~~~~~~~~~~^~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/site_symmetry.h:6: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/site_symmetry.h:203:75: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/site_symmetry.h:214:75: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] In file included from /usr/include/boost/assert.hpp:58, from /usr/include/boost/move/detail/type_traits.hpp:33, from /usr/include/boost/move/traits.hpp:31, @@ -7555,16 +7590,16 @@ from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/shared_plain.h:31, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/shared.h:4, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/shared_wrapper.h:12, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/dihedral_bpl.cpp:11: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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::dihedral_proxy; GetitemReturnValuePolicy = boost::python::return_internal_reference<>; std::string = std::__cxx11::basic_string]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/dihedral_bpl.cpp:84:65: required from here + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/chirality_bpl.cpp:11: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/chirality_bpl.cpp:75:60: required from here /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/nonbonded_bpl.cpp g++ -o cctbx/geometry_restraints/nonbonded_sorted_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/nonbonded_sorted_bpl.cpp -g++ -o cctbx/geometry_restraints/parallelity_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/parallelity_bpl.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -7585,16 +7620,6 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/wyckoff.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/sym_equiv_sites.h:5, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/crystal/direct_space_asu.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/asu_cache.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/nonbonded.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/nonbonded_bpl.cpp:11: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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::shared_plain(const size_type&) [with ElementType = scitbx::vec3]’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/shared_plain.h:132:34: warning: ‘’ may be used uninitialized [-Wmaybe-uninitialized] 132 | std::uninitialized_fill_n(begin(), sz, ElementType()); @@ -7617,6 +7642,17 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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/parallelity_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/parallelity_bpl.cpp +In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/wyckoff.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/sym_equiv_sites.h:5, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/crystal/direct_space_asu.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/asu_cache.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/nonbonded.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/nonbonded_bpl.cpp:11: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ @@ -7628,7 +7664,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]’ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/site_symmetry.h:214:75: required from here /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] -g++ -o cctbx/geometry_restraints/planarity_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/planarity_bpl.cpp In file included from /usr/include/boost/assert.hpp:58, from /usr/include/boost/move/detail/type_traits.hpp:33, from /usr/include/boost/move/traits.hpp:31, @@ -7684,25 +7719,7 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy; PyObject = _object]’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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::parallelity_proxy; GetitemReturnValuePolicy = boost::python::return_value_policy; std::string = std::__cxx11::basic_string]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/parallelity_bpl.cpp:82:60: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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/planarity_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/planarity_bpl.cpp In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/site_symmetry.h:6: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ @@ -7723,6 +7740,27 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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; | ~~^~~~~~~~~~~~~~~~~~ +g++ -o cctbx/maptbx/asymmetric_map_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/maptbx/asymmetric_map_ext.cpp +In file included from /usr/include/boost/assert.hpp:58, + 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:53, + from /usr/include/boost/optional.hpp:15, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/ref_reductions.h:8, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny.h:5, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/shared_plain.h:31, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/shared.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/shared_wrapper.h:12, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/parallelity_bpl.cpp:11: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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::parallelity_proxy; GetitemReturnValuePolicy = boost::python::return_value_policy; std::string = std::__cxx11::basic_string]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/parallelity_bpl.cpp:82:60: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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/maptbx/bcr/bcr_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/maptbx/bcr/bcr_ext.cpp In file included from /usr/include/boost/assert.hpp:58, from /usr/include/boost/move/detail/type_traits.hpp:33, from /usr/include/boost/move/traits.hpp:31, @@ -7742,8 +7780,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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/maptbx/asymmetric_map_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/maptbx/asymmetric_map_ext.cpp -g++ -o cctbx/maptbx/bcr/bcr_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/maptbx/bcr/bcr_ext.cpp g++ -o cctbx/maptbx/boost_python/coordinate_transformers.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/maptbx/boost_python/coordinate_transformers.cpp g++ -o cctbx/maptbx/boost_python/grid_indices_around_sites.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/maptbx/boost_python/grid_indices_around_sites.cpp g++ -o cctbx/maptbx/boost_python/grid_tags.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/maptbx/boost_python/grid_tags.cpp @@ -7868,6 +7904,15 @@ g++ -o cctbx/xray/boost_python/fast_gradients.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/boost_python/fast_gradients.cpp In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/scatterer.h:5, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/scattering_type_registry.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/gradients_direct.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/each_hkl_gradients_direct.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/boost_python/each_hkl_gradients_direct.cpp:3: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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::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]’ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/site_symmetry.h:214:75: required from here /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] -In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/scatterer.h:5, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/scattering_type_registry.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/gradients_direct.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/each_hkl_gradients_direct.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/boost_python/each_hkl_gradients_direct.cpp:3: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ @@ -7971,6 +8007,7 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/boost_python/parameter_map.cpp In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/miller/match_indices.h:4, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/miller/lookup_utils.h:11, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/f_model.h:11, @@ -8013,16 +8050,6 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/cctbx/xray/boost_python/f_model_bpl.cpp:174:32: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/f_model.h:732:38: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘scitbx::af::shared_plain >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] - 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-2022.9+ds2+~3.11.2+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]’ @@ -8057,29 +8083,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/cctbx/xray/scatterer.h:5, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/minimization.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/boost_python/minimization.cpp:8: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/site_symmetry.h:203:75: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/site_symmetry.h:214:75: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] -g++ -o cctbx/xray/boost_python/sampling_base.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/boost_python/sampling_base.cpp -g++ -o cctbx/xray/boost_python/scatterer.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/boost_python/scatterer.cpp -g++ -o cctbx/xray/boost_python/scatterer_flags.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/boost_python/scatterer_flags.cpp -g++ -o cctbx/xray/boost_python/scattering_type_registry.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/boost_python/scattering_type_registry.cpp In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/miller/match_indices.h:4, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/miller/lookup_utils.h:11, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/grouped_data.h:14, @@ -8122,6 +8125,26 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/cctbx/xray/boost_python/f_model_bpl.cpp:174:32: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/f_model.h:732:38: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘scitbx::af::shared_plain >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] + 732 | CCTBX_ASSERT( iselection[ii]::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] + 100 | for (int i=0; i::bic() [with FloatType = double]’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/boost_python/grouped_data.cpp:68:29: required from here /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/grouped_data.h:257:30: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘scitbx::af::shared_plain >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] @@ -8138,6 +8161,17 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/grouped_data.h:213:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 213 | for (int ii=1;ii::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-2022.9+ds2+~3.11.2+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]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/site_symmetry.h:203:75: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/site_symmetry.h:214:75: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/grouped_data.h:231:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 231 | for (int ii=1;ii::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 167 | for (int ii=0; ii + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ +g++ -o cctbx/xray/boost_python/scattering_type_registry.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/boost_python/scattering_type_registry.cpp In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/scatterer.h:5, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/boost_python/parameter_map.cpp:10: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ @@ -8229,7 +8256,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]’ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/site_symmetry.h:214:75: required from here /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] -g++ -o cctbx/xray/boost_python/sigmaa.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/boost_python/sigmaa.cpp In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/boost_python/parameter_map.cpp:9: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/parameter_map.h: In instantiation of ‘void cctbx::xray::parameter_map::init_scatterer_part(const scitbx::af::const_ref&) [with XRayScattererType = cctbx::xray::scatterer<>]’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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<>]’ @@ -8247,12 +8273,30 @@ 61 | for(int i_sc=0; i_sc < scatterers.size(); ++i_sc) { | ~~~~~^~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/scatterer.h:5, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/scattering_type_registry.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/sampling_base.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/boost_python/sampling_base.cpp:3: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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::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-2022.9+ds2+~3.11.2+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]’ @@ -8264,28 +8308,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]’ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/site_symmetry.h:214:75: required from here /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] -In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/scatterer.h:5, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/scattering_type_registry.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/sampling_base.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/boost_python/sampling_base.cpp:3: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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::small_plain(const OtherElementType*, const OtherElementType*) [with OtherElementType = float; ElementType = double; long unsigned int N = 10]’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/scattering_type_registry.h:192:40: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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(); - | ~~^~~~~~~~~~~~~~ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/cctbx/xray/boost_python/scatterer.cpp:349:54: required from here /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] @@ -8305,19 +8327,20 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]’ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/site_symmetry.h:214:75: required from here /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] -In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/scatterer.h:5, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/boost_python/scatterer_flags.cpp:7: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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::small_plain(const OtherElementType*, const OtherElementType*) [with OtherElementType = float; ElementType = double; long unsigned int N = 10]’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/scattering_type_registry.h:192:40: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/site_symmetry.h:6: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ @@ -8343,6 +8366,12 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/cctbx/xray/scatterer.h:5, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/boost_python/scatterer_flags.cpp:7: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ @@ -8354,6 +8383,25 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]’ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/site_symmetry.h:214:75: required from here /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] +In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/scatterer.h:5, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/scattering_type_registry.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/boost_python/scattering_type_registry.cpp:3: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy; PyObject = _object]’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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::xray::scatterer_flags; GetitemReturnValuePolicy = boost::python::return_internal_reference<>; std::string = std::__cxx11::basic_string]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/boost_python/scatterer_flags.cpp:142:44: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/cctbx/xray/boost_python/scattering_type_registry.cpp: At global scope: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 @@ -8377,18 +8425,6 @@ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ -In file included from /usr/include/boost/assert.hpp:58, - from /usr/include/boost/smart_ptr/shared_array.hpp:21, - from /usr/include/boost/shared_array.hpp:17, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/tensor_rank_2.h:9, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/site_symmetry.h:5: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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::xray::scatterer_flags; GetitemReturnValuePolicy = boost::python::return_internal_reference<>; std::string = std::__cxx11::basic_string]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/boost_python/scatterer_flags.cpp:142:44: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/site_symmetry.h:6: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ @@ -8400,6 +8436,7 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]’ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/site_symmetry.h:214:75: required from here /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] +g++ -o cctbx/xray/boost_python/structure_factors_direct.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/boost_python/structure_factors_direct.cpp In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/small.h:4, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/uctbx.h:11, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/change_of_basis_op.h:6, @@ -8414,7 +8451,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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/structure_factors_direct.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/boost_python/structure_factors_direct.cpp g++ -o cctbx/xray/boost_python/structure_factors_simple.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/boost_python/structure_factors_simple.cpp g++ -o cctbx/xray/boost_python/targets.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/boost_python/targets.cpp In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/scatterer.h:5, @@ -8424,6 +8460,7 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ @@ -8435,7 +8472,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]’ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/site_symmetry.h:214:75: required from here /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] -g++ -o cctbx/xray/boost_python/twin_components.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/boost_python/twin_components.cpp g++ -o cctbx/xray/boost_python/twin_targets.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/boost_python/twin_targets.cpp g++ -o cctbx/xray/boost_python/xray_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/boost_python/xray_ext.cpp g++ -o cctbx/xray/observations/boost_python/observations.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/observations/boost_python/observations.cpp @@ -8457,6 +8493,18 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/site_symmetry.h:203:75: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/site_symmetry.h:214:75: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/site_symmetry.h:6: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ @@ -8482,13 +8530,21 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/site_symmetry.h:6: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/site_symmetry.h:203:75: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/small.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/uctbx.h:11, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/change_of_basis_op.h:6, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/tr_group.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/space_group.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/site_constraints.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/site_symmetry.h:4: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/scattering_type_registry.h:192:40: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 chiltbx/handle_test -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -pthread chiltbx/handle_test.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lboost_thread -lboost_system In file included from /usr/include/boost/assert.hpp:58, from /usr/include/boost/smart_ptr/shared_ptr.hpp:24, from /usr/include/boost/shared_ptr.hpp:17, @@ -8508,33 +8564,33 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/site_symmetry.h:214:75: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/boost_python/container_conversions.h:270:7: required from ‘scitbx::boost_python::container_conversions::tuple_mapping::tuple_mapping() [with ContainerType = scitbx::af::shared*>; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy]’ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/boost_python/container_conversions.h:300:7: required from ‘scitbx::boost_python::container_conversions::tuple_mapping_variable_capacity::tuple_mapping_variable_capacity() [with ContainerType = scitbx::af::shared*>]’ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/boost_python/twin_components.cpp:92:78: required from here /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] -In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/small.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/uctbx.h:11, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/change_of_basis_op.h:6, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/tr_group.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/space_group.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/site_constraints.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/site_symmetry.h:4: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/scattering_type_registry.h:192:40: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 chiltbx/handle_test.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/chiltbx/handle_test.cpp -g++ -o chiltbx/handle_test -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -pthread chiltbx/handle_test.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lboost_thread -lboost_system g++ -o cma_es/cma/cmaes.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cma_es/cma/cmaes.cpp +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + 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/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/targets/shelxl_wght_ls_bpl.cpp:22: +/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/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/miller/match_indices.h:4, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/miller/lookup_utils.h:11, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/twin_targets.h:14, @@ -8577,6 +8633,43 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem/io.hpp:8, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem/close_chain.hpp:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem/common.hpp:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem/read.hpp:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem/major_types.hpp:6, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem.hpp:10, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/targets/shelxl_wght_ls.hpp:1, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/targets/shelxl_wght_ls_bpl.cpp:23: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/fable/fem/common.hpp: In member function ‘void fem::common::getarg(int, fem::str_ref) const’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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()) { + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem/utils/string_to_double_fmt.hpp:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem/read.hpp:9: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem/utils/string_to_double.hpp: In member function ‘void fem::utils::string_to_double::convert(fem::utils::simple_istream&, unsigned int, int)’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem/utils/string_to_double.hpp:115:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare] + 115 | if (dexp <= ad_hoc_limits::max_digit_count) { + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem/read.hpp: In member function ‘double fem::read_loop::read_fmt_double()’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem/read.hpp:652:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] + 652 | if (iw+1 != ed.size()) { + | ~~~~~^~~~~~~~~~~~ +In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem/variant.hpp:5, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem/major_types.hpp:7: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem/utils/equivalence.hpp: In member function ‘void fem::utils::equivalence::array_alignment::infer_diffs0_from_diff_matrix()’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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) { + | ~~~~~~~^~~~~ +In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem/major_types.hpp:8: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem/write.hpp: In destructor ‘fem::write_loop::~write_loop()’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/cctbx/xray/twin_targets.h: In instantiation of ‘scitbx::af::shared cctbx::xray::twin_targets::twin_completion::get_free_model_selection(scitbx::af::const_ref >, const scitbx::af::const_ref&) [with FloatType = double]’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/boost_python/twin_targets.cpp:42:50: required from here /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/twin_targets.h:128:31: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘scitbx::af::const_ref::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] @@ -8763,63 +8856,7 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/twin_targets.h:948:17: note: in expansion of macro ‘CCTBX_ASSERT’ 948 | CCTBX_ASSERT(f_model.size() > loc_twin_calc); // XXX trap for long standing seg. fault bug | ^~~~~~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - 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/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/targets/shelxl_wght_ls_bpl.cpp:22: -/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/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem/io.hpp:8, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem/close_chain.hpp:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem/common.hpp:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem/read.hpp:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem/major_types.hpp:6, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem.hpp:10, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/targets/shelxl_wght_ls.hpp:1, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/targets/shelxl_wght_ls_bpl.cpp:23: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/fable/fem/common.hpp: In member function ‘void fem::common::getarg(int, fem::str_ref) const’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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()) { - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem/utils/string_to_double_fmt.hpp:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem/read.hpp:9: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem/utils/string_to_double.hpp: In member function ‘void fem::utils::string_to_double::convert(fem::utils::simple_istream&, unsigned int, int)’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem/utils/string_to_double.hpp:115:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare] - 115 | if (dexp <= ad_hoc_limits::max_digit_count) { - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem/read.hpp: In member function ‘double fem::read_loop::read_fmt_double()’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem/read.hpp:652:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] - 652 | if (iw+1 != ed.size()) { - | ~~~~~^~~~~~~~~~~~ -In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem/variant.hpp:5, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem/major_types.hpp:7: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem/utils/equivalence.hpp: In member function ‘void fem::utils::equivalence::array_alignment::infer_diffs0_from_diff_matrix()’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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) { - | ~~~~~~~^~~~~ -In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem/major_types.hpp:8: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem/write.hpp: In destructor ‘fem::write_loop::~write_loop()’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 cma_es/cma_es_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cma_es/cma_es_ext.cpp /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/twin_targets.h: In instantiation of ‘cctbx::xray::twin_targets::hemihedral_r_values::hemihedral_r_values(const scitbx::af::const_ref >&, const scitbx::af::const_ref >&, const cctbx::sgtbx::space_group&, const bool&, const scitbx::mat3&) [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) [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&>; Value = cctbx::xray::twin_targets::hemihedral_r_values; PyObject = _object]’ /usr/include/boost/python/object/make_holder.hpp:94:18: required from ‘static void boost::python::objects::make_holder<5>::apply::execute(PyObject*, t0, t1, t2, t3, t4) [with Holder = boost::python::objects::value_holder >; ArgList = boost::mpl::vector5 >&, const scitbx::af::const_ref >&, const cctbx::sgtbx::space_group&, const bool&, const scitbx::mat3&>; PyObject = _object; t0 = const scitbx::af::const_ref >&; t1 = const scitbx::af::const_ref >&; t2 = const cctbx::sgtbx::space_group&; t3 = const bool&; t4 = const scitbx::mat3&]’ @@ -8850,18 +8887,18 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -8952,6 +8988,9 @@ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ g++ -o dxtbx/src/dxtbx/model/boost_python/beam.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_CBF -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/base/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -I/usr/include/cbflib -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cbflib_adaptbx -I/usr/include/python3.11 -I/usr/include/hdf5/serial /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/beam.cc +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/format/boost_python/cbf_read_buffer.cpp:11:1: warning: ‘typedef’ was ignored in this declaration + 11 | typedef struct cbf_handle_struct; + | ^~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -8965,16 +9004,13 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/format/boost_python/cbf_read_buffer.cpp:6: + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/format/boost_python/nexus_ext.cc:11: /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/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/format/boost_python/cbf_read_buffer.cpp:11:1: warning: ‘typedef’ was ignored in this declaration - 11 | typedef struct cbf_handle_struct; - | ^~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -8988,27 +9024,13 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/format/boost_python/nexus_ext.cc:11: + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc:11: /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( | ^~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc: In instantiation of ‘boost::shared_ptr > dxtbx::format::boost_python::make_image_from_tuple(boost::python::tuple) [with T = bool]’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc:127:40: required from ‘void dxtbx::format::boost_python::image_wrapper(const char*) [with T = bool]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc:143:24: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc:53:31: 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] - 53 | for (std::size_t i = 0; i < boost::python::len(data); ++i) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc: In instantiation of ‘boost::shared_ptr > dxtbx::format::boost_python::make_image_from_tuple(boost::python::tuple) [with T = int]’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc:127:40: required from ‘void dxtbx::format::boost_python::image_wrapper(const char*) [with T = int]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc:144:23: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc:53:31: 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] -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc: In instantiation of ‘boost::shared_ptr > dxtbx::format::boost_python::make_image_from_tuple(boost::python::tuple) [with T = double]’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc:127:40: required from ‘void dxtbx::format::boost_python::image_wrapper(const char*) [with T = double]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc:145:26: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc:53:31: 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] In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -9029,6 +9051,21 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +g++ -o dxtbx/src/dxtbx/model/boost_python/crystal.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_CBF -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/base/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -I/usr/include/cbflib -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cbflib_adaptbx -I/usr/include/python3.11 -I/usr/include/hdf5/serial /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/crystal.cc +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc: In instantiation of ‘boost::shared_ptr > dxtbx::format::boost_python::make_image_from_tuple(boost::python::tuple) [with T = bool]’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc:127:40: required from ‘void dxtbx::format::boost_python::image_wrapper(const char*) [with T = bool]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc:143:24: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc:53:31: 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] + 53 | for (std::size_t i = 0; i < boost::python::len(data); ++i) { + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc: In instantiation of ‘boost::shared_ptr > dxtbx::format::boost_python::make_image_from_tuple(boost::python::tuple) [with T = int]’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc:127:40: required from ‘void dxtbx::format::boost_python::image_wrapper(const char*) [with T = int]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc:144:23: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc:53:31: 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] +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc: In instantiation of ‘boost::shared_ptr > dxtbx::format::boost_python::make_image_from_tuple(boost::python::tuple) [with T = double]’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc:127:40: required from ‘void dxtbx::format::boost_python::image_wrapper(const char*) [with T = double]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc:145:26: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc:53:31: 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] /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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>]’ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc:136:18: required from ‘void dxtbx::format::boost_python::image_wrapper(const char*) [with T = bool]’ @@ -9046,15 +9083,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc:136:18: required from ‘void dxtbx::format::boost_python::image_wrapper(const char*) [with T = double]’ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc:145:26: required from here /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc:100:33: 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] -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:220:31: 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 > >}; PyObject = _object]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:227:36: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:62:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 62 | for (int i = 0; i < flex.accessor().nd(); ++i) { - | ~~^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:64:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 64 | for (int j = i + 1; j < flex.accessor().nd(); ++j) { - | ~~^~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/panel.h:22, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/detector.h:27, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/imageset.h:24, @@ -9079,9 +9107,8 @@ 449 | if (i >= dx_.accessor()[1]) i = dx_.accessor()[1] - 1; /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:220:31: 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 > >}; PyObject = _object]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:222:32: 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 > >}; PyObject = _object]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:220:31: 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 > >}; PyObject = _object]’ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:227:36: required from here /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:62:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 62 | for (int i = 0; i < flex.accessor().nd(); ++i) { @@ -9112,6 +9139,23 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/scan.h:39:5: warning: when initialized here [-Wreorder] 39 | Scan() | ^~~~ +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + 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/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/masking/boost_python/ext.cc: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( + | ^~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/error.h:16, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/ref.h:4, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny_plain.h:4, @@ -9138,6 +9182,9 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/scan.h:100:7: note: in expansion of macro ‘DXTBX_ASSERT’ 100 | DXTBX_ASSERT(epochs_.size() == num_images_); | ^~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/scan.h: In member function ‘void dxtbx::model::Scan::set_exposure_times(scitbx::af::shared)’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/scan.h:231:42: warning: comparison of integer expressions of different signedness: ‘scitbx::af::shared_plain::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 231 | DXTBX_ASSERT(exposure_times.size() == num_images_); @@ -9158,6 +9205,16 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/scan.h:237:7: note: in expansion of macro ‘DXTBX_ASSERT’ 237 | DXTBX_ASSERT(epochs.size() == num_images_); | ^~~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:220:31: 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 > >}; PyObject = _object]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:222:32: 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 > >}; PyObject = _object]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:227:36: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:62:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 62 | for (int i = 0; i < flex.accessor().nd(); ++i) { + | ~~^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:64:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 64 | for (int j = i + 1; j < flex.accessor().nd(); ++j) { + | ~~^~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/geometry/geometry.hpp: At global scope: /usr/include/boost/geometry/geometry.hpp:27:1: note: ‘#pragma message: CAUTION: Boost.Geometry in Boost 1.73 deprecates support for C++03 and will require C++14 from Boost 1.75 onwards.’ 27 | BOOST_PRAGMA_MESSAGE("CAUTION: Boost.Geometry in Boost 1.73 deprecates support for C++03 and will require C++14 from Boost 1.75 onwards.") @@ -9175,7 +9232,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:64:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 64 | for (int j = i + 1; j < flex.accessor().nd(); ++j) { | ~~^~~~~~~~~~~~~~~~~~~~~~ -g++ -o dxtbx/src/dxtbx/model/boost_python/crystal.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_CBF -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/base/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -I/usr/include/cbflib -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cbflib_adaptbx -I/usr/include/python3.11 -I/usr/include/hdf5/serial /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/crystal.cc /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:222:32: 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 > >}; PyObject = _object]’ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:222:32: 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 > >}; PyObject = _object]’ @@ -9186,6 +9242,27 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:64:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 64 | for (int j = i + 1; j < flex.accessor().nd(); ++j) { | ~~^~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/panel.h:22, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/masking/masking.h:17, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/masking/boost_python/ext.cc:4: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:222:32: 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 > >}; PyObject = _object]’ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:222:32: 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 > >}; PyObject = _object]’ @@ -9196,6 +9273,40 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:64:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 64 | for (int j = i + 1; j < flex.accessor().nd(); ++j) { | ~~^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/panel.h:368:36: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 368 | for (std::size_t y = y0; y < y1; ++y) { + | ~~^~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/panel.h:369:38: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 369 | for (std::size_t x = x0; x < x1; ++x) { + | ~~^~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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) { + | ~~^~~~ +/usr/include/boost/geometry/geometry.hpp: At global scope: +/usr/include/boost/geometry/geometry.hpp:27:1: note: ‘#pragma message: CAUTION: Boost.Geometry in Boost 1.73 deprecates support for C++03 and will require C++14 from Boost 1.75 onwards.’ + 27 | BOOST_PRAGMA_MESSAGE("CAUTION: Boost.Geometry in Boost 1.73 deprecates support for C++03 and will require C++14 from Boost 1.75 onwards.") + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/geometry/geometry.hpp:28:1: note: ‘#pragma message: CAUTION: Define BOOST_GEOMETRY_DISABLE_DEPRECATED_03_WARNING to suppress this message.’ + 28 | BOOST_PRAGMA_MESSAGE("CAUTION: Define BOOST_GEOMETRY_DISABLE_DEPRECATED_03_WARNING to suppress this message.") + | ^~~~~~~~~~~~~~~~~~~~ +g++ -o dxtbx/src/dxtbx/model/boost_python/detector.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_CBF -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/base/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -I/usr/include/cbflib -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cbflib_adaptbx -I/usr/include/python3.11 -I/usr/include/hdf5/serial /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/detector.cc +/usr/include/boost/detail/no_exceptions_support.hpp:17:1: note: ‘#pragma message: This header is deprecated. Use instead.’ + 17 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:222:32: 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 > >}; PyObject = _object]’ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:222:32: 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 > >}; PyObject = _object]’ @@ -9236,9 +9347,7 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:64:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 64 | for (int j = i + 1; j < flex.accessor().nd(); ++j) { | ~~^~~~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/no_exceptions_support.hpp:17:1: note: ‘#pragma message: This header is deprecated. Use instead.’ - 17 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ +g++ -o dxtbx/src/dxtbx/model/boost_python/experiment.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_CBF -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/base/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -I/usr/include/cbflib -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cbflib_adaptbx -I/usr/include/python3.11 -I/usr/include/hdf5/serial /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/experiment.cc /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc: In instantiation of ‘pybind11::buffer_info get_buffer_specific(grid) [with T = float; grid = scitbx::af::versa >]’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:222:32: 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 > >}; PyObject = _object]’ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:222:32: 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 > >}; PyObject = _object]’ @@ -9335,8 +9444,9 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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) { | ~~^~~~ -g++ -o dxtbx/src/dxtbx/model/boost_python/detector.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_CBF -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/base/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -I/usr/include/cbflib -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cbflib_adaptbx -I/usr/include/python3.11 -I/usr/include/hdf5/serial /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/detector.cc -g++ -o dxtbx/src/dxtbx/model/boost_python/experiment.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_CBF -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/base/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -I/usr/include/cbflib -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cbflib_adaptbx -I/usr/include/python3.11 -I/usr/include/hdf5/serial /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/experiment.cc +/usr/include/boost/detail/no_exceptions_support.hpp:17:1: note: ‘#pragma message: This header is deprecated. Use instead.’ + 17 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/imageset.h: In member function ‘dxtbx::format::ImageBuffer dxtbx::ImageSet::get_raw_data(std::size_t)’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/imageset.h:646:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 646 | if (data_cache_.index == index) { @@ -9375,6 +9485,23 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/imageset.h:1397:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1397 | if (scan->get_num_images() != size()) { | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + 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/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/beam.cc:11: +/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( + | ^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/imageset.h:1413:41: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1413 | DXTBX_ASSERT(scan->get_num_images() == size()); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ @@ -9384,6 +9511,9 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/imageset.h:1413:5: note: in expansion of macro ‘DXTBX_ASSERT’ 1413 | DXTBX_ASSERT(scan->get_num_images() == size()); | ^~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/imageset.h:467:56: required from here /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/imageset.h:500:31: 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] @@ -9427,54 +9557,7 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/boost_python/imageset_ext.cc:236:33: 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] 236 | for (std::size_t i = 0; i < boost::python::len(indices); ++i) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - 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/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/masking/boost_python/ext.cc: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/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - 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/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/beam.cc:11: -/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/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/panel.h:22, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/masking/masking.h:17, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/masking/boost_python/ext.cc:4: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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; +g++ -o dxtbx/src/dxtbx/model/boost_python/experiment_list.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_CBF -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/base/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -I/usr/include/cbflib -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cbflib_adaptbx -I/usr/include/python3.11 -I/usr/include/hdf5/serial /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/experiment_list.cc In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/panel.h:22, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/detector.h:27, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/to_from_dict.h:18, @@ -9484,6 +9567,7 @@ 288 | if (i >= dx_.accessor()[1]) i = dx_.accessor()[1] - 1; /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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; +g++ -o dxtbx/src/dxtbx/model/boost_python/goniometer.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_CBF -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/base/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -I/usr/include/cbflib -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cbflib_adaptbx -I/usr/include/python3.11 -I/usr/include/hdf5/serial /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/goniometer.cc /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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; @@ -9506,49 +9590,26 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/panel.h:369:38: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 369 | for (std::size_t x = x0; x < x1; ++x) { | ~~^~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/panel.h:368:36: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 368 | for (std::size_t y = y0; y < y1; ++y) { - | ~~^~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/panel.h:369:38: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 369 | for (std::size_t x = x0; x < x1; ++x) { - | ~~^~~~ -/usr/include/boost/geometry/geometry.hpp: At global scope: -/usr/include/boost/geometry/geometry.hpp:27:1: note: ‘#pragma message: CAUTION: Boost.Geometry in Boost 1.73 deprecates support for C++03 and will require C++14 from Boost 1.75 onwards.’ - 27 | BOOST_PRAGMA_MESSAGE("CAUTION: Boost.Geometry in Boost 1.73 deprecates support for C++03 and will require C++14 from Boost 1.75 onwards.") - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/geometry/geometry.hpp:28:1: note: ‘#pragma message: CAUTION: Define BOOST_GEOMETRY_DISABLE_DEPRECATED_03_WARNING to suppress this message.’ - 28 | BOOST_PRAGMA_MESSAGE("CAUTION: Define BOOST_GEOMETRY_DISABLE_DEPRECATED_03_WARNING to suppress this message.") +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + 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/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/crystal.cc:11: +/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/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/scan.h:22, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/to_from_dict.h:20: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/scan_helpers.h: In function ‘scitbx::af::shared dxtbx::model::get_mod2pi_angles_in_range(scitbx::vec2, double)’: @@ -9611,27 +9672,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/scan.h:237:7: note: in expansion of macro ‘DXTBX_ASSERT’ 237 | DXTBX_ASSERT(epochs.size() == num_images_); | ^~~~~~~~~~~~ -g++ -o dxtbx/src/dxtbx/model/boost_python/experiment_list.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_CBF -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/base/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -I/usr/include/cbflib -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cbflib_adaptbx -I/usr/include/python3.11 -I/usr/include/hdf5/serial /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/experiment_list.cc -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - 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/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/crystal.cc:11: -/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/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/beam.cc: In function ‘void dxtbx::model::boost_python::Beam_set_s0_at_scan_points_from_tuple(dxtbx::model::Beam&, boost::python::tuple)’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/beam.cc:161:31: 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] 161 | for (std::size_t i = 0; i < boost::python::len(l); ++i) { @@ -9640,7 +9680,19 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/beam.cc:170:31: 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] 170 | for (std::size_t i = 0; i < boost::python::len(l); ++i) { | ~~^~~~~~~~~~~~~~~~~~~~~~~ -g++ -o dxtbx/src/dxtbx/model/boost_python/goniometer.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_CBF -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/base/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -I/usr/include/cbflib -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cbflib_adaptbx -I/usr/include/python3.11 -I/usr/include/hdf5/serial /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/goniometer.cc +g++ -o dxtbx/src/dxtbx/model/boost_python/kappa_goniometer.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_CBF -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/base/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -I/usr/include/cbflib -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cbflib_adaptbx -I/usr/include/python3.11 -I/usr/include/hdf5/serial /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/kappa_goniometer.cc +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/crystal.cc:118:31: 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] + 118 | for (std::size_t i = 0; i < boost::python::len(l); ++i) { + | ~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/crystal.cc:128:31: 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] + 128 | for (std::size_t i = 0; i < boost::python::len(l); ++i) { + | ~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/crystal.cc:140:31: 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] + 140 | for (std::size_t i = 0; i < boost::python::len(obj); ++i) { + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/assert.hpp:58, from /usr/include/boost/variant/detail/forced_return.hpp:17, from /usr/include/boost/variant/variant.hpp:29, @@ -9659,18 +9711,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = dxtbx::model::Beam; 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-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/beam.cc:304:56: required from here /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/crystal.cc:118:31: 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] - 118 | for (std::size_t i = 0; i < boost::python::len(l); ++i) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/crystal.cc:128:31: 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] - 128 | for (std::size_t i = 0; i < boost::python::len(l); ++i) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/crystal.cc:140:31: 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] - 140 | for (std::size_t i = 0; i < boost::python::len(obj); ++i) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_wrapper.h:18, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/beam.cc:18: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/slice.h: In instantiation of ‘scitbx::af::versa > scitbx::af::copy_slice(const const_ref >&, small) [with T = dxtbx::model::Beam]’: @@ -9697,10 +9737,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/beam.cc:304:56: required from here /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 dxtbx/src/dxtbx/model/boost_python/kappa_goniometer.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_CBF -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/base/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -I/usr/include/cbflib -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cbflib_adaptbx -I/usr/include/python3.11 -I/usr/include/hdf5/serial /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/kappa_goniometer.cc -/usr/include/boost/detail/no_exceptions_support.hpp:17:1: note: ‘#pragma message: This header is deprecated. Use instead.’ - 17 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -9864,46 +9900,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/panel.h:369:38: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 369 | for (std::size_t x = x0; x < x1; ++x) { | ~~^~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/detector.cc: In function ‘void dxtbx::model::boost_python::node_from_dict(boost::python::dict, dxtbx::model::Detector::Node*, boost::python::list, scitbx::af::ref)’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/detector.cc:86:32: 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] - 86 | DXTBX_ASSERT(used.size() == boost::python::len(panels)); - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/detector.cc:86:7: note: in expansion of macro ‘DXTBX_ASSERT’ - 86 | DXTBX_ASSERT(used.size() == boost::python::len(panels)); - | ^~~~~~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/detector.cc:87:24: 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] - 87 | DXTBX_ASSERT(idx < boost::python::len(panels)); - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/detector.cc:87:7: note: in expansion of macro ‘DXTBX_ASSERT’ - 87 | DXTBX_ASSERT(idx < boost::python::len(panels)); - | ^~~~~~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/detector.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(obj["children"]); ++i) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/detector.cc: In function ‘dxtbx::model::Detector* dxtbx::model::boost_python::detector_from_dict(dxtbx::model::Detector*, boost::python::dict)’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/detector.cc:134:33: 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] - 134 | for (std::size_t i = 0; i < boost::python::len(hierarchy["children"]); ++i) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/detector.cc:144:33: 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] - 144 | for (std::size_t i = 0; i < boost::python::len(panels); ++i) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/detector.cc: In function ‘dxtbx::model::Detector* dxtbx::model::boost_python::detector_from_dict(dxtbx::model::Detector*, boost::python::dict, const dxtbx::format::Image&, const dxtbx::format::Image&)’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/detector.cc:168:33: 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] - 168 | for (std::size_t i = 0; i < boost::python::len(hierarchy["children"]); ++i) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/detector.cc:178:33: 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] - 178 | for (std::size_t i = 0; i < boost::python::len(panels); ++i) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/detector.cc: In static member function ‘static void dxtbx::model::boost_python::DetectorPickleSuite::copy_node(dxtbx::model::Detector::Node::pointer, boost::python::dict, boost::python::list)’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/detector.cc:250:33: 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] - 250 | for (std::size_t i = 0; i < boost::python::len(node["children"]); ++i) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/scan.h:22, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/experiment.h:25: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/scan_helpers.h: In function ‘scitbx::af::shared dxtbx::model::get_mod2pi_angles_in_range(scitbx::vec2, double)’: @@ -9985,6 +9981,66 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + 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/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/goniometer.cc:11: +/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/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/detector.cc: In function ‘void dxtbx::model::boost_python::node_from_dict(boost::python::dict, dxtbx::model::Detector::Node*, boost::python::list, scitbx::af::ref)’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/detector.cc:86:32: 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] + 86 | DXTBX_ASSERT(used.size() == boost::python::len(panels)); + | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/detector.cc:86:7: note: in expansion of macro ‘DXTBX_ASSERT’ + 86 | DXTBX_ASSERT(used.size() == boost::python::len(panels)); + | ^~~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/detector.cc:87:24: 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] + 87 | DXTBX_ASSERT(idx < boost::python::len(panels)); + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/detector.cc:87:7: note: in expansion of macro ‘DXTBX_ASSERT’ + 87 | DXTBX_ASSERT(idx < boost::python::len(panels)); + | ^~~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/detector.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(obj["children"]); ++i) { + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/detector.cc: In function ‘dxtbx::model::Detector* dxtbx::model::boost_python::detector_from_dict(dxtbx::model::Detector*, boost::python::dict)’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/detector.cc:134:33: 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] + 134 | for (std::size_t i = 0; i < boost::python::len(hierarchy["children"]); ++i) { + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/detector.cc:144:33: 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] + 144 | for (std::size_t i = 0; i < boost::python::len(panels); ++i) { + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/detector.cc: In function ‘dxtbx::model::Detector* dxtbx::model::boost_python::detector_from_dict(dxtbx::model::Detector*, boost::python::dict, const dxtbx::format::Image&, const dxtbx::format::Image&)’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/detector.cc:168:33: 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] + 168 | for (std::size_t i = 0; i < boost::python::len(hierarchy["children"]); ++i) { + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/detector.cc:178:33: 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] + 178 | for (std::size_t i = 0; i < boost::python::len(panels); ++i) { + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/detector.cc: In static member function ‘static void dxtbx::model::boost_python::DetectorPickleSuite::copy_node(dxtbx::model::Detector::Node::pointer, boost::python::dict, boost::python::list)’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/detector.cc:250:33: 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] + 250 | for (std::size_t i = 0; i < boost::python::len(node["children"]); ++i) { + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/panel.h:22, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/detector.h:27, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/experiment.h:23, @@ -10017,6 +10073,43 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/panel.h:369:38: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 369 | for (std::size_t x = x0; x < x1; ++x) { | ~~^~~~ +In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/panel.h:22, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/detector.h:27, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/to_from_dict.h:18, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/goniometer.cc:21: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/panel.h:368:36: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 368 | for (std::size_t y = y0; y < y1; ++y) { + | ~~^~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/panel.h:369:38: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 369 | for (std::size_t x = x0; x < x1; ++x) { + | ~~^~~~ +In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/scan.h:22, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/experiment.h:25: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/scan_helpers.h:85:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 85 | for (std::size_t i = 0; i < n_angles; ++i) { + | ~~^~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -10030,19 +10123,10 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/goniometer.cc:11: + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/kappa_goniometer.cc:11: /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/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/scan.h:22, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/experiment.h:25: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/scan_helpers.h:85:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 85 | for (std::size_t i = 0; i < n_angles; ++i) { - | ~~^~~~~~~~~~ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/scan.h: In constructor ‘dxtbx::model::Scan::Scan()’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/scan.h:504:32: warning: ‘dxtbx::model::Scan::epochs_’ will be initialized after [-Wreorder] 504 | scitbx::af::shared epochs_; @@ -10053,6 +10137,9 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/scan.h:39:5: warning: when initialized here [-Wreorder] 39 | Scan() | ^~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/error.h:16, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/ref.h:4, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny_plain.h:4, @@ -10088,6 +10175,12 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/scan.h:231:7: note: in expansion of macro ‘DXTBX_ASSERT’ 231 | DXTBX_ASSERT(exposure_times.size() == num_images_); | ^~~~~~~~~~~~ +In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/scan.h:22, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/to_from_dict.h:20: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/scan_helpers.h:85:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 85 | for (std::size_t i = 0; i < n_angles; ++i) { + | ~~^~~~~~~~~~ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/scan.h: In member function ‘void dxtbx::model::Scan::set_epochs(const scitbx::af::shared&)’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/scan.h:237:34: warning: comparison of integer expressions of different signedness: ‘scitbx::af::shared_plain::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 237 | DXTBX_ASSERT(epochs.size() == num_images_); @@ -10098,83 +10191,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/scan.h:237:7: note: in expansion of macro ‘DXTBX_ASSERT’ 237 | DXTBX_ASSERT(epochs.size() == num_images_); | ^~~~~~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - 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/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/kappa_goniometer.cc:11: -/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/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/experiment_list.cc:29:31: 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] - 29 | for (std::size_t i = 0; i < boost::python::len(items); ++i) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/panel.h:22, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/detector.h:27, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/to_from_dict.h:18, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/goniometer.cc:21: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/panel.h:368:36: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 368 | for (std::size_t y = y0; y < y1; ++y) { - | ~~^~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/panel.h:369:38: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 369 | for (std::size_t x = x0; x < x1; ++x) { - | ~~^~~~ -In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/scan.h:22, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/to_from_dict.h:20: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/scan_helpers.h:85:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 85 | for (std::size_t i = 0; i < n_angles; ++i) { - | ~~^~~~~~~~~~ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/scan.h: In constructor ‘dxtbx::model::Scan::Scan()’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/scan.h:504:32: warning: ‘dxtbx::model::Scan::epochs_’ will be initialized after [-Wreorder] 504 | scitbx::af::shared epochs_; @@ -10185,23 +10201,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/scan.h:39:5: warning: when initialized here [-Wreorder] 39 | Scan() | ^~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - 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/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/model_ext.cc:11: -/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( - | ^~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/error.h:16, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/ref.h:4, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny_plain.h:4, @@ -10228,9 +10227,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/scan.h:100:7: note: in expansion of macro ‘DXTBX_ASSERT’ 100 | DXTBX_ASSERT(epochs_.size() == num_images_); | ^~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/scan.h: In member function ‘void dxtbx::model::Scan::set_exposure_times(scitbx::af::shared)’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/scan.h:231:42: warning: comparison of integer expressions of different signedness: ‘scitbx::af::shared_plain::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 231 | DXTBX_ASSERT(exposure_times.size() == num_images_); @@ -10259,7 +10255,48 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/goniometer.cc:88:31: 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] 88 | for (std::size_t i = 0; i < boost::python::len(l); ++i) { | ~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/experiment_list.cc:29:31: 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] + 29 | for (std::size_t i = 0; i < boost::python::len(items); ++i) { + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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 /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + 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/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/model_ext.cc:11: +/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/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ g++ -o dxtbx/src/dxtbx/model/boost_python/multi_axis_goniometer.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_CBF -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/base/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -I/usr/include/cbflib -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cbflib_adaptbx -I/usr/include/python3.11 -I/usr/include/hdf5/serial /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/multi_axis_goniometer.cc +g++ -o dxtbx/src/dxtbx/model/boost_python/panel.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_CBF -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/base/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -I/usr/include/cbflib -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cbflib_adaptbx -I/usr/include/python3.11 -I/usr/include/hdf5/serial /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/panel.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -10280,7 +10317,6 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -g++ -o dxtbx/src/dxtbx/model/boost_python/panel.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_CBF -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/base/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -I/usr/include/cbflib -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cbflib_adaptbx -I/usr/include/python3.11 -I/usr/include/hdf5/serial /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/panel.cc /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/multi_axis_goniometer.cc: In function ‘dxtbx::model::MultiAxisGoniometer* dxtbx::model::boost_python::from_dict(boost::python::dict)’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/multi_axis_goniometer.cc:102:33: 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] 102 | for (std::size_t i = 0; i < boost::python::len(l); ++i) { @@ -10397,9 +10433,6 @@ 237 | DXTBX_ASSERT(epochs.size() == num_images_); | ^~~~~~~~~~~~ g++ -o dxtbx/src/dxtbx/model/boost_python/pixel_to_millimeter.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_CBF -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/base/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -I/usr/include/cbflib -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cbflib_adaptbx -I/usr/include/python3.11 -I/usr/include/hdf5/serial /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/pixel_to_millimeter.cc -g++ -o dxtbx/src/dxtbx/model/boost_python/scan.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_CBF -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/base/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -I/usr/include/cbflib -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cbflib_adaptbx -I/usr/include/python3.11 -I/usr/include/hdf5/serial /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/scan.cc -g++ -o dxtbx/src/dxtbx/model/boost_python/scan_helpers.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_CBF -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/base/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -I/usr/include/cbflib -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cbflib_adaptbx -I/usr/include/python3.11 -I/usr/include/hdf5/serial /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/scan_helpers.cc -g++ -o dxtbx/src/dxtbx/model/boost_python/spectrum.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_CBF -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/base/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -I/usr/include/cbflib -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cbflib_adaptbx -I/usr/include/python3.11 -I/usr/include/hdf5/serial /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/spectrum.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -10420,14 +10453,8 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -g++ -o lib/libcbf-private.so.0.0.1 -shared -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -Wl,-soname=libcbf-private.so.0 cbflib_adaptbx/detectors/mar_adaptor.o cbflib_adaptbx/detectors/cbf_adaptor.o cbflib_adaptbx/detectors/cbf_byte_offset_optimized.o cbflib_adaptbx/detectors/buffer_based_service.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lboost_thread -lboost_system -lhdf5 -lcbf -Create symlinks for: 'lib/libcbf-private.so.0.0.1' - 'lib/libcbf-private.so.0'->'lib/libcbf-private.so.0.0.1' - 'lib/libcbf-private.so'->'lib/libcbf-private.so.0.0.1' -g++ -o exe_dev/cbflib.tst_memory -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -pthread cbflib_adaptbx/detectors/tst_memory.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lcbf -lcbf-private -lm -lhdf5 -g++ -o exe_dev/cctbx.convert_ccp4_symop_lib -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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++11 -pthread cctbx/examples/find_distances.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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++11 -pthread cctbx/examples/getting_started.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx_sgtbx_asu -lcctbx -lboost_thread -lboost_system -lm +g++ -o dxtbx/src/dxtbx/model/boost_python/scan.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_CBF -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/base/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -I/usr/include/cbflib -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cbflib_adaptbx -I/usr/include/python3.11 -I/usr/include/hdf5/serial /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/scan.cc +g++ -o dxtbx/src/dxtbx/model/boost_python/scan_helpers.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_CBF -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/base/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -I/usr/include/cbflib -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cbflib_adaptbx -I/usr/include/python3.11 -I/usr/include/hdf5/serial /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/scan_helpers.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -10448,9 +10475,7 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -g++ -o exe_dev/cctbx.lattice_symmetry -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -pthread cctbx/examples/lattice_symmetry.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx_sgtbx_asu -lcctbx -lboost_thread -lboost_system -lm +g++ -o dxtbx/src/dxtbx/model/boost_python/spectrum.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_CBF -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/base/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -I/usr/include/cbflib -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cbflib_adaptbx -I/usr/include/python3.11 -I/usr/include/hdf5/serial /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/spectrum.cc In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/panel.h:22, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/pixel_to_millimeter.cc:13: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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’: @@ -10473,6 +10498,7 @@ 449 | if (i >= dx_.accessor()[1]) i = dx_.accessor()[1] - 1; /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 lib/libcbf-private.so.0.0.1 -shared -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -Wl,-soname=libcbf-private.so.0 cbflib_adaptbx/detectors/mar_adaptor.o cbflib_adaptbx/detectors/cbf_adaptor.o cbflib_adaptbx/detectors/cbf_byte_offset_optimized.o cbflib_adaptbx/detectors/buffer_based_service.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lboost_thread -lboost_system -lhdf5 -lcbf /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/panel.h:368:36: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 368 | for (std::size_t y = y0; y < y1; ++y) { @@ -10480,8 +10506,21 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/panel.h:369:38: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 369 | for (std::size_t x = x0; x < x1; ++x) { | ~~^~~~ +g++ -o exe_dev/cctbx.convert_ccp4_symop_lib -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx_sgtbx_asu -lcctbx -lboost_thread -lboost_system -lm +Create symlinks for: 'lib/libcbf-private.so.0.0.1' + 'lib/libcbf-private.so.0'->'lib/libcbf-private.so.0.0.1' + 'lib/libcbf-private.so'->'lib/libcbf-private.so.0.0.1' +g++ -o exe_dev/cbflib.tst_memory -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -pthread cbflib_adaptbx/detectors/tst_memory.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lcbf -lcbf-private -lm -lhdf5 +g++ -o exe_dev/cctbx.find_distances -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -pthread cctbx/examples/find_distances.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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++11 -pthread cctbx/examples/getting_started.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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++11 -pthread cctbx/examples/lattice_symmetry.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/ext.cpp g++ -o gltbx/font_ucs_10x20.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 gltbx/font_ucs_10x20.cpp +g++ -o gltbx/font_ucs_8x13.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 gltbx/font_ucs_8x13.cpp +g++ -o gltbx/font_ucs_9x15.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 gltbx/font_ucs_9x15.cpp +g++ -o gltbx/fonts_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/gltbx/fonts_ext.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -10502,6 +10541,7 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +g++ -o gltbx/gl_defines_00_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 gltbx/gl_defines_00_bpl.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -10519,26 +10559,6 @@ /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( | ^~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - 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/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/spectrum.cc:4: -/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/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ @@ -10627,6 +10647,11 @@ 449 | if (i >= dx_.accessor()[1]) i = dx_.accessor()[1] - 1; /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/scan_helpers.cc:17: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/scan_helpers.h:85:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 85 | for (std::size_t i = 0; i < n_angles; ++i) { + | ~~^~~~~~~~~~ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/panel.h:368:36: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 368 | for (std::size_t y = y0; y < y1; ++y) { @@ -10634,6 +10659,56 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/panel.h:369:38: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 369 | for (std::size_t x = x0; x < x1; ++x) { | ~~^~~~ +g++ -o gltbx/gl_defines_01_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 gltbx/gl_defines_01_bpl.cpp +g++ -o gltbx/gl_defines_02_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 gltbx/gl_defines_02_bpl.cpp +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + 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/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/spectrum.cc:4: +/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/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/scan.cc: In function ‘boost::python::dict dxtbx::model::boost_python::MaptoPythonDict(dxtbx::model::ExpImgRangeMap)’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/scan.cc:62:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] + 62 | for (int k = 0; k < val.size(); ++k) { + | ~~^~~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/scan.cc: In function ‘boost::python::list dxtbx::model::boost_python::get_valid_image_ranges(dxtbx::model::Scan&, std::string)’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/scan.cc:191:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] + 191 | for (int k = 0; k < ranges.size(); ++k) { + | ~~^~~~~~~~~~~~~~~ +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + 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/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/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( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/panel.h:22, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/detector.h:27, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/to_from_dict.h:18, @@ -10658,8 +10733,37 @@ 449 | if (i >= dx_.accessor()[1]) i = dx_.accessor()[1] - 1; /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 gltbx/font_ucs_8x13.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 gltbx/font_ucs_8x13.cpp -g++ -o gltbx/font_ucs_9x15.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 gltbx/font_ucs_9x15.cpp +In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/ext.cpp:5: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem/utils/equivalence.hpp: In member function ‘void fem::utils::equivalence::array_alignment::infer_diffs0_from_diff_matrix()’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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) { + | ~~~~~~~^~~~~ +In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem/utils/string_to_double.hpp:5, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem/utils/string_to_double_fmt.hpp:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/ext.cpp:6: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/fable/fem/utils/string_to_double.hpp: In member function ‘void fem::utils::string_to_double::convert(fem::utils::simple_istream&, unsigned int, int)’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem/utils/string_to_double.hpp:115:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare] + 115 | if (dexp <= ad_hoc_limits::max_digit_count) { + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem/utils/string.hpp:6, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem/str_ref.hpp:5, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem/format.hpp:5, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/ext.cpp:4: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/ext.cpp: In function ‘unsigned int fable::ext::get_code_stop(const boost::python::api::object&, int)’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/ext.cpp:24:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] + 24 | TBXX_ASSERT(stop <= len_code); + | ~~~~~^~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/tbxx/error_utils.hpp:59:9: note: in definition of macro ‘TBXX_ASSERT’ + 59 | if (!(condition)) { \ + | ^~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/ext.cpp: In function ‘int fable::ext::floating_point_scan_after_dot(const boost::python::api::object&, unsigned int, int)’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/ext.cpp:71:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] + 71 | if (i < code_stop) { + | ~~^~~~~~~~~~~ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/panel.h:368:36: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 368 | for (std::size_t y = y0; y < y1; ++y) { @@ -10667,13 +10771,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/panel.h:369:38: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 369 | for (std::size_t x = x0; x < x1; ++x) { | ~~^~~~ -In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/scan_helpers.cc:17: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/scan_helpers.h:85:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 85 | 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-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/gltbx/fonts_ext.cpp -g++ -o gltbx/gl_defines_00_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 gltbx/gl_defines_00_bpl.cpp In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/scan.h:22, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/to_from_dict.h:20: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/scan_helpers.h: In function ‘scitbx::af::shared dxtbx::model::get_mod2pi_angles_in_range(scitbx::vec2, double)’: @@ -10737,16 +10834,8 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/scan.h:237:7: note: in expansion of macro ‘DXTBX_ASSERT’ 237 | DXTBX_ASSERT(epochs.size() == num_images_); | ^~~~~~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/scan.cc: In function ‘boost::python::dict dxtbx::model::boost_python::MaptoPythonDict(dxtbx::model::ExpImgRangeMap)’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/scan.cc:62:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] - 62 | for (int k = 0; k < val.size(); ++k) { - | ~~^~~~~~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/scan.cc: In function ‘boost::python::list dxtbx::model::boost_python::get_valid_image_ranges(dxtbx::model::Scan&, std::string)’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/scan.cc:191:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] - 191 | for (int k = 0; k < ranges.size(); ++k) { - | ~~^~~~~~~~~~~~~~~ -g++ -o gltbx/gl_defines_01_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 gltbx/gl_defines_01_bpl.cpp -g++ -o gltbx/gl_defines_02_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 gltbx/gl_defines_02_bpl.cpp +g++ -o gltbx/gl_defines_03_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 gltbx/gl_defines_03_bpl.cpp +g++ -o gltbx/gl_defines_04_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 gltbx/gl_defines_04_bpl.cpp In file included from /usr/include/boost/assert.hpp:58, from /usr/include/boost/variant/detail/forced_return.hpp:17, from /usr/include/boost/variant/variant.hpp:29, @@ -10765,27 +10854,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = dxtbx::model::Spectrum; 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-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/spectrum.cc:80:60: required from here /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] -g++ -o gltbx/gl_defines_03_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 gltbx/gl_defines_03_bpl.cpp -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - 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/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/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( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_wrapper.h:18, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/spectrum.cc:10: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/slice.h: In instantiation of ‘scitbx::af::versa > scitbx::af::copy_slice(const const_ref >&, small) [with T = dxtbx::model::Spectrum]’: @@ -10804,37 +10872,8 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = dxtbx::model::Spectrum]’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/slice.h:119:35: required from ‘void scitbx::af::copy_to_slice(versa >&, small, const const_ref >&) [with T = dxtbx::model::Spectrum]’ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = dxtbx::model::Spectrum; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >]’ @@ -10843,9 +10882,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/spectrum.cc:80:60: required from here /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 gltbx/gl_defines_04_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 gltbx/gl_defines_04_bpl.cpp -g++ -o gltbx/gl_defines_05_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 gltbx/gl_defines_05_bpl.cpp -g++ -o gltbx/gl_defines_06_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 gltbx/gl_defines_06_bpl.cpp g++ -o gltbx/gl_defines_07_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 gltbx/gl_defines_07_bpl.cpp g++ -o gltbx/gl_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/gltbx/gl_ext.cpp g++ -o gltbx/gl_functions_00_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 gltbx/gl_functions_00_bpl.cpp @@ -10854,6 +10890,7 @@ g++ -o gltbx/gl_functions_03_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 gltbx/gl_functions_03_bpl.cpp g++ -o gltbx/gl_functions_04_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 gltbx/gl_functions_04_bpl.cpp g++ -o gltbx/gl_functions_05_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 gltbx/gl_functions_05_bpl.cpp +g++ -o gltbx/gl_functions_06_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 gltbx/gl_functions_06_bpl.cpp In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/shared.h:4, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/scan.h:18: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/shared_plain.h: In constructor ‘scitbx::af::shared_plain::shared_plain(const size_type&) [with ElementType = scitbx::vec2]’: @@ -10876,7 +10913,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/shared_plain.h:132:48: note: ‘’ declared here 132 | std::uninitialized_fill_n(begin(), sz, ElementType()); | ^~~~~~~~~~~~~ -g++ -o gltbx/gl_functions_06_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 gltbx/gl_functions_06_bpl.cpp g++ -o gltbx/gl_functions_07_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 gltbx/gl_functions_07_bpl.cpp g++ -o gltbx/gl_functions_08_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 gltbx/gl_functions_08_bpl.cpp g++ -o gltbx/gl_functions_09_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 gltbx/gl_functions_09_bpl.cpp @@ -10901,6 +10937,7 @@ g++ -o iotbx/detectors/bruker.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/ccp4 -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/detectors/bruker.cpp g++ -o iotbx/detectors/bruker_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/ccp4 -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/detectors/bruker_ext.cpp g++ -o iotbx/detectors/detectors_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/ccp4 -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/detectors/detectors_ext.cpp +g++ -o iotbx/detectors/image_divider.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/ccp4 -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/detectors/image_divider.cpp /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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++) { @@ -10925,7 +10962,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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/image_divider.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/ccp4 -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/detectors/image_divider.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -10949,6 +10985,7 @@ g++ -o iotbx/dsn6/ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/ccp4 -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/dsn6/ext.cpp g++ -o iotbx/misc/boost_python/dtrek_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/ccp4 -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/misc/boost_python/dtrek_ext.cpp g++ -o iotbx/misc/boost_python/scalepack_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/ccp4 -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/misc/boost_python/scalepack_ext.cpp +g++ -o iotbx/mtz/batch_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/ccp4 -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/mtz/batch_bpl.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -10965,11 +11002,9 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -g++ -o iotbx/mtz/batch_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/ccp4 -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/mtz/batch_bpl.cpp g++ -o iotbx/mtz/column.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/ccp4 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/mtz/column.cpp g++ -o iotbx/mtz/column_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/ccp4 -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/mtz/column_bpl.cpp g++ -o iotbx/mtz/crystal.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/ccp4 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/mtz/crystal.cpp -g++ -o iotbx/mtz/crystal_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/ccp4 -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/mtz/crystal_bpl.cpp In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/ref.h:8, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny_plain.h:4, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny.h:4, @@ -11012,7 +11047,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/ccp4 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/mtz/dataset.cpp /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/shared_plain.h: In member function ‘ElementType& scitbx::af::shared_plain::at(size_type)’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]; \ @@ -11065,6 +11099,8 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/ccp4 -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/mtz/crystal_bpl.cpp +g++ -o iotbx/mtz/dataset.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/ccp4 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/mtz/dataset.cpp In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/ref.h:8, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny_plain.h:4, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny.h:4, @@ -11218,20 +11254,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/mtz/object.h:594:11: note: in expansion of macro ‘IOTBX_ASSERT’ 594 | IOTBX_ASSERT(iref[i] < oldsize); | ^~~~~~~~~~~~ -g++ -o iotbx/mtz/ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/ccp4 -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/mtz/ext.cpp -In file included from /usr/include/boost/assert.hpp:58, - from /usr/include/boost/smart_ptr/shared_array.hpp:21, - from /usr/include/boost/shared_array.hpp:17, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/hendrickson_lattman.h:9, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/mtz/object.h:13: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/mtz/batch_bpl.cpp:78:60: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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/object.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/ccp4 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/mtz/object.cpp In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/ref.h:8, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny_plain.h:4, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny.h:4, @@ -11274,7 +11296,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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/object_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/ccp4 -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/mtz/object_bpl.cpp In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/error.h:16, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/mat3.h:5: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/mtz/object.h: In member function ‘void iotbx::mtz::object::delete_reflections(const scitbx::af::const_ref&)’: @@ -11346,64 +11367,21 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/ref.h:8, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny_plain.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/hendrickson_lattman.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/miller/sym_equiv.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/miller/asu.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/mtz/object.cpp:5: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny_plain.h: In member function ‘ElementType& scitbx::af::tiny_plain::at(size_type)’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny_plain.h: In member function ‘const ElementType& scitbx::af::tiny_plain::at(size_type) const’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/shared_plain.h: In member function ‘ElementType& scitbx::af::shared_plain::at(size_type)’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/shared_plain.h: In member function ‘const ElementType& scitbx::af::shared_plain::at(size_type) const’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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:21, + from /usr/include/boost/shared_array.hpp:17, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/hendrickson_lattman.h:9, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/mtz/object.h:13: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/mtz/batch_bpl.cpp:78:60: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/ccp4 -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/mtz/ext.cpp +g++ -o iotbx/mtz/object.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/ccp4 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/mtz/object.cpp +g++ -o iotbx/mtz/object_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/ccp4 -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/mtz/object_bpl.cpp In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/error.h:16, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/mat3.h:5, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/sym_mat3.h:4, @@ -11434,18 +11412,10 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/mtz/object.h:594:11: note: in expansion of macro ‘IOTBX_ASSERT’ 594 | IOTBX_ASSERT(iref[i] < oldsize); | ^~~~~~~~~~~~ +g++ -o iotbx/pdb/atom_selection.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/ccp4 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/atom_selection.cpp +g++ -o iotbx/pdb/common_residue_names_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/ccp4 -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/common_residue_names_bpl.cpp In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/error.h:16, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/mat3.h:5, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/sym_mat3.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/rot_mx.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/rt_mx.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/change_of_basis_op.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/tr_group.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/space_group.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/mtz/object.h:12, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/mtz/crystal.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/mtz/dataset.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/mtz/crystal_bpl.cpp:6: + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/mat3.h:5: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/mtz/object.h: In member function ‘void iotbx::mtz::object::delete_reflections(const scitbx::af::const_ref&)’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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); @@ -11463,21 +11433,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/mtz/object.h:594:11: note: in expansion of macro ‘IOTBX_ASSERT’ 594 | IOTBX_ASSERT(iref[i] < oldsize); | ^~~~~~~~~~~~ -g++ -o iotbx/pdb/atom_selection.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/ccp4 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/atom_selection.cpp -g++ -o iotbx/pdb/common_residue_names_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/ccp4 -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/common_residue_names_bpl.cpp -g++ -o iotbx/pdb/construct_hierarchy.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/ccp4 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/construct_hierarchy.cpp -In file included from /usr/include/boost/assert.hpp:58, - from /usr/include/boost/smart_ptr/shared_array.hpp:21, - from /usr/include/boost/shared_array.hpp:17, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/hendrickson_lattman.h:9, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/mtz/object.h:13: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/mtz/crystal_bpl.cpp:42:60: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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/boost/assert.hpp:58, from /usr/include/boost/smart_ptr/shared_array.hpp:21, from /usr/include/boost/shared_array.hpp:17, @@ -11490,25 +11445,7 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/error.h:16, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/mat3.h:5: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/mtz/object.h: In member function ‘void iotbx::mtz::object::delete_reflections(const scitbx::af::const_ref&)’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/iotbx/mtz/object.h:591:9: note: in expansion of macro ‘IOTBX_ASSERT’ - 591 | IOTBX_ASSERT(iref[0] < oldsize); - | ^~~~~~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/iotbx/mtz/object.h:594:11: note: in expansion of macro ‘IOTBX_ASSERT’ - 594 | IOTBX_ASSERT(iref[i] < oldsize); - | ^~~~~~~~~~~~ +g++ -o iotbx/pdb/construct_hierarchy.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/ccp4 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/construct_hierarchy.cpp In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/ref.h:8, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny_plain.h:4, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny.h:4, @@ -11543,31 +11480,63 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/small_plain.h: In member function ‘ElementType& scitbx::af::small_plain::at(size_type)’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/shared_plain.h: In member function ‘ElementType& scitbx::af::shared_plain::at(size_type)’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/small_plain.h: In member function ‘const ElementType& scitbx::af::small_plain::at(size_type) const’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/shared_plain.h: In member function ‘const ElementType& scitbx::af::shared_plain::at(size_type) const’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/ref.h:8, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny_plain.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/hendrickson_lattman.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/miller/sym_equiv.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/miller/asu.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/mtz/object.cpp:5: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny_plain.h: In member function ‘ElementType& scitbx::af::tiny_plain::at(size_type)’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny_plain.h: In member function ‘const ElementType& scitbx::af::tiny_plain::at(size_type) const’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/shared_plain.h: In member function ‘ElementType& scitbx::af::shared_plain::at(size_type)’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] @@ -11595,46 +11564,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/error.h:16, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/ref.h:4: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/mtz/object.h: In member function ‘void iotbx::mtz::object::delete_reflections(const scitbx::af::const_ref&)’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/iotbx/mtz/object.h:591:9: note: in expansion of macro ‘IOTBX_ASSERT’ - 591 | IOTBX_ASSERT(iref[0] < oldsize); - | ^~~~~~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/iotbx/mtz/object.h:594:11: note: in expansion of macro ‘IOTBX_ASSERT’ - 594 | IOTBX_ASSERT(iref[i] < oldsize); - | ^~~~~~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/mtz/object.cpp: In member function ‘void iotbx::mtz::object::replace_miller_indices(const scitbx::af::const_ref >&)’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/shared_plain.h: In member function ‘const ElementType& scitbx::af::shared_plain::at(size_type) const’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/error.h:16, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/mat3.h:5, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/sym_mat3.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/rot_mx.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/rt_mx.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/change_of_basis_op.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/tr_group.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/space_group.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/mtz/object.h:12, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/mtz/crystal.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/mtz/dataset.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/mtz/crystal_bpl.cpp:6: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/mtz/object.h: In member function ‘void iotbx::mtz::object::delete_reflections(const scitbx::af::const_ref&)’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/iotbx/mtz/object.h:591:9: note: in expansion of macro ‘IOTBX_ASSERT’ + 591 | IOTBX_ASSERT(iref[0] < oldsize); + | ^~~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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:21, + from /usr/include/boost/shared_array.hpp:17, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/hendrickson_lattman.h:9, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/mtz/object.h:13: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/mtz/crystal_bpl.cpp:42:60: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/error.h:16, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/mat3.h:5, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/sym_mat3.h:4, @@ -11700,31 +11697,31 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/mtz/object.h:594:11: note: in expansion of macro ‘IOTBX_ASSERT’ 594 | IOTBX_ASSERT(iref[i] < oldsize); | ^~~~~~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/shared_plain.h: In member function ‘ElementType& scitbx::af::shared_plain::at(size_type)’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/small_plain.h: In member function ‘ElementType& scitbx::af::small_plain::at(size_type)’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/shared_plain.h: In member function ‘const ElementType& scitbx::af::shared_plain::at(size_type) const’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/small_plain.h: In member function ‘const ElementType& scitbx::af::small_plain::at(size_type) const’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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:21, @@ -11738,7 +11735,48 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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/ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/ccp4 -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/ext.cpp +In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/error.h:16, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/ref.h:4: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/mtz/object.h: In member function ‘void iotbx::mtz::object::delete_reflections(const scitbx::af::const_ref&)’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/iotbx/mtz/object.h:591:9: note: in expansion of macro ‘IOTBX_ASSERT’ + 591 | IOTBX_ASSERT(iref[0] < oldsize); + | ^~~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/iotbx/mtz/object.h:594:11: note: in expansion of macro ‘IOTBX_ASSERT’ + 594 | IOTBX_ASSERT(iref[i] < oldsize); + | ^~~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/mtz/object.cpp: In member function ‘void iotbx::mtz::object::replace_miller_indices(const scitbx::af::const_ref >&)’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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 auto_ptr; | ^~~~~~~~ +g++ -o iotbx/pdb/hierarchy_atoms_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/ccp4 -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/hierarchy_atoms_bpl.cpp g++ -o iotbx/pdb/hierarchy_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/ccp4 -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/hierarchy_ext.cpp g++ -o iotbx/pdb/hierarchy_select.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/ccp4 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/hierarchy_select.cpp g++ -o iotbx/pdb/hierarchy_write.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/ccp4 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/hierarchy_write.cpp @@ -12036,7 +12072,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/ccp4 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/hybrid_36_c.c /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/shared_plain.h: In member function ‘ElementType& scitbx::af::shared_plain::at(size_type)’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]; \ @@ -12063,7 +12098,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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_cpp.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/ccp4 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/hybrid_36_cpp.cpp /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/hierarchy_atoms.h: At global scope: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 @@ -12080,69 +12114,11 @@ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ -In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/scatterer.h:5, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/hierarchy_atoms_bpl.cpp:2: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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++/12/memory:76, - 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-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/hierarchy_ext.cpp:4: -/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here - 64 | template class auto_ptr; - | ^~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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++/12/bits/unique_ptr.h:64:28: note: declared here - 64 | template class auto_ptr; - | ^~~~~~~~ g++ -o iotbx/pdb/input_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/ccp4 -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/input_bpl.cpp -In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/hierarchy_atoms_bpl.cpp:13: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/hierarchy_atoms.h: At global scope: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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++/12/memory:76, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/detail/misc.h:5, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny_plain.h:5, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/vec3.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/mat3.h:6, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/sym_mat3.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/scatterer_flags.h:5, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/scatterer.h:4: -/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here - 64 | template class auto_ptr; - | ^~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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++/12/bits/unique_ptr.h:64:28: note: declared here - 64 | template class auto_ptr; - | ^~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/hierarchy_atoms_bpl.cpp: In function ‘void iotbx::pdb::hierarchy::atoms::bpl_wrap()’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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++/12/bits/unique_ptr.h:64:28: note: declared here - 64 | template class auto_ptr; - | ^~~~~~~~ In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem/io.hpp:8, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem/close_chain.hpp:4, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem/common.hpp:4, @@ -12154,44 +12130,12 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/site_symmetry.h:6: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/site_symmetry.h:203:75: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/site_symmetry.h:214:75: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] g++ -o iotbx/pdb/input_write.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/ccp4 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/input_write.cpp /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem/common.hpp: In member function ‘void fem::common::getarg(int, fem::str_ref) const’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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()) { | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/assert.hpp:58, - from /usr/include/boost/function/function_base.hpp:19, - from /usr/include/boost/function/detail/prologue.hpp:17, - 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/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-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/hierarchy_atoms_bpl.cpp:6: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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::pdb::hierarchy::atom; GetitemReturnValuePolicy = boost::python::return_value_policy; std::string = std::__cxx11::basic_string]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/hierarchy_atoms_bpl.cpp:87:36: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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/overall_counts.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/ccp4 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/overall_counts.cpp In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem/utils/string_to_double_fmt.hpp:4, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem/read.hpp:9: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem/utils/string_to_double.hpp: In member function ‘void fem::utils::string_to_double::convert(fem::utils::simple_istream&, unsigned int, int)’: @@ -12202,12 +12146,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem/read.hpp:652:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 652 | if (iw+1 != ed.size()) { | ~~~~~^~~~~~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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::pdb::hierarchy::atom_with_labels; GetitemReturnValuePolicy = boost::python::return_value_policy; std::string = std::__cxx11::basic_string]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/hierarchy_atoms_bpl.cpp:91:44: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] -g++ -o iotbx/pdb/overall_counts.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/ccp4 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/overall_counts.cpp In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem/variant.hpp:5, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem/major_types.hpp:7: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem/utils/equivalence.hpp: In member function ‘void fem::utils::equivalence::array_alignment::infer_diffs0_from_diff_matrix()’: @@ -12280,6 +12218,54 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/cctbx/xray/scatterer.h:5, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/hierarchy_atoms_bpl.cpp:2: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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++/12/memory:76, + 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-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/hierarchy_ext.cpp:4: +/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here + 64 | template class auto_ptr; + | ^~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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++/12/bits/unique_ptr.h:64:28: note: declared here + 64 | template class auto_ptr; + | ^~~~~~~~ +In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/misc/file_utils.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/input.cpp:3: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/ref.h:8, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny_plain.h:4, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny.h:4, @@ -12375,24 +12361,36 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/misc/file_utils.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/input.cpp:3: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/hierarchy_atoms_bpl.cpp:13: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/hierarchy_atoms.h: At global scope: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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++/12/memory:76, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/detail/misc.h:5, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny_plain.h:5, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/vec3.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/mat3.h:6, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/sym_mat3.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/scatterer_flags.h:5, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/scatterer.h:4: +/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here + 64 | template class auto_ptr; + | ^~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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++/12/bits/unique_ptr.h:64:28: note: declared here + 64 | template class auto_ptr; + | ^~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/hierarchy_atoms_bpl.cpp: In function ‘void iotbx::pdb::hierarchy::atoms::bpl_wrap()’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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++/12/bits/unique_ptr.h:64:28: note: declared here + 64 | template class auto_ptr; + | ^~~~~~~~ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/shared_plain.h: In member function ‘ElementType& scitbx::af::shared_plain::at(size_type)’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]; \ @@ -12419,7 +12417,45 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/site_symmetry.h:6: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/site_symmetry.h:203:75: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/site_symmetry.h:214:75: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] +In file included from /usr/include/boost/assert.hpp:58, + from /usr/include/boost/function/function_base.hpp:19, + from /usr/include/boost/function/detail/prologue.hpp:17, + 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/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-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/hierarchy_atoms_bpl.cpp:6: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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::pdb::hierarchy::atom; GetitemReturnValuePolicy = boost::python::return_value_policy; std::string = std::__cxx11::basic_string]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/hierarchy_atoms_bpl.cpp:87:36: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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/rna_dna_atom_names_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/ccp4 -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/rna_dna_atom_names_bpl.cpp +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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::pdb::hierarchy::atom_with_labels; GetitemReturnValuePolicy = boost::python::return_value_policy; std::string = std::__cxx11::basic_string]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/hierarchy_atoms_bpl.cpp:91:44: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] g++ -o iotbx/pdb/utils.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/ccp4 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/utils.cpp g++ -o iotbx/pdb/write_utils.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/ccp4 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/write_utils.cpp In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/ref.h:8, @@ -12494,25 +12530,7 @@ g++ -o iotbx/shelx/shelx_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/ccp4 -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/shelx/shelx_ext.cpp g++ -o iotbx/wildcard_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/wildcard_ext.cpp g++ -o iotbx/xplor/boost_python/xplor_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/ccp4 -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/xplor/boost_python/xplor_ext.cpp -In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/scatterer.h:5, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/xray_structure.h:6, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/xray_structure_bpl.cpp:7: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/site_symmetry.h:203:75: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/site_symmetry.h:214:75: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] Create symlinks for: 'lib/libann_adaptor.so.0.0.1' 'lib/libann_adaptor.so.0'->'lib/libann_adaptor.so.0.0.1' 'lib/libann_adaptor.so'->'lib/libann_adaptor.so.0.0.1' @@ -12521,10 +12539,17 @@ 'lib/annlib_ext.so.0'->'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++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lboost_thread -lboost_system -lboost_python311 -lm +g++ -o lib/boost_adaptbx_graph_breadth_first_search_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lboost_thread -lboost_system -lboost_python311 -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_breadth_first_search_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lboost_thread -lboost_system -lboost_python311 -lm +In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/scatterer.h:5, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/xray_structure.h:6, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/xray_structure_bpl.cpp:7: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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/boost_adaptbx_graph_breadth_first_search_ext.so.0.0.1' @@ -12534,6 +12559,17 @@ '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_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lboost_thread -lboost_system -lboost_python311 -lm +In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/site_symmetry.h:6: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/site_symmetry.h:203:75: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/site_symmetry.h:214:75: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] 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' @@ -12547,59 +12583,59 @@ '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_graph_min_cut_max_flow_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lboost_thread -lboost_system -lboost_python311 -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' 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++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lboost_thread -lboost_system -lboost_python311 -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_python_streambuf_test_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lboost_thread -lboost_system -lboost_python311 -lm 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++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lboost_thread -lboost_system -lboost_python311 -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_optional_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lboost_thread -lboost_system -lboost_python311 -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_optional_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lboost_thread -lboost_system -lboost_python311 -lm g++ -o lib/boost_python_hybrid_times_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lboost_thread -lboost_system -lboost_python311 -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_python_meta_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lboost_thread -lboost_system -lboost_python311 -lm g++ -o lib/boost_rational_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lboost_thread -lboost_system -lboost_python311 -lm 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_tuple_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lboost_thread -lboost_system -lboost_python311 -lm -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_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/cbflib_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lcbf-private -lcbf -lboost_thread -lboost_system -lboost_python311 -lm -lhdf5 -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' -g++ -o lib/libccp4io.so.0.0.1 -shared -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lboost_thread -lboost_system -lm -lccp4c -g++ -o scitbx/boost_python/utils.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/boost_python/utils.cpp 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' +g++ -o lib/libccp4io.so.0.0.1 -shared -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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' +g++ -o scitbx/boost_python/utils.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/boost_python/utils.cpp +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' +g++ -o scitbx/boost_python/slice.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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' -g++ -o scitbx/boost_python/slice.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/boost_python/slice.cpp g++ -o lib/ccp4io_adaptbx_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lccp4io -lccp4c -lssm -lmmdb2 -lboost_thread -lboost_system -lboost_python311 -lm 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/array_family/boost_python/utils.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/utils.cpp -g++ -o lib/cma_es_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lboost_thread -lboost_system -lboost_python311 -lm 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 lib/cma_es_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lboost_thread -lboost_system -lboost_python311 -lm g++ -o lib/dxtbx_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/base/lib -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lm -ltiff -lboost_python311 -lcbf 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' @@ -12609,19 +12645,7 @@ '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++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/base/lib -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lm -ltiff -lboost_python311 -lcbf -lhdf5 -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' -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' g++ -o lib/dxtbx_imageset_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/base/lib -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lm -ltiff -lboost_python311 -lcbf -lhdf5 -g++ -o lib/fable_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lboost_thread -lboost_system -lboost_python311 -lm -g++ -o lib/iotbx_ccp4_map_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lccp4c -lboost_thread -lboost_system -lboost_python311 -lm -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/cifParser.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/ccp4 -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/ucif/cifParser.cpp In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/ref.h:8, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny_plain.h:4, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny.h:4, @@ -12682,10 +12706,9 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 ucif/cifLexer.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/ccp4 -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/ucif/cifLexer.cpp +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' /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/shared_plain.h: In member function ‘ElementType& scitbx::af::shared_plain::at(size_type)’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]; \ @@ -12738,311 +12761,324 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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/fable_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lboost_thread -lboost_system -lboost_python311 -lm +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++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lccp4c -lboost_thread -lboost_system -lboost_python311 -lm +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/cifParser.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/ccp4 -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/ucif/cifParser.cpp +g++ -o ucif/cifLexer.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/ccp4 -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/ucif/cifLexer.cpp +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_bruker_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lboost_thread -lboost_system -lboost_python311 -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_detectors_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lboost_thread -lboost_system -lboost_python311 -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' +g++ -o lib/iotbx_detectors_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lboost_thread -lboost_system -lboost_python311 -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++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lboost_thread -lboost_system -lboost_python311 -lm -g++ -o lib/iotbx_dtrek_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lboost_thread -lboost_system -lboost_python311 -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++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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' 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_scalepack_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lboost_thread -lboost_system -lboost_python311 -lm -g++ -o lib/iotbx_shelx_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lboost_thread -lboost_system -lboost_python311 -lm +g++ -o lib/iotbx_dtrek_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lboost_thread -lboost_system -lboost_python311 -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++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lccp4io -lccp4c -lm -lboost_thread -lboost_system 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' -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/iotbx_scalepack_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lboost_thread -lboost_system -lboost_python311 -lm g++ -o lib/iotbx_wildcard_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lboost_thread -lboost_system -lboost_python311 -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' +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' 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' +g++ -o spotfinder/dxtbx_toolbox/libdistl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -Ispotfinder/src -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/spotfinder/src -Ispotfinder/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/spotfinder/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/spotfinder/dxtbx_toolbox/libdistl.cpp +g++ -o spotfinder/dxtbx_toolbox/distl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -Ispotfinder/src -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/spotfinder/src -Ispotfinder/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/spotfinder/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/spotfinder/dxtbx_toolbox/distl.cpp 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' -g++ -o spotfinder/dxtbx_toolbox/libdistl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -Ispotfinder/src -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/spotfinder/src -Ispotfinder/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/spotfinder/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/spotfinder/dxtbx_toolbox/libdistl.cpp -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 spotfinder/dxtbx_toolbox/distl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -Ispotfinder/src -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/spotfinder/src -Ispotfinder/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/spotfinder/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/spotfinder/dxtbx_toolbox/distl.cpp -g++ -o lib/iotbx_cif_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lboost_thread -lboost_system -lboost_python311 -lm -lantlr3c -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++11 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lboost_thread -lboost_system -lboost_python311 g++ -o spotfinder/core_toolbox/spot.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -Ispotfinder/src -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/spotfinder/src -Ispotfinder/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/spotfinder/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/spotfinder/core_toolbox/spot.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++11 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lboost_thread -lboost_system -lboost_python311 +g++ -o lib/iotbx_shelx_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lboost_thread -lboost_system -lboost_python311 -lm g++ -o spotfinder/core_toolbox/libdistl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -Ispotfinder/src -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/spotfinder/src -Ispotfinder/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/spotfinder/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/spotfinder/core_toolbox/libdistl.cpp -g++ -o spotfinder/core_toolbox/hough.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -Ispotfinder/src -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/spotfinder/src -Ispotfinder/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/spotfinder/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/spotfinder/core_toolbox/hough.cpp -g++ -o spotfinder/core_toolbox/distl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -Ispotfinder/src -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/spotfinder/src -Ispotfinder/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/spotfinder/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/spotfinder/core_toolbox/distl.cpp -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/spotfilter.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -Ispotfinder/src -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/spotfinder/src -Ispotfinder/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/spotfinder/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/spotfinder/core_toolbox/spotfilter.cpp 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_anharmonic_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -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/gltbx_gl_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lGLU -lGL -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/iotbx_xplor_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -liotbx_xplor -lcctbx -lboost_thread -lboost_system -lboost_python311 -lm -g++ -o lib/dxtbx_flumpy.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/base/lib -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lm -ltiff -lboost_python311 -lcbf -lboost_thread -lboost_system -lm -lcctbx -lscitbx_boost_python -ltiff -lboost_python311 -lcbf -lhdf5 -g++ -o lib/cctbx_eltbx_sasaki_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -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/libiotbx_pdb.so.0.0.1 -shared -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lboost_thread -lboost_system -g++ -o lib/cctbx_symmetry_search_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lomptbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -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/cctbx_miller_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -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' -g++ -o lib/cctbx_eltbx_wavelengths_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -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_translation_search_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lomptbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -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/cctbx_geometry_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -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' -g++ -o lib/iotbx_pdb_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -liotbx_pdb -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -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_covalent_radii_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -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_crystal_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm +g++ -o lib/iotbx_cif_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lboost_thread -lboost_system -lboost_python311 -lm -lantlr3c +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' +g++ -o lib/gltbx_glu_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lGLU -lGL -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_statistics_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -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' -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_sgtbx_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm -g++ -o lib/iotbx_mtz_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -liotbx_mtz -lcctbx -lccp4io -lccp4c -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm -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_orientation_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm -g++ -o lib/cctbx_eltbx_fp_fdp_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm -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/cctbx_adp_restraints_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm -g++ -o lib/gltbx_glu_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lGLU -lGL -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_sgtbx_asu_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx_sgtbx_asu -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm +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 lib/determine_unit_cell_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lomptbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -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/gltbx_viewer_utils_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lGLU -lGL -lm -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' -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/cctbx_eltbx_henke_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -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_covariance_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm -g++ -o lib/cctbx_multipolar_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm -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' -g++ -o lib/cctbx_dmtbx_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -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_array_family_flex_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm -g++ -o lib/cctbx_eltbx_chemical_elements_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -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' +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/dxtbx_model_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/base/lib -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lm -ltiff -lboost_python311 -lcbf -lboost_thread -lboost_system -lm -lcctbx -lscitbx_boost_python -ltiff -lboost_python311 -lcbf -lhdf5 +g++ -o lib/cctbx_xray_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lomptbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm +g++ -o lib/iotbx_xplor_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -liotbx_xplor -lcctbx -lboost_thread -lboost_system -lboost_python311 -lm +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/cctbx_eltbx_henke_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -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_symmetry_search_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lomptbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm +g++ -o lib/cctbx_emma_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm 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_geometry_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -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_french_wilson_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm +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_geometry_restraints_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm +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' +g++ -o lib/cctbx_masks_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lomptbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -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_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' +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' g++ -o lib/gltbx_fonts_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lGLU -lGL -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' -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' -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++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lomptbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm -g++ -o lib/cctbx_merging_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm -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/cctbx_adp_restraints_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm g++ -o lib/cctbx_eltbx_neutron_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm -g++ -o lib/cctbx_uctbx_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm 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++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lomptbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm +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_uctbx_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -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' +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_eltbx_tiny_pse_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -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/cctbx_eltbx_xray_scattering_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm +g++ -o lib/dxtbx_masking_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/base/lib -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lboost_thread -lboost_system -lm -lcctbx -lscitbx_boost_python -ltiff -lboost_python311 -lcbf -lhdf5 +g++ -o lib/cctbx_maptbx_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lomptbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -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_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' 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_xray_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lomptbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -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' -g++ -o lib/cctbx_eltbx_icsd_radii_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm -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_eltbx_attenuation_coefficient_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm -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' -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_emma_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm -g++ -o lib/cctbx_xray_observations_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm -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 lib/cctbx_math_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm +g++ -o lib/cctbx_eltbx_xray_scattering_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm +g++ -o lib/cctbx_covariance_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm +g++ -o lib/cctbx_adptbx_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -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++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lboost_thread -lboost_system +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_multipolar_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm +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' 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' -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/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_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/cctbx_eltbx_attenuation_coefficient_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm +g++ -o lib/cctbx_eltbx_icsd_radii_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm +g++ -o lib/cctbx_math_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm +g++ -o lib/cctbx_eltbx_fp_fdp_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm g++ -o lib/gltbx_util_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lGLU -lGL -lm -g++ -o lib/cctbx_french_wilson_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -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' +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_quadrics_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lGLU -lGL -lm +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 lib/cctbx_maptbx_bcr_bcr_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -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/dxtbx_flumpy.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/base/lib -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lm -ltiff -lboost_python311 -lcbf -lboost_thread -lboost_system -lm -lcctbx -lscitbx_boost_python -ltiff -lboost_python311 -lcbf -lhdf5 +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_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' -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_geometry_restraints_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm -g++ -o lib/cctbx_masks_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lomptbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm -g++ -o lib/cctbx_asymmetric_map_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lasymmetric_map -liotbx_xplor -lcctbx_sgtbx_asu -lcctbx -lomptbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm -g++ -o lib/gltbx_quadrics_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lGLU -lGL -lm -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' -g++ -o lib/dxtbx_masking_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/base/lib -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lboost_thread -lboost_system -lm -lcctbx -lscitbx_boost_python -ltiff -lboost_python311 -lcbf -lhdf5 -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/iotbx_pdb_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -liotbx_pdb -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm +g++ -o lib/cctbx_crystal_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm 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_adptbx_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm -g++ -o lib/cctbx_maptbx_bcr_bcr_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -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' -g++ -o lib/cctbx_maptbx_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lomptbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm -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_merging_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm +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' 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++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm +g++ -o lib/cctbx_sgtbx_asu_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx_sgtbx_asu -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -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' +g++ -o lib/cctbx_orientation_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -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' +g++ -o lib/cctbx_asymmetric_map_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lasymmetric_map -liotbx_xplor -lcctbx_sgtbx_asu -lcctbx -lomptbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -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' +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++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -liotbx_mtz -lcctbx -lccp4io -lccp4c -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm +g++ -o lib/gltbx_gl_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lGLU -lGL -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' +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_chemical_elements_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm +g++ -o lib/cctbx_anharmonic_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm +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_xray_observations_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm +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/cctbx_dmtbx_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -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_eltbx_sasaki_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -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_miller_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm +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/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' +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' +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' +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_wavelengths_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm +g++ -o spotfinder/core_toolbox/hough.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -Ispotfinder/src -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/spotfinder/src -Ispotfinder/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/spotfinder/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/spotfinder/core_toolbox/hough.cpp +g++ -o spotfinder/core_toolbox/distl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -Ispotfinder/src -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/spotfinder/src -Ispotfinder/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/spotfinder/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/spotfinder/core_toolbox/distl.cpp +g++ -o spotfinder/core_toolbox/spotfilter.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -Ispotfinder/src -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/spotfinder/src -Ispotfinder/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/spotfinder/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/spotfinder/core_toolbox/spotfilter.cpp +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' +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 mmtbx/masks/atom_mask.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/masks/atom_mask.cpp -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' -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' g++ -o mmtbx/tls/decompose.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/tls/decompose.cpp -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/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' g++ -o rstbx/dps_core/dps_core.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -Irstbx/src -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/src -Irstbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -Irstbx/src -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/src -Irstbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/dps_core/directional_fft.cpp g++ -o rstbx/dps_core/direction.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -Irstbx/src -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/src -Irstbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/dps_core/direction.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' g++ -o rstbx/indexing_api/indexing_api.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -Irstbx/src -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/src -Irstbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/indexing_api/indexing_api.cpp -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 rstbx/diffraction/ewald_sphere.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -Irstbx/src -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/src -Irstbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/diffraction/ewald_sphere.cpp -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 lib/libspotfinder.so.0.0.1 -shared -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lann-cctbx -lomptbx -lm g++ -o rstbx/diffraction/partial_spot_position_partial_H.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -Irstbx/src -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/src -Irstbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/diffraction/partial_spot_position_partial_H.cpp -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' g++ -o scitbx/minpack/raw.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/minpack/raw.cpp -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++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lspotfinder -lann-cctbx -lomptbx -lm -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' 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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -Ismtbx/refinement/constraints -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/refinement/constraints /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/refinement/constraints/affine.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++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lm g++ -o smtbx/refinement/constraints/geometrical_hydrogens.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -Ismtbx/refinement/constraints -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/refinement/constraints /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/refinement/constraints/geometrical_hydrogens.cpp +g++ -o smtbx/refinement/constraints/occupancy.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -Ismtbx/refinement/constraints -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/refinement/constraints /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/refinement/constraints/occupancy.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++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lboost_thread -lboost_system -lm +Create symlinks for: 'lib/libmmtbx_tls.so.0.0.1' + 'lib/libmmtbx_tls.so.0'->'lib/libmmtbx_tls.so.0.0.1' + 'lib/libmmtbx_tls.so'->'lib/libmmtbx_tls.so.0.0.1' Create symlinks for: 'lib/libscitbx_slatec.so.0.0.1' 'lib/libscitbx_slatec.so.0'->'lib/libscitbx_slatec.so.0.0.1' 'lib/libscitbx_slatec.so'->'lib/libscitbx_slatec.so.0.0.1' -g++ -o smtbx/refinement/constraints/occupancy.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -Ismtbx/refinement/constraints -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/refinement/constraints /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/refinement/constraints/occupancy.cpp +g++ -o smtbx/refinement/constraints/reparametrisation.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -Ismtbx/refinement/constraints -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/refinement/constraints /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/refinement/constraints/reparametrisation.cpp +g++ -o smtbx/refinement/constraints/rigid.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -Ismtbx/refinement/constraints -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/refinement/constraints /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/refinement/constraints/rigid.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++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lboost_thread -lboost_system -lm 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-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -Ismtbx/refinement/constraints -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/refinement/constraints /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/refinement/constraints/reparametrisation.cpp -g++ -o smtbx/refinement/constraints/rigid.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -Ismtbx/refinement/constraints -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/refinement/constraints /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/refinement/constraints/rigid.cpp g++ -o smtbx/refinement/constraints/same_group.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -Ismtbx/refinement/constraints -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/refinement/constraints /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/refinement/constraints/same_group.cpp g++ -o smtbx/refinement/constraints/scaled_adp.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -Ismtbx/refinement/constraints -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/refinement/constraints /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/refinement/constraints/scaled_adp.cpp g++ -o smtbx/refinement/constraints/shared.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -Ismtbx/refinement/constraints -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/refinement/constraints /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/refinement/constraints/shared.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++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lm +g++ -o lib/libspotfinder.so.0.0.1 -shared -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lann-cctbx -lomptbx -lm g++ -o lib/librstbx.so.0.0.1 -shared -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -Wl,-soname=librstbx.so.0 rstbx/dps_core/dps_core.o rstbx/dps_core/directional_fft.o rstbx/dps_core/direction.o rstbx/indexing_api/indexing_api.o rstbx/diffraction/ewald_sphere.o rstbx/diffraction/partial_spot_position_partial_H.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lboost_thread -lboost_system -lcctbx -lm -Create symlinks for: 'lib/libmmtbx_tls.so.0.0.1' - 'lib/libmmtbx_tls.so.0'->'lib/libmmtbx_tls.so.0.0.1' - 'lib/libmmtbx_tls.so'->'lib/libmmtbx_tls.so.0.0.1' -g++ -o smtbx/refinement/constraints/special_position.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -Ismtbx/refinement/constraints -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/refinement/constraints /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/refinement/constraints/special_position.cpp +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++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lspotfinder -lann-cctbx -lomptbx -lm Create symlinks for: 'lib/librstbx.so.0.0.1' 'lib/librstbx.so.0'->'lib/librstbx.so.0.0.1' 'lib/librstbx.so'->'lib/librstbx.so.0.0.1' +g++ -o smtbx/refinement/constraints/special_position.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -Ismtbx/refinement/constraints -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/refinement/constraints /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/refinement/constraints/special_position.cpp +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/symmetry_equivalent.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -Ismtbx/refinement/constraints -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/refinement/constraints /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/refinement/constraints/symmetry_equivalent.cpp g++ -o smtbx/refinement/constraints/u_eq_dependent_u_iso.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -Ismtbx/refinement/constraints -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/refinement/constraints /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/refinement/constraints/u_eq_dependent_u_iso.cpp g++ -o smtbx/refinement/constraints/u_iso_dependent_u_iso.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -Ismtbx/refinement/constraints -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/refinement/constraints /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/refinement/constraints/u_iso_dependent_u_iso.cpp @@ -13061,7 +13097,19 @@ 'lib/libsmtbx_refinement_constraints.so'->'lib/libsmtbx_refinement_constraints.so.0.0.1' g++ -o mmtbx/f_model/f_model_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/f_model/f_model_ext.cpp g++ -o mmtbx/geometry/boost_python/asa_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/geometry/boost_python/asa_ext.cpp +In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/wyckoff.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/sym_equiv_sites.h:5, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/crystal/direct_space_asu.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/asu_cache.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/bond.h:5, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/den/den.h:2, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/den/boost_python/den_ext.cpp:12: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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 instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/wyckoff.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/sym_equiv_sites.h:5, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/crystal/direct_space_asu.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/asu_cache.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/bond.h:5, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/den/den.h:2, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/den/boost_python/den_ext.cpp:12: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ @@ -13103,7 +13140,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]’ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/site_symmetry.h:214:75: required from here /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] -g++ -o lib/iotbx_pdb_hierarchy_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -liotbx_pdb -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm In file included from /usr/include/boost/assert.hpp:58, from /usr/include/boost/smart_ptr/shared_array.hpp:21, from /usr/include/boost/shared_array.hpp:17, @@ -13120,31 +13156,32 @@ '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/indexing_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/geometry/boost_python/indexing_ext.cpp +g++ -o lib/mmtbx_alignment_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm g++ -o lib/mmtbx_dssp_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -liotbx_pdb -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm +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/primitive_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/geometry/boost_python/primitive_ext.cpp 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-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/geometry/boost_python/primitive_ext.cpp -g++ -o lib/mmtbx_cablam_align_utils_ext.so.0.0.1 -shared -rdynamic -std=c++11 -Wl,-soname=mmtbx_cablam_align_utils_ext.so.0 mmtbx/cablam/boost_python/cablam_align_utils_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm -Create symlinks for: 'lib/mmtbx_cablam_align_utils_ext.so.0.0.1' - 'lib/mmtbx_cablam_align_utils_ext.so.0'->'lib/mmtbx_cablam_align_utils_ext.so.0.0.1' - 'lib/mmtbx_cablam_align_utils_ext.so'->'lib/mmtbx_cablam_align_utils_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-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/geometry/boost_python/shared_types_ext.cpp g++ -o lib/libmmtbx_masks.so.0.0.1 -shared -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -Wl,-soname=libmmtbx_masks.so.0 mmtbx/masks/atom_mask.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lomptbx -lcctbx_sgtbx_asu -lm -g++ -o lib/mmtbx_dynamics_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm -g++ -o lib/mmtbx_alignment_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm 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/geometry/boost_python/sphere_surface_sampling_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/geometry/boost_python/sphere_surface_sampling_ext.cpp +g++ -o lib/mmtbx_cablam_align_utils_ext.so.0.0.1 -shared -rdynamic -std=c++11 -Wl,-soname=mmtbx_cablam_align_utils_ext.so.0 mmtbx/cablam/boost_python/cablam_align_utils_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm +g++ -o lib/mmtbx_dynamics_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm +Create symlinks for: 'lib/mmtbx_cablam_align_utils_ext.so.0.0.1' + 'lib/mmtbx_cablam_align_utils_ext.so.0'->'lib/mmtbx_cablam_align_utils_ext.so.0.0.1' + 'lib/mmtbx_cablam_align_utils_ext.so'->'lib/mmtbx_cablam_align_utils_ext.so.0.0.1' +g++ -o mmtbx/hydrogens/hydrogens_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/hydrogens/hydrogens_ext.cpp Create symlinks for: 'lib/mmtbx_dynamics_ext.so.0.0.1' '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' -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/hydrogens/hydrogens_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/hydrogens/hydrogens_ext.cpp g++ -o mmtbx/masks/masks_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/masks/masks_ext.cpp +g++ -o lib/mmtbx_building_loop_closure_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -liotbx_pdb -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -13162,13 +13199,12 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -/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++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -liotbx_pdb -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm 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' +/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/max_lik/max_lik_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/max_lik/max_lik_ext.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, @@ -13187,6 +13223,9 @@ /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/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -13198,8 +13237,9 @@ 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/extract.hpp:16, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/geometry/boost_python/indexing_ext.cpp:2: + from /usr/include/boost/python/object/class.hpp:9, + from /usr/include/boost/python/class.hpp:13, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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( | ^~~~~~~~~~~~~~~~~~~~ @@ -13214,18 +13254,14 @@ 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/class.hpp:9, - from /usr/include/boost/python/class.hpp:13, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/geometry/boost_python/shared_types_ext.cpp:2: + from /usr/include/boost/python/extract.hpp:16, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -13239,13 +13275,13 @@ 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-2022.9+ds2+~3.11.2+ds1/mmtbx/hydrogens/hydrogens_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( - | ^~~~~~~~~~~~~~~~~~~~ + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/geometry/boost_python/sphere_surface_sampling_ext.cpp:2: /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +/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( + | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -13259,13 +13295,13 @@ 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-2022.9+ds2+~3.11.2+ds1/mmtbx/geometry/boost_python/sphere_surface_sampling_ext.cpp:2: -/usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/hydrogens/hydrogens_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( | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ g++ -o lib/mmtbx_geometry_primitive_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm g++ -o lib/mmtbx_geometry_shared_types_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm Create symlinks for: 'lib/mmtbx_geometry_primitive_ext.so.0.0.1' @@ -13281,21 +13317,22 @@ 'lib/mmtbx_den_restraints_ext.so.0'->'lib/mmtbx_den_restraints_ext.so.0.0.1' 'lib/mmtbx_den_restraints_ext.so'->'lib/mmtbx_den_restraints_ext.so.0.0.1' g++ -o mmtbx/ncs/cartesian_restraints_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/ncs/cartesian_restraints_ext.cpp -g++ -o lib/mmtbx_f_model_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm -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-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/ncs/tncs_ext.cpp g++ -o lib/mmtbx_geometry_sphere_surface_sampling_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm 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-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/ncs/tncs_ext.cpp +g++ -o lib/mmtbx_f_model_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm +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/pair_interaction/interaction_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/pair_interaction/interaction_ext.cpp g++ -o lib/mmtbx_hydrogens_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm 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-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/probe/boost_python/probe_bpl.cpp +g++ -o mmtbx/probe/Scoring.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/probe/Scoring.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -13316,17 +13353,6 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -g++ -o mmtbx/probe/Scoring.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/probe/Scoring.cpp -g++ -o lib/mmtbx_ncs_cartesian_restraints_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm -g++ -o lib/mmtbx_masks_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lmmtbx_masks -lcctbx_sgtbx_asu -lcctbx -lomptbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm -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/DotSpheres.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/probe/DotSpheres.cpp -Create symlinks for: 'lib/mmtbx_masks_ext.so.0.0.1' - 'lib/mmtbx_masks_ext.so.0'->'lib/mmtbx_masks_ext.so.0.0.1' - 'lib/mmtbx_masks_ext.so'->'lib/mmtbx_masks_ext.so.0.0.1' -g++ -o mmtbx/probe/SpatialQuery.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/probe/SpatialQuery.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -13347,6 +13373,17 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +g++ -o lib/mmtbx_mosaic_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm +g++ -o lib/mmtbx_ncs_cartesian_restraints_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm +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/probe/DotSpheres.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/probe/DotSpheres.cpp +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-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/probe/SpatialQuery.cpp +g++ -o lib/mmtbx_masks_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lmmtbx_masks -lcctbx_sgtbx_asu -lcctbx -lomptbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -13367,21 +13404,26 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -g++ -o lib/mmtbx_mosaic_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm -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_masks_ext.so.0.0.1' + 'lib/mmtbx_masks_ext.so.0'->'lib/mmtbx_masks_ext.so.0.0.1' + 'lib/mmtbx_masks_ext.so'->'lib/mmtbx_masks_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-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/ccp4 -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/geometry_restraints/boost_python/ramachandran_ext.cpp -g++ -o mmtbx/geometry_restraints/boost_python/reference_coordinate_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/ccp4 -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/geometry_restraints/boost_python/reference_coordinate_ext.cpp g++ -o lib/mmtbx_bulk_solvent_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm -g++ -o lib/mmtbx_geometry_indexing_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -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' +g++ -o mmtbx/geometry_restraints/boost_python/reference_coordinate_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/ccp4 -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/geometry_restraints/boost_python/reference_coordinate_ext.cpp +g++ -o lib/mmtbx_max_lik_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm +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' g++ -o mmtbx/rotamer/fit_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/rotamer/fit_ext.cpp +g++ -o mmtbx/rsr/rsr_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/rsr/rsr_ext.cpp +g++ -o lib/mmtbx_geometry_indexing_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -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/scaling/scaling_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/scaling/scaling_ext.cpp In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/scatterer.h:5, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/restraints.h:6, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/dihedral.h:6, @@ -13391,10 +13433,7 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 mmtbx::geometry_restraints::target_phi_psi(const scitbx::af::const_ref, scitbx::af::trivial_accessor>&, const scitbx::af::const_ref, scitbx::af::trivial_accessor>&, const phi_psi_proxy&) [with FloatType = double]’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/geometry_restraints/ramachandran.h:314:35: required from here /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/geometry_restraints/ramachandran.h:269:19: 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] @@ -13403,7 +13442,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/geometry_restraints/ramachandran.h:284:19: 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] 284 | 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-2022.9+ds2+~3.11.2+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]’ @@ -13415,27 +13453,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]’ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/site_symmetry.h:214:75: required from here /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] -g++ -o lib/mmtbx_max_lik_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm -In file included from /usr/include/boost/assert.hpp:58, - from /usr/include/boost/format/parsing.hpp:21, - from /usr/include/boost/format.hpp:50, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/dihedral.h:8: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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 = mmtbx::geometry_restraints::phi_psi_proxy; GetitemReturnValuePolicy = boost::python::return_internal_reference<>; std::string = std::__cxx11::basic_string]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/geometry_restraints/boost_python/ramachandran_ext.cpp:52:75: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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); - | ~~^~~~~~~~~~~ -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' -g++ -o mmtbx/scaling/relative_scaling_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/scaling/relative_scaling_bpl.cpp -g++ -o lib/mmtbx_ncs_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm -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/scaling/outlier_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/scaling/outlier_bpl.cpp In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/wyckoff.h:4, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/sgtbx/sym_equiv_sites.h:5, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/crystal/direct_space_asu.h:4, @@ -13447,7 +13464,20 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy; PyObject = _object]’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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 = mmtbx::geometry_restraints::phi_psi_proxy; GetitemReturnValuePolicy = boost::python::return_internal_reference<>; std::string = std::__cxx11::basic_string]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/geometry_restraints/boost_python/ramachandran_ext.cpp:52:75: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/mmtbx/geometry_restraints/boost_python/reference_coordinate_ext.cpp:14: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/proxy_select.h: In instantiation of ‘scitbx::af::shared 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-2022.9+ds2+~3.11.2+ds1/mmtbx/geometry_restraints/boost_python/reference_coordinate_ext.cpp:80:41: required from here @@ -13477,9 +13507,15 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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_geometry_clash_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm +g++ -o lib/mmtbx_ncs_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm 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' +g++ -o mmtbx/scaling/outlier_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/scaling/outlier_bpl.cpp +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/secondary_structure/ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/ccp4 -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/secondary_structure/ext.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, @@ -13501,15 +13537,15 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -g++ -o lib/mmtbx_pair_interaction_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm -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/tls/decompose_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/tls/decompose_ext.cpp g++ -o lib/mmtbx_secondary_structure_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -liotbx_pdb -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm 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/decompose_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/tls/decompose_ext.cpp +g++ -o lib/mmtbx_pair_interaction_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm +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/tls/tls_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/tls/tls_ext.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, @@ -13536,10 +13572,12 @@ 'lib/mmtbx_rsr_ext.so.0'->'lib/mmtbx_rsr_ext.so.0.0.1' 'lib/mmtbx_rsr_ext.so'->'lib/mmtbx_rsr_ext.so.0.0.1' g++ -o mmtbx/tls/optimise_amplitudes.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/tls/optimise_amplitudes.cpp -g++ -o lib/mmtbx_tls_decompose_ext.so.0.0.1 -shared -rdynamic -std=c++11 -Wl,-soname=mmtbx_tls_decompose_ext.so.0 mmtbx/tls/decompose_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lmmtbx_tls -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm -Create symlinks for: 'lib/mmtbx_tls_decompose_ext.so.0.0.1' - 'lib/mmtbx_tls_decompose_ext.so.0'->'lib/mmtbx_tls_decompose_ext.so.0.0.1' - 'lib/mmtbx_tls_decompose_ext.so'->'lib/mmtbx_tls_decompose_ext.so.0.0.1' +g++ -o lib/mmtbx_reference_coordinate_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm +g++ -o mmtbx/tls/optimise_amplitudes_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/tls/optimise_amplitudes_ext.cpp +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/utils.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/tls/utils.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -13557,34 +13595,30 @@ /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/tls/optimise_amplitudes_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/tls/optimise_amplitudes_ext.cpp /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -g++ -o mmtbx/tls/utils.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/tls/utils.cpp -g++ -o mmtbx/tls/utils_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/tls/utils_ext.cpp -g++ -o lib/mmtbx_probe_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -Lprobe/lib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/probe/lib -lprobelib -liotbx_pdb -lcctbx -lscitbx_boost_python -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm g++ -o lib/mmtbx_rotamer_fit_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm -g++ -o lib/mmtbx_reference_coordinate_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm 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/utils_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/tls/utils_ext.cpp g++ -o mmtbx/utils/utils_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/utils/utils_ext.cpp +g++ -o lib/mmtbx_tls_decompose_ext.so.0.0.1 -shared -rdynamic -std=c++11 -Wl,-soname=mmtbx_tls_decompose_ext.so.0 mmtbx/tls/decompose_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lmmtbx_tls -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm +Create symlinks for: 'lib/mmtbx_tls_decompose_ext.so.0.0.1' + 'lib/mmtbx_tls_decompose_ext.so.0'->'lib/mmtbx_tls_decompose_ext.so.0.0.1' + 'lib/mmtbx_tls_decompose_ext.so'->'lib/mmtbx_tls_decompose_ext.so.0.0.1' +g++ -o mmtbx/validation/ramachandran/rama_eval_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/validation/ramachandran/rama_eval_bpl.cpp +g++ -o lib/mmtbx_probe_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -Lprobe/lib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/probe/lib -lprobelib -liotbx_pdb -lcctbx -lscitbx_boost_python -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm +g++ -o lib/mmtbx_geometry_asa_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm 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/validation/ramachandran/rama_eval_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/validation/ramachandran/rama_eval_bpl.cpp -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 omptbx/ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/omptbx/ext.cpp +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' g++ -o rstbx/array_family/ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -Irstbx/src -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/src -Irstbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/array_family/ext.cpp -g++ -o lib/mmtbx_ramachandran_restraints_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm -g++ -o rstbx/array_family/flex_rstbx_arrays.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -Irstbx/src -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/src -Irstbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/array_family/flex_rstbx_arrays.cpp -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 rstbx/bandpass/ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -Irstbx/bandpass/src -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/src -Irstbx/bandpass/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -13605,6 +13639,13 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +g++ -o rstbx/array_family/flex_rstbx_arrays.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -Irstbx/src -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/src -Irstbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/array_family/flex_rstbx_arrays.cpp +g++ -o lib/mmtbx_ramachandran_restraints_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm +g++ -o rstbx/bandpass/ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -Irstbx/bandpass/src -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/src -Irstbx/bandpass/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp +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 rstbx/bpcx/detector_model/detector_model_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -Irstbx/bpcx/src -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bpcx/src -Irstbx/bpcx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bpcx/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bpcx/detector_model/detector_model_ext.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -13625,14 +13666,11 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -g++ -o lib/mmtbx_geometry_asa_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm g++ -o lib/omptbx_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lomptbx -lboost_thread -lboost_system -lboost_python311 -lm 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' -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' +g++ -o rstbx/bpcx/detector_model/sensor.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -Irstbx/bpcx/src -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bpcx/src -Irstbx/bpcx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bpcx/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bpcx/detector_model/sensor.cpp In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp:10: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/parameters.h: In constructor ‘rstbx::bandpass::active_area_filter::active_area_filter(scitbx::af::shared)’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/parameters.h:100:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] @@ -13726,8 +13764,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp:933:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 933 | for (int idx = 0; idx < indices.size(); ++idx){ | ~~~~^~~~~~~~~~~~~~~~ -g++ -o rstbx/bpcx/detector_model/detector_model_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -Irstbx/bpcx/src -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bpcx/src -Irstbx/bpcx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bpcx/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -Irstbx/bpcx/src -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bpcx/src -Irstbx/bpcx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bpcx/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bpcx/detector_model/sensor.cpp /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp: In instantiation of ‘void rstbx::bandpass::use_case_bp3::enclosed_pixels_and_margin_pixels_detail() [with pixel_accept_policy = resolution_limited_pixel_accept_policy]’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp:616:87: required from here /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp:631:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] @@ -13768,19 +13804,37 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + 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/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bpcx/detector_model/detector_model_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( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ g++ -o lib/mmtbx_tls_optimise_amplitudes_ext.so.0.0.1 -shared -rdynamic -std=c++11 -Wl,-soname=mmtbx_tls_optimise_amplitudes_ext.so.0 mmtbx/tls/optimise_amplitudes.o mmtbx/tls/optimise_amplitudes_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lmmtbx_tls -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -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/diffraction/fastbragg/fastbragg_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -Irstbx/diffraction/fastbragg/src -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/diffraction/fastbragg/src -Irstbx/diffraction/fastbragg/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/diffraction/fastbragg/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/diffraction/fastbragg/fastbragg_ext.cpp g++ -o rstbx/diffraction/fastbragg/fastbragg.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -Irstbx/diffraction/fastbragg/src -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/diffraction/fastbragg/src -Irstbx/diffraction/fastbragg/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/diffraction/fastbragg/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/diffraction/fastbragg/fastbragg.cpp -g++ -o rstbx/ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -Irstbx/src -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/src -Irstbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/ext.cpp g++ -o lib/mmtbx_validation_ramachandran_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm 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/indexing_api/ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -Irstbx/indexing_api/src -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/indexing_api/src -Irstbx/indexing_api/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/indexing_api/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/indexing_api/ext.cpp -g++ -o lib/mmtbx_scaling_ext.so.0.0.1 -shared -rdynamic -std=c++11 -Wl,-soname=mmtbx_scaling_ext.so.0 mmtbx/scaling/scaling_ext.o mmtbx/scaling/twinning_bpl.o mmtbx/scaling/relative_scaling_bpl.o mmtbx/scaling/outlier_bpl.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm +g++ -o rstbx/ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -Irstbx/src -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/src -Irstbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/ext.cpp In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/ref.h:8, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny_plain.h:4, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny.h:4, @@ -13911,37 +13965,25 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/diffraction/fastbragg/fastbragg.h:176:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 176 | for (int i = 0; i < miller.size(); ++i){ | ~~^~~~~~~~~~~~~~~ +g++ -o rstbx/indexing_api/ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -Irstbx/indexing_api/src -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/indexing_api/src -Irstbx/indexing_api/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/indexing_api/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/indexing_api/ext.cpp /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/diffraction/fastbragg/fastbragg.h: In member function ‘void rstbx::diffraction::fastbragg::fast_bragg_simulation::sweep_over_detector(const bool&)’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/diffraction/fastbragg/fastbragg.h:305:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 305 | for(int i_lambda=0; i_lambda < lambdas.size(); ++i_lambda){ | ~~~~~~~~~^~~~~~~~~~~~~~~~ +g++ -o rstbx/apps/integration_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -Irstbx/apps/src -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/apps/src -Irstbx/apps/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/apps/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/apps/integration_ext.cpp +g++ -o lib/mmtbx_scaling_ext.so.0.0.1 -shared -rdynamic -std=c++11 -Wl,-soname=mmtbx_scaling_ext.so.0 mmtbx/scaling/scaling_ext.o mmtbx/scaling/twinning_bpl.o mmtbx/scaling/relative_scaling_bpl.o mmtbx/scaling/outlier_bpl.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm +g++ -o lib/mmtbx_utils_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm +g++ -o lib/rstbx_bpcx_detector_model_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lrstbx -lann-cctbx -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -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' +Create symlinks for: 'lib/rstbx_bpcx_detector_model_ext.so.0.0.1' + 'lib/rstbx_bpcx_detector_model_ext.so.0'->'lib/rstbx_bpcx_detector_model_ext.so.0.0.1' + 'lib/rstbx_bpcx_detector_model_ext.so'->'lib/rstbx_bpcx_detector_model_ext.so.0.0.1' +g++ -o rstbx/simage/ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -Irstbx/simage/src -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/simage/src -Irstbx/simage/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/simage/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/simage/ext.cpp 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 /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - 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/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bpcx/detector_model/detector_model_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( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -g++ -o rstbx/apps/integration_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -Irstbx/apps/src -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/apps/src -Irstbx/apps/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/apps/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/apps/integration_ext.cpp -g++ -o rstbx/simage/ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -Irstbx/simage/src -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/simage/src -Irstbx/simage/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/simage/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/simage/ext.cpp -g++ -o rstbx/simulation/ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -Irstbx/simulation/src -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/simulation/src -Irstbx/simulation/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/simulation/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/simulation/ext.cpp -g++ -o lib/mmtbx_utils_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/diffraction/fastbragg/fastbragg_ext.cpp:10: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/diffraction/fastbragg/fastbragg.h: In member function ‘scitbx::af::versa > rstbx::diffraction::fastbragg::detector::intdata()’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] @@ -13967,13 +14009,11 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/diffraction/fastbragg/fastbragg.h:176:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 176 | for (int i = 0; i < miller.size(); ++i){ | ~~^~~~~~~~~~~~~~~ +g++ -o rstbx/simulation/ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -Irstbx/simulation/src -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/simulation/src -Irstbx/simulation/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/simulation/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/simulation/ext.cpp /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/diffraction/fastbragg/fastbragg.h: In member function ‘void rstbx::diffraction::fastbragg::fast_bragg_simulation::sweep_over_detector(const bool&)’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/diffraction/fastbragg/fastbragg.h:305:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 305 | for(int i_lambda=0; i_lambda < lambdas.size(); ++i_lambda){ | ~~~~~~~~~^~~~~~~~~~~~~~~~ -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' /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/diffraction/fastbragg/fastbragg.h: In instantiation of ‘scitbx::af::shared rstbx::diffraction::fastbragg::fast_bragg_simulation::sweep_over_detector_get_indices(const bool&) [with IndexType = scitbx::vec3; MillerConversionPolicy = rstbx::diffraction::fastbragg::vec3_double_miller_index_policy]’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/diffraction/fastbragg/fastbragg_ext.cpp:134:11: required from here /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] @@ -13982,6 +14022,7 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/diffraction/fastbragg/fastbragg.h: In instantiation of ‘scitbx::af::shared rstbx::diffraction::fastbragg::fast_bragg_simulation::sweep_over_detector_get_indices(const bool&) [with IndexType = cctbx::miller::index<>; MillerConversionPolicy = rstbx::diffraction::fastbragg::integer_miller_index_policy]’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/diffraction/fastbragg/fastbragg_ext.cpp:138:11: required from here /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] +g++ -o rstbx/symmetry/constraints/ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -Irstbx/symmetry/constraints/src -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/symmetry/constraints/src -Irstbx/symmetry/constraints/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/symmetry/constraints/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/symmetry/constraints/ext.cpp /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/shared_plain.h:132:34: warning: ‘’ may be used uninitialized [-Wmaybe-uninitialized] 132 | std::uninitialized_fill_n(begin(), sz, ElementType()); @@ -14003,11 +14044,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/shared_plain.h:132:48: note: ‘’ declared here 132 | std::uninitialized_fill_n(begin(), sz, ElementType()); | ^~~~~~~~~~~~~ -g++ -o rstbx/symmetry/constraints/ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -Irstbx/symmetry/constraints/src -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/symmetry/constraints/src -Irstbx/symmetry/constraints/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/symmetry/constraints/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/symmetry/constraints/ext.cpp -g++ -o lib/rstbx_bpcx_detector_model_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lrstbx -lann-cctbx -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm -Create symlinks for: 'lib/rstbx_bpcx_detector_model_ext.so.0.0.1' - 'lib/rstbx_bpcx_detector_model_ext.so.0'->'lib/rstbx_bpcx_detector_model_ext.so.0.0.1' - 'lib/rstbx_bpcx_detector_model_ext.so'->'lib/rstbx_bpcx_detector_model_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-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_ext.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, @@ -14049,6 +14085,54 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/fftpack/real_to_complex.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/dps_core/directional_fft.h:5, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/dps_core/dps_core.h:11, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/indexing_api/indexing_api.h:9, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/indexing_api/ext.cpp:4: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/fftpack/factorization.h: In constructor ‘scitbx::fftpack::factorization::factorization(std::size_t, bool)’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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++) { + | ~~^~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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++) { + | ~~^~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/spotfinder/core_toolbox/libdistl.h:81, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/spotfinder/core_toolbox/distl.h:14, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/apps/stills/simple_integration.h:9, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/apps/integration_ext.cpp:3: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/detectors/scanbox.h: In member function ‘Distl::interval_list Distl::scanbox_tiling_explicit::generate_defined_x_tiles(const int&)’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/detectors/scanbox.h:268:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 268 | for (int tile = 0 ; tile < tile_count; ++tile){ + | ~~~~~^~~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/apps/stills/simple_integration.h: In member function ‘void rstbx::integration::simple_integration::append_ISmask(scitbx::af::shared)’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/apps/stills/simple_integration.h:222:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] + 222 | for (int i=0; i < mask.size(); i+=2){ + | ~~^~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/apps/stills/simple_integration.h: In member function ‘void rstbx::integration::simple_integration::positional_correction_mapping(scitbx::af::shared >, scitbx::af::shared >, const annlib_adaptbx::AnnAdaptor&, const annlib_adaptbx::AnnAdaptor&, scitbx::af::shared)’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/apps/stills/simple_integration.h:273:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] + 273 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] + 287 | for (int p=0; p >, scitbx::af::shared >, const annlib_adaptbx::AnnAdaptor&, scitbx::af::shared)’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/apps/stills/simple_integration.h:310:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] + 310 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] + 320 | for (int p=0; p > rstbx::integration::simple_integration::safe_background(const scitbx::af::flex_int&, scitbx::af::shared >, const annlib_adaptbx::AnnAdaptor&, scitbx::af::shared)’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/apps/stills/simple_integration.h:366:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] + 366 | for (int isort=0; isort >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] + 378 | for (int isort=0; isort >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] + 395 | for (int i=0; i + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/apps/stills/simple_integration.h:495:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] + 495 | for (int isort=0; isort >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] + 550 | for (int i=0; i >, scitbx::af::shared >, scitbx::af::shared >)’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/apps/stills/simple_integration.h:575:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] + 575 | for (int i=0; i instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/fftpack/real_to_complex.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/dps_core/directional_fft.h:5, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/dps_core/dps_core.h:11, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/indexing_api/indexing_api.h:9, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/indexing_api/ext.cpp:4: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/fftpack/factorization.h: In constructor ‘scitbx::fftpack::factorization::factorization(std::size_t, bool)’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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++) { - | ~~^~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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++) { - | ~~^~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/apps/stills/simple_integration.h:631:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] + 631 | for (int k=0; k::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] + 638 | for (int k=0; k= dx_.accessor()[1]) i = dx_.accessor()[1] - 1; /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/spotfinder/core_toolbox/libdistl.h:81, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/spotfinder/core_toolbox/distl.h:14, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/apps/stills/simple_integration.h:9, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/apps/integration_ext.cpp:3: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/detectors/scanbox.h: In member function ‘Distl::interval_list Distl::scanbox_tiling_explicit::generate_defined_x_tiles(const int&)’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/detectors/scanbox.h:268:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 268 | for (int tile = 0 ; tile < tile_count; ++tile){ - | ~~~~~^~~~~~~~~~~~ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/panel.h:368:36: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 368 | for (std::size_t y = y0; y < y1; ++y) { @@ -14142,10 +14222,21 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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){ | ~~^~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/apps/stills/simple_integration.h: In member function ‘void rstbx::integration::simple_integration::append_ISmask(scitbx::af::shared)’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/apps/stills/simple_integration.h:222:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] - 222 | for (int i=0; i < mask.size(); i+=2){ - | ~~^~~~~~~~~~~~~ +In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/simulation/ext.cpp:11: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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){ + | ~~^~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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] + 230 | for (int isel = 0; isel < selected.size(); ++isel){ + | ~~~~~^~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/simulation/sim_xfel1.h:231:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] + 231 | for (int imos = 0; imos < mosaic_perturbations.size(); ++imos){ + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/simage/ext.cpp:2: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/rstbx/simage/image_simple.hpp:144:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] @@ -14154,13 +14245,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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++) { | ~^~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/apps/stills/simple_integration.h: In member function ‘void rstbx::integration::simple_integration::positional_correction_mapping(scitbx::af::shared >, scitbx::af::shared >, const annlib_adaptbx::AnnAdaptor&, const annlib_adaptbx::AnnAdaptor&, scitbx::af::shared)’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/apps/stills/simple_integration.h:273:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] - 273 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] - 287 | for (int p=0; p >, scitbx::af::shared >, const annlib_adaptbx::AnnAdaptor&, scitbx::af::shared)’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/apps/stills/simple_integration.h:310:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] - 310 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] - 320 | for (int p=0; p > rstbx::integration::simple_integration::safe_background(const scitbx::af::flex_int&, scitbx::af::shared >, const annlib_adaptbx::AnnAdaptor&, scitbx::af::shared)’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/apps/stills/simple_integration.h:366:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] - 366 | for (int isort=0; isort >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] - 378 | for (int isort=0; isort >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] - 395 | for (int i=0; i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] - 495 | for (int isort=0; isort >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] - 550 | for (int i=0; i >, scitbx::af::shared >, scitbx::af::shared >)’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/apps/stills/simple_integration.h:575:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] - 575 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] - 631 | for (int k=0; k::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] - 638 | for (int k=0; k 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-2022.9+ds2+~3.11.2+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){ - | ~~^~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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] - 230 | for (int isel = 0; isel < selected.size(); ++isel){ - | ~~~~~^~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/simulation/sim_xfel1.h:231:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] - 231 | for (int imos = 0; imos < mosaic_perturbations.size(); ++imos){ - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o lib/mmtbx_tls_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lmmtbx_tls -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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) { @@ -14228,10 +14263,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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/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-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_grid.cpp In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/error.h:16, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/ref.h:4, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny_plain.h:4, @@ -14652,6 +14683,11 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/boost_python/container_conversions.h:290:7: required from ‘scitbx::boost_python::container_conversions::tuple_mapping_fixed_capacity::tuple_mapping_fixed_capacity() [with ContainerType = scitbx::af::small, 8>]’ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_ext.cpp:159:59: required from here /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] +g++ -o lib/mmtbx_tls_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lmmtbx_tls -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm +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-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_grid.cpp In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/shared_plain.h:307, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/versa_plain.h:5, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/versa.h:4, @@ -14667,8 +14703,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/detail/push_back_etc.h:175:26: note: ‘’ declared here 175 | resize(new_size, ElementType()); | ^~~~~~~~~~~~~ -g++ -o lib/rstbx_symmetry_constraints_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lrstbx -lann-cctbx -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm -g++ -o lib/rstbx_bandpass_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lann-cctbx -lann_adaptor -lrstbx -lann-cctbx -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/detail/push_back_etc.h:175:15: warning: ‘’ may be used uninitialized [-Wmaybe-uninitialized] 175 | resize(new_size, ElementType()); @@ -14679,35 +14713,26 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/detail/push_back_etc.h:175:26: note: ‘’ declared here 175 | resize(new_size, ElementType()); | ^~~~~~~~~~~~~ -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_bool.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_bool.cpp +g++ -o lib/rstbx_bandpass_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lann-cctbx -lann_adaptor -lrstbx -lann-cctbx -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm +g++ -o lib/rstbx_symmetry_constraints_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lrstbx -lann-cctbx -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm 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_bool.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_bool.cpp +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-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_size_t.cpp +g++ -o lib/rstbx_simulation_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lrstbx -lann-cctbx -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm g++ -o lib/rstbx_simage_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lrstbx -lann-cctbx -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm +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_int.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_int.cpp 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-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_int.cpp -g++ -o lib/rstbx_indexing_api_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lrstbx -lann-cctbx -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm -g++ -o lib/rstbx_diffraction_fastbragg_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lrstbx -lann-cctbx -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm -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-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_float.cpp -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.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_double.cpp -g++ -o lib/rstbx_simulation_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lrstbx -lann-cctbx -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm -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_matrix.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_double_matrix.cpp -g++ -o lib/rstbx_integration_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lann-cctbx -lann_adaptor -lspotfinder -lrstbx -lann-cctbx -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/error.h:16, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/accessors/flex_grid.h:4, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/flex_types.h:6, @@ -14723,56 +14748,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - 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/to_python_value.hpp:20, - 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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_wrapper.h:6: -/usr/include/boost/bind.hpp: At global scope: -/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/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -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-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_complex_double.cpp -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = bool; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >; e_t = bool]’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_bool.cpp:429:8: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = bool]’ 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++/12/bits/stl_function.h:1438, - from /usr/include/c++/12/functional:49, - from /usr/include/boost/config/no_tr1/functional.hpp:21, - from /usr/include/boost/function/detail/prologue.hpp:14, - 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: -/usr/include/c++/12/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = bool; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >; e_t = bool]’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_bool.cpp:430:8: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = bool]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] - 621 | return last_index(a, std::bind2nd(std::equal_to(), x)); - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/error.h:16, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/accessors/flex_grid.h:4, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/flex_types.h:6, @@ -14808,69 +14783,6 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/assert.hpp:58, - 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:53, - from /usr/include/boost/optional.hpp:15, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/ref_reductions.h:8, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny.h:5, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/small_plain.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/small.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/accessors/flex_grid.h:5: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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 = bool; 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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_bool.cpp:367:15: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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 = bool; 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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_bool.cpp:367:15: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] -In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_wrapper.h:18: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/slice.h: In instantiation of ‘scitbx::af::versa > scitbx::af::copy_slice(const const_ref >&, small) [with T = bool]’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = bool; GetitemReturnValuePolicy = boost::python::return_value_policy]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = bool; GetitemReturnValuePolicy = boost::python::return_value_policy]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = bool; 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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_bool.cpp:367:15: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = bool]’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = bool; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = bool; GetitemReturnValuePolicy = boost::python::return_value_policy]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = bool; 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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_bool.cpp:367:15: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = bool]’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/slice.h:119:35: required from ‘void scitbx::af::copy_to_slice(versa >&, small, const const_ref >&) [with T = bool]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = bool; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = bool; GetitemReturnValuePolicy = boost::python::return_value_policy]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = bool; 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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_bool.cpp:367:15: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -14891,6 +14803,12 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +g++ -o lib/rstbx_diffraction_fastbragg_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lrstbx -lann-cctbx -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm +g++ -o lib/rstbx_indexing_api_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lrstbx -lann-cctbx -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm +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.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_double.cpp /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 unsigned int]’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_size_t.cpp:140:3: required from here /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] @@ -14901,6 +14819,32 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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 = bool; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >; e_t = bool]’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_bool.cpp:429:8: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = bool]’ 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++/12/bits/stl_function.h:1438, + from /usr/include/c++/12/functional:49, + from /usr/include/boost/config/no_tr1/functional.hpp:21, + from /usr/include/boost/function/detail/prologue.hpp:14, + 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: +/usr/include/c++/12/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = bool; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >; e_t = bool]’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_bool.cpp:430:8: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = bool]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] + 621 | return last_index(a, std::bind2nd(std::equal_to(), x)); + | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = unsigned char]’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_size_t.cpp:141:3: required from here /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] @@ -14931,6 +14875,33 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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); | ^~~~~~~~~~~~~ +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_double_matrix.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_double_matrix.cpp +In file included from /usr/include/boost/assert.hpp:58, + 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:53, + from /usr/include/boost/optional.hpp:15, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/ref_reductions.h:8, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny.h:5, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/small_plain.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/small.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/accessors/flex_grid.h:5: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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 = bool; 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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_bool.cpp:367:15: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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 = bool; 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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_bool.cpp:367:15: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]’ @@ -15011,6 +14982,15 @@ /usr/include/c++/12/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ +In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_wrapper.h:18: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/slice.h: In instantiation of ‘scitbx::af::versa > scitbx::af::copy_slice(const const_ref >&, small) [with T = bool]’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = bool; GetitemReturnValuePolicy = boost::python::return_value_policy]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = bool; GetitemReturnValuePolicy = boost::python::return_value_policy]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = bool; 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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_bool.cpp:367:15: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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::flex_wrapper::last_index_a_s(const f_t&, e_t) [with ElementType = unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >; e_t = unsigned int]’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = 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-2022.9+ds2+~3.11.2+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]’ @@ -15021,46 +15001,23 @@ /usr/include/c++/12/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_int.cpp:319:3: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_int.cpp:320:3: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_int.cpp:321:3: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_int.cpp:322:3: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/slice.h: In instantiation of ‘void scitbx::af::copy_to_slice(versa >&, small, const const_ref >&) [with T = bool]’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = bool; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = bool; GetitemReturnValuePolicy = boost::python::return_value_policy]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = bool; 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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_bool.cpp:367:15: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = bool]’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/slice.h:119:35: required from ‘void scitbx::af::copy_to_slice(versa >&, small, const const_ref >&) [with T = bool]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = bool; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = bool; GetitemReturnValuePolicy = boost::python::return_value_policy]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = bool; 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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_bool.cpp:367:15: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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_integration_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lann-cctbx -lann_adaptor -lspotfinder -lrstbx -lann-cctbx -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm In file included from /usr/include/boost/assert.hpp:58, from /usr/include/boost/move/detail/type_traits.hpp:33, from /usr/include/boost/move/traits.hpp:31, @@ -15090,6 +15047,10 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_size_t.cpp:140:3: required from here /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] +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-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_complex_double.cpp /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ @@ -15138,47 +15099,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_size_t.cpp:143:3: required from here /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] -In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/error.h:16, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/accessors/flex_grid.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/flex_types.h:6, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_wrapper.h:15, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_float.cpp:1: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_double_matrix.cpp:4: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_double_matrix.cpp:119:74: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_wrapper.h:18: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ @@ -15202,22 +15122,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_double_matrix.cpp:177:11: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 instead.’ - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/matrix/norms.h: In instantiation of ‘FloatType scitbx::matrix::norm_frobenius(const scitbx::af::const_ref >&) [with FloatType = double]’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_double_matrix.cpp:178:11: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]’ @@ -15240,14 +15144,21 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = int; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >; e_t = int]’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_int.cpp:319:3: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/error.h:16, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/accessors/flex_grid.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/flex_types.h:6, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_wrapper.h:15, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_int.cpp:1: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]’ @@ -15259,30 +15170,21 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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::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-2022.9+ds2+~3.11.2+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]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_int.cpp:319:3: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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++/12/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ +In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/error.h:16, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/accessors/flex_grid.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/flex_types.h:6, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_wrapper.h:15, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_float.cpp:1: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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 >]’ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]’ @@ -15294,6 +15196,26 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/slice.h: In instantiation of ‘scitbx::af::versa > scitbx::af::copy_slice(const const_ref >&, small) [with T = unsigned int]’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]’ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]’ @@ -15316,32 +15238,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = long unsigned int]’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 >]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_size_t.cpp:140:3: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -15362,6 +15258,47 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 >]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_size_t.cpp:140:3: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_size_t.cpp:141:3: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 >]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_size_t.cpp:142:3: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_size_t.cpp:143:3: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = 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]’ @@ -15392,102 +15329,46 @@ /usr/include/c++/12/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 int; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >; e_t = long int]’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 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-2022.9+ds2+~3.11.2+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 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-2022.9+ds2+~3.11.2+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 = long 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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_int.cpp:320:3: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = long int]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] - 616 | return first_index(a, std::bind2nd(std::equal_to(), x)); - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = long int; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >; e_t = long int]’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = long 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-2022.9+ds2+~3.11.2+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 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-2022.9+ds2+~3.11.2+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 = long 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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_int.cpp:319:3: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_int.cpp:320:3: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = long int]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] - 621 | return last_index(a, std::bind2nd(std::equal_to(), x)); - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_size_t.cpp:141:3: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = signed char; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >; e_t = signed char]’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = signed 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-2022.9+ds2+~3.11.2+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 = signed 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-2022.9+ds2+~3.11.2+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 = signed 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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_int.cpp:321:3: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = signed char]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] - 616 | return first_index(a, std::bind2nd(std::equal_to(), x)); - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = signed char; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >; e_t = signed char]’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = signed 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-2022.9+ds2+~3.11.2+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 = signed 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-2022.9+ds2+~3.11.2+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 = signed 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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_int.cpp:321:3: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = signed char]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] - 621 | return last_index(a, std::bind2nd(std::equal_to(), x)); - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 >]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_size_t.cpp:142:3: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = short int; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >; e_t = short int]’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = short 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-2022.9+ds2+~3.11.2+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 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-2022.9+ds2+~3.11.2+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 = short 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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_int.cpp:322:3: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = short int]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] - 616 | return first_index(a, std::bind2nd(std::equal_to(), x)); - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = short int; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >; e_t = short int]’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = short 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-2022.9+ds2+~3.11.2+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 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-2022.9+ds2+~3.11.2+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 = short 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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_int.cpp:322:3: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = short int]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] - 621 | return last_index(a, std::bind2nd(std::equal_to(), x)); - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_size_t.cpp:143:3: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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 /usr/include/boost/assert.hpp:58, from /usr/include/boost/move/detail/type_traits.hpp:33, from /usr/include/boost/move/traits.hpp:31, @@ -15517,26 +15398,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = 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]’ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_float.cpp:12:33: required from here /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_wrapper.h:18: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ @@ -15560,12 +15421,38 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_double.cpp:365:26: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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::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-2022.9+ds2+~3.11.2+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]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_int.cpp:319:3: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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++/12/bits/stl_function.h:1438, + from /usr/include/c++/12/functional:49, + from /usr/include/boost/config/no_tr1/functional.hpp:21, + from /usr/include/boost/function/detail/prologue.hpp:14, + 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: +/usr/include/c++/12/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_int.cpp:319:3: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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++/12/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = float]’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/slice.h:119:35: required from ‘void scitbx::af::copy_to_slice(versa >&, small, const const_ref >&) [with T = float]’ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 >]’ @@ -15577,22 +15464,99 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_float.cpp:12:33: required from here /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_double.cpp:536:8: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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 scitbx/array_family/boost_python/flex_std_string.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_std_string.cpp +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 int; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >; e_t = long int]’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 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-2022.9+ds2+~3.11.2+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 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-2022.9+ds2+~3.11.2+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 = long 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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_int.cpp:320:3: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = long int]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] + 616 | return first_index(a, std::bind2nd(std::equal_to(), x)); + | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = long int; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >; e_t = long int]’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = long 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-2022.9+ds2+~3.11.2+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 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-2022.9+ds2+~3.11.2+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 = long 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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_int.cpp:320:3: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = long int]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] + 621 | return last_index(a, std::bind2nd(std::equal_to(), x)); + | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = signed char; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >; e_t = signed char]’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = signed 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-2022.9+ds2+~3.11.2+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 = signed 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-2022.9+ds2+~3.11.2+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 = signed 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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_int.cpp:321:3: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = signed char]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] + 616 | return first_index(a, std::bind2nd(std::equal_to(), x)); + | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = signed char; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >; e_t = signed char]’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = signed 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-2022.9+ds2+~3.11.2+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 = signed 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-2022.9+ds2+~3.11.2+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 = signed 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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_int.cpp:321:3: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = signed char]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] + 621 | return last_index(a, std::bind2nd(std::equal_to(), x)); + | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = short int; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >; e_t = short int]’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = short 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-2022.9+ds2+~3.11.2+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 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-2022.9+ds2+~3.11.2+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 = short 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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_int.cpp:322:3: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = short int]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] + 616 | return first_index(a, std::bind2nd(std::equal_to(), x)); + | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = short int; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >; e_t = short int]’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = short 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-2022.9+ds2+~3.11.2+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 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-2022.9+ds2+~3.11.2+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 = short 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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_int.cpp:322:3: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = short int]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] + 621 | return last_index(a, std::bind2nd(std::equal_to(), x)); + | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ +In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_double_matrix.cpp:4: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_double_matrix.cpp:119:74: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_double_matrix.cpp:177:11: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_double_matrix.cpp:178:11: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/error.h:16, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/accessors/flex_grid.h:4, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/flex_types.h:6, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_wrapper.h:15, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_complex_double.cpp:1: + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_double.cpp:1: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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); @@ -15603,36 +15567,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_double.cpp:477:42: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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++/12/bits/stl_function.h:1438, - from /usr/include/c++/12/functional:49, - from /usr/include/boost/config/no_tr1/functional.hpp:21, - from /usr/include/boost/function/detail/prologue.hpp:14, - 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: -/usr/include/c++/12/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_double.cpp:477:42: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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++/12/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -15653,6 +15587,32 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_double.cpp:7: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_double.cpp:365:26: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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::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]’ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_int.cpp:319:3: required from here /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] -In file included from /usr/include/boost/assert.hpp:58, - 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:53, - from /usr/include/boost/optional.hpp:15, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/ref_reductions.h:8, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny.h:5, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/small_plain.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/small.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/accessors/flex_grid.h:5: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_double.cpp:477:42: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_double.cpp:477:42: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_double.cpp:536:8: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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 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]’ @@ -15731,29 +15672,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = long 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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_int.cpp:320:3: required from here /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] -In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_wrapper.h:18: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/slice.h: In instantiation of ‘scitbx::af::versa > scitbx::af::copy_slice(const const_ref >&, small) [with T = double]’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_double.cpp:477:42: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_double.cpp:477:42: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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 = signed 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]’ @@ -15772,36 +15690,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = signed 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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_int.cpp:321:3: required from here /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_double.cpp:477:42: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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/boost/assert.hpp:58, - 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:53, - from /usr/include/boost/optional.hpp:15, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/ref_reductions.h:8, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny.h:5, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/small_plain.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/small.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/accessors/flex_grid.h:5: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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 = std::complex; 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-2022.9+ds2+~3.11.2+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 = std::complex; 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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_complex_double.cpp:117:24: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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 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]’ @@ -15811,12 +15699,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = short 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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_int.cpp:322:3: required from here /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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 = std::complex; 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-2022.9+ds2+~3.11.2+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 = std::complex; 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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_complex_double.cpp:117:24: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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 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]’ @@ -15826,6 +15708,36 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = short 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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_int.cpp:322:3: required from here /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_double.cpp:477:42: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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++/12/bits/stl_function.h:1438, + from /usr/include/c++/12/functional:49, + from /usr/include/boost/config/no_tr1/functional.hpp:21, + from /usr/include/boost/function/detail/prologue.hpp:14, + 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: +/usr/include/c++/12/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_double.cpp:477:42: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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++/12/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_wrapper.h:18: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ @@ -15875,25 +15787,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = std::complex]’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = std::complex; GetitemReturnValuePolicy = boost::python::return_value_policy]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = std::complex; GetitemReturnValuePolicy = boost::python::return_value_policy]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = std::complex; 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-2022.9+ds2+~3.11.2+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 = std::complex; 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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_complex_double.cpp:117:24: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = std::complex]’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = std::complex; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa, scitbx::af::flex_grid<> >]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = std::complex; GetitemReturnValuePolicy = boost::python::return_value_policy]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = std::complex; 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-2022.9+ds2+~3.11.2+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 = std::complex; 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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_complex_double.cpp:117:24: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = signed char]’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = signed char; GetitemReturnValuePolicy = boost::python::return_value_policy]’ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = signed char; GetitemReturnValuePolicy = boost::python::return_value_policy]’ @@ -15942,6 +15835,21 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/slice.h:119:35: required from ‘void scitbx::af::copy_to_slice(versa >&, small, const const_ref >&) [with T = int]’ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = int; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >]’ @@ -15954,15 +15862,26 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_int.cpp:319:3: required from here /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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 = std::complex]’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/slice.h:119:35: required from ‘void scitbx::af::copy_to_slice(versa >&, small, const const_ref >&) [with T = std::complex]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = std::complex; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa, scitbx::af::flex_grid<> >]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = std::complex; GetitemReturnValuePolicy = boost::python::return_value_policy]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = std::complex; 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-2022.9+ds2+~3.11.2+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 = std::complex; 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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_complex_double.cpp:117:24: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + 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/to_python_value.hpp:20, + 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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_wrapper.h:6: +/usr/include/boost/bind.hpp: At global scope: +/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/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 int; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >]’ @@ -15974,7 +15893,95 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = long 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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_int.cpp:320:3: required from here /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] -g++ -o lib/mmtbx_tls_utils_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lmmtbx_tls -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm +In file included from /usr/include/boost/assert.hpp:58, + 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:53, + from /usr/include/boost/optional.hpp:15, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/ref_reductions.h:8, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny.h:5, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/small_plain.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/small.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/accessors/flex_grid.h:5: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_double.cpp:477:42: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_double.cpp:477:42: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] +g++ -o scitbx/array_family/boost_python/flex_std_string.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_std_string.cpp +In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_wrapper.h:18: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/slice.h: In instantiation of ‘scitbx::af::versa > scitbx::af::copy_slice(const const_ref >&, small) [with T = double]’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_double.cpp:477:42: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_double.cpp:477:42: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = double]’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_double.cpp:477:42: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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/boost/assert.hpp:58, + 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:53, + from /usr/include/boost/optional.hpp:15, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/ref_reductions.h:8, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny.h:5, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/small_plain.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/small.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/accessors/flex_grid.h:5: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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 = std::complex; 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-2022.9+ds2+~3.11.2+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 = std::complex; 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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_complex_double.cpp:117:24: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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 = std::complex; 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-2022.9+ds2+~3.11.2+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 = std::complex; 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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_complex_double.cpp:117:24: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = signed char]’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/slice.h:119:35: required from ‘void scitbx::af::copy_to_slice(versa >&, small, const const_ref >&) [with T = signed char]’ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = signed char; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >]’ @@ -15986,10 +15993,25 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = signed 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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_int.cpp:321:3: required from here /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] -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_random.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_random.cpp +In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_wrapper.h:18: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/slice.h: In instantiation of ‘scitbx::af::versa > scitbx::af::copy_slice(const const_ref >&, small) [with T = std::complex]’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = std::complex; GetitemReturnValuePolicy = boost::python::return_value_policy]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = std::complex; GetitemReturnValuePolicy = boost::python::return_value_policy]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = std::complex; 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-2022.9+ds2+~3.11.2+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 = std::complex; 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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_complex_double.cpp:117:24: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = std::complex]’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = std::complex; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa, scitbx::af::flex_grid<> >]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = std::complex; GetitemReturnValuePolicy = boost::python::return_value_policy]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = std::complex; 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-2022.9+ds2+~3.11.2+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 = std::complex; 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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_complex_double.cpp:117:24: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = short int]’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]’ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 int; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >]’ @@ -16001,6 +16023,25 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = short 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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_int.cpp:322:3: required from here /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = std::complex]’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/slice.h:119:35: required from ‘void scitbx::af::copy_to_slice(versa >&, small, const const_ref >&) [with T = std::complex]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = std::complex; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa, scitbx::af::flex_grid<> >]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = std::complex; GetitemReturnValuePolicy = boost::python::return_value_policy]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = std::complex; 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-2022.9+ds2+~3.11.2+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 = std::complex; 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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_complex_double.cpp:117:24: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lmmtbx_tls -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm +g++ -o lib/rstbx_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lrstbx -lann-cctbx -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm +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_random.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_random.cpp +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-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_sort.cpp In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_std_string.cpp:3: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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] @@ -16110,20 +16151,11 @@ Create symlinks for: 'lib/rstbx_array_family_flex_ext.so.0.0.1' 'lib/rstbx_array_family_flex_ext.so.0'->'lib/rstbx_array_family_flex_ext.so.0.0.1' 'lib/rstbx_array_family_flex_ext.so'->'lib/rstbx_array_family_flex_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-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_sort.cpp -g++ -o lib/rstbx_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lrstbx -lann-cctbx -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm g++ -o scitbx/array_family/boost_python/flex_histogram.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_histogram.cpp -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_weighted_histogram.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_weighted_histogram.cpp g++ -o scitbx/array_family/boost_python/flex_mean_and_variance.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_mean_and_variance.cpp g++ -o scitbx/array_family/boost_python/flex_median.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_median.cpp g++ -o scitbx/array_family/boost_python/flex_linear_interpolation.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_linear_interpolation.cpp -g++ -o scitbx/array_family/boost_python/flex_vec3_double.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_vec3_double.cpp -g++ -o scitbx/array_family/boost_python/flex_vec2_double.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_vec2_double.cpp -g++ -o scitbx/array_family/boost_python/flex_vec3_int.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_vec3_int.cpp -g++ -o scitbx/array_family/boost_python/flex_sym_mat3_double.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_sym_mat3_double.cpp In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_median.cpp:2: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/math/basic_statistics.h: In instantiation of ‘scitbx::math::median_statistics scitbx::math::median_functor::dispersion(const scitbx::af::ref&) [with FloatType = double]’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_median.cpp:31:26: required from ‘static scitbx::math::median_statistics scitbx::af::boost_python::median_functor_wrapper::dispersion(wt&, const scitbx::af::const_ref&) [with FloatType = double; wt = scitbx::math::median_functor]’ @@ -16132,7 +16164,12 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/math/basic_statistics.h:210:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::const_ref::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 210 | for (int i=0; i < data.size(); ++i) { | ~~^~~~~~~~~~~~~ +g++ -o scitbx/array_family/boost_python/flex_vec3_double.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_vec3_double.cpp +g++ -o scitbx/array_family/boost_python/flex_vec2_double.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_vec2_double.cpp +g++ -o scitbx/array_family/boost_python/flex_vec3_int.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_vec3_int.cpp +g++ -o scitbx/array_family/boost_python/flex_sym_mat3_double.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_sym_mat3_double.cpp g++ -o scitbx/array_family/boost_python/flex_mat3_double.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_mat3_double.cpp +g++ -o scitbx/array_family/boost_python/flex_tiny_size_t_2.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_tiny_size_t_2.cpp In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/error.h:16, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/accessors/flex_grid.h:4, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/flex_types.h:6, @@ -16148,6 +16185,27 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/loops.cpp +In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/error.h:16, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/accessors/flex_grid.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/flex_types.h:6, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_wrapper.h:15, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_vec2_double.cpp:3: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = scitbx::vec3; 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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_vec3_double.cpp:567:15: required from here /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] +In file included from /usr/include/boost/assert.hpp:58, + 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:53, + from /usr/include/boost/optional.hpp:15, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/ref_reductions.h:8, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny.h:5, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/small_plain.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/small.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/accessors/flex_grid.h:5: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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::vec2; 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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_vec2_double.cpp:440:15: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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::vec2; 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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_vec2_double.cpp:440:15: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] +In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_wrapper.h:18: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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::vec2; GetitemReturnValuePolicy = boost::python::return_value_policy]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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::vec2; 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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_vec2_double.cpp:440:15: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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::copy_slice(const const_ref >&, small) [with T = scitbx::vec3]’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]’ @@ -16180,6 +16270,14 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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::vec2]’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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::vec2; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa, scitbx::af::flex_grid<> >]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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::vec2; GetitemReturnValuePolicy = boost::python::return_value_policy]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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::vec2; 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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_vec2_double.cpp:440:15: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 >&, small, const const_ref >&) [with T = scitbx::vec3]’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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<> >]’ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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::vec3; GetitemReturnValuePolicy = boost::python::return_value_policy]’ @@ -16188,6 +16286,29 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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::vec2; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa, scitbx::af::flex_grid<> >]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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::vec2; GetitemReturnValuePolicy = boost::python::return_value_policy]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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::vec2; 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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_vec2_double.cpp:440:15: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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<> >]’ @@ -16200,7 +16321,7 @@ from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/accessors/flex_grid.h:4, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/flex_types.h:6, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_wrapper.h:15, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_sym_mat3_double.cpp:3: + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_vec3_int.cpp:3: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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); @@ -16234,23 +16355,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]’ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_sym_mat3_double.cpp:124:15: required from here /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] -g++ -o scitbx/array_family/boost_python/flex_tiny_size_t_2.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_tiny_size_t_2.cpp -g++ -o scitbx/array_family/boost_python/loops.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/loops.cpp -In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/error.h:16, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/accessors/flex_grid.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/flex_types.h:6, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_wrapper.h:15, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_vec2_double.cpp:3: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_wrapper.h:18: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ @@ -16268,11 +16372,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 >::type* scitbx::af::{anonymous}::array_indices_as_double_from_array_focus_dimensions(const scitbx::vec2&)’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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::small, const scitbx::af::const_ref >&) [with T = scitbx::sym_mat3]’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]’ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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<> >]’ @@ -16281,61 +16380,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_sym_mat3_double.cpp:124:15: required from here /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/error.h:16, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/accessors/flex_grid.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/flex_types.h:6, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_wrapper.h:15, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_vec3_int.cpp:3: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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/boost/assert.hpp:58, - 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:53, - from /usr/include/boost/optional.hpp:15, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/ref_reductions.h:8, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny.h:5, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/small_plain.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/small.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/accessors/flex_grid.h:5: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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::vec2; 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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_vec2_double.cpp:440:15: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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::vec2; 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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_vec2_double.cpp:440:15: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] -In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_wrapper.h:18: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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::vec2; GetitemReturnValuePolicy = boost::python::return_value_policy]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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::vec2; 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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_vec2_double.cpp:440:15: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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::vec2]’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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::vec2; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa, scitbx::af::flex_grid<> >]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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::vec2; GetitemReturnValuePolicy = boost::python::return_value_policy]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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::vec2; 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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_vec2_double.cpp:440:15: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = scitbx::vec3; 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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_vec3_int.cpp:117:15: required from here /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] -g++ -o scitbx/array_family/boost_python/show_sizes.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/show_sizes.cpp -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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::vec2]’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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::vec2; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa, scitbx::af::flex_grid<> >]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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::vec2; GetitemReturnValuePolicy = boost::python::return_value_policy]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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::vec2; 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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_vec2_double.cpp:440:15: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_wrapper.h:18: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ @@ -16393,6 +16428,7 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_vec3_int.cpp:117:15: required from here /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/show_sizes.cpp g++ -o scitbx/array_family/boost_python/numpy_bridge.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/numpy_bridge.cpp In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/error.h:16, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/accessors/flex_grid.h:4, @@ -16432,31 +16468,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]’ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_mat3_double.cpp:180:15: required from here /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] -In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_wrapper.h:18: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_mat3_double.cpp:180:15: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_mat3_double.cpp:180:15: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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::mat3]’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_mat3_double.cpp:180:15: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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/boost/assert.hpp:58, from /usr/include/boost/move/detail/type_traits.hpp:33, from /usr/include/boost/move/traits.hpp:31, @@ -16483,28 +16494,31 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]’ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_tiny_size_t_2.cpp:32:47: required from here /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - 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/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /usr/include/boost/python/numpy/dtype.hpp:15, - from /usr/include/boost/python/numpy.hpp:10, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/numpy_bridge.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/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_wrapper.h:18: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_mat3_double.cpp:180:15: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_mat3_double.cpp:180:15: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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::mat3]’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_mat3_double.cpp:180:15: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_wrapper.h:18: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ @@ -16530,6 +16544,30 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_tiny_size_t_2.cpp:32:47: required from here /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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/shared_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/shared_ext.cpp +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + 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/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /usr/include/boost/python/numpy/dtype.hpp:15, + from /usr/include/boost/python/numpy.hpp:10, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/numpy_bridge.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/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +g++ -o scitbx/cubicle_neighbors_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/cubicle_neighbors_ext.cpp /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/numpy_bridge.cpp:202:3: required from here /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/numpy_bridge.cpp:86:23: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] @@ -16836,7 +16874,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/shared_plain.h:132:48: note: ‘’ declared here 132 | std::uninitialized_fill_n(begin(), sz, ElementType()); | ^~~~~~~~~~~~~ -g++ -o scitbx/array_family/boost_python/shared_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/shared_ext.cpp In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/versa_plain.h:5, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/versa.h:4, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/flex_types.h:7: @@ -16863,22 +16900,10 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/shared_plain.h:132:48: note: ‘’ declared here 132 | std::uninitialized_fill_n(begin(), sz, ElementType()); | ^~~~~~~~~~~~~ -g++ -o scitbx/cubicle_neighbors_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/cubicle_neighbors_ext.cpp -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/shared_plain.h:307: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/versa_plain.h:5, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/versa.h:4, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/flex_types.h:7: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/shared_plain.h:132:34: warning: ‘’ may be used uninitialized [-Wmaybe-uninitialized] 132 | std::uninitialized_fill_n(begin(), sz, ElementType()); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -16895,7 +16920,7 @@ from /usr/include/boost/python/make_function.hpp:10, from /usr/include/boost/python/def.hpp:11, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_wrapper.h:6: -/usr/include/c++/12/bits/stl_uninitialized.h:312:5: 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++/12/bits/stl_uninitialized.h:312:5: 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 312 | uninitialized_fill_n(_ForwardIterator __first, _Size __n, const _Tp& __x) | ^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/shared_plain.h:132:48: note: ‘’ declared here @@ -16912,40 +16937,12 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/versa_plain.h:5, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/versa.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/flex_types.h:7: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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++/12/memory:66, - from /usr/include/boost/function/function_base.hpp:16, - from /usr/include/boost/function/detail/prologue.hpp:17, - 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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_wrapper.h:6: -/usr/include/c++/12/bits/stl_uninitialized.h:312:5: 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 - 312 | uninitialized_fill_n(_ForwardIterator __first, _Size __n, const _Tp& __x) - | ^~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/fftpack/boost_python/fftpack_ext.cpp -g++ -o scitbx/glmtbx/boost_python/ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/glmtbx/boost_python/ext.cc -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/shared_plain.h:307: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/versa_plain.h:168:50: note: ‘’ declared here @@ -17000,10 +16997,11 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 = scitbx::af::tiny; GetitemReturnValuePolicy = boost::python::return_value_policy; std::string = std::__cxx11::basic_string]’ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/shared_ext.cpp:51:40: required from here /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] +g++ -o scitbx/fftpack/boost_python/fftpack_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/fftpack/boost_python/fftpack_ext.cpp In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/versa_plain.h:5, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/versa.h:4, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/flex_types.h:7: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/shared_plain.h:132:34: warning: ‘’ may be used uninitialized [-Wmaybe-uninitialized] 132 | std::uninitialized_fill_n(begin(), sz, ElementType()); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -17020,12 +17018,23 @@ from /usr/include/boost/python/make_function.hpp:10, from /usr/include/boost/python/def.hpp:11, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_wrapper.h:6: -/usr/include/c++/12/bits/stl_uninitialized.h:312:5: 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 +/usr/include/c++/12/bits/stl_uninitialized.h:312:5: 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 312 | uninitialized_fill_n(_ForwardIterator __first, _Size __n, const _Tp& __x) | ^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/shared_plain.h:132:48: note: ‘’ declared here 132 | std::uninitialized_fill_n(begin(), sz, ElementType()); | ^~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/shared_plain.h:307: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -17046,17 +17055,32 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/shared_plain.h:307: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/versa_plain.h:5, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/versa.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/flex_types.h:7: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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++/12/memory:66, + from /usr/include/boost/function/function_base.hpp:16, + from /usr/include/boost/function/detail/prologue.hpp:17, + 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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_wrapper.h:6: +/usr/include/c++/12/bits/stl_uninitialized.h:312:5: 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 + 312 | uninitialized_fill_n(_ForwardIterator __first, _Size __n, const _Tp& __x) + | ^~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/cubicle_neighbors_ext.cpp:3: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/cubicle_neighbors_ext.cpp:23:36: required from here @@ -17069,7 +17093,7 @@ In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/versa_plain.h:5, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/versa.h:4, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/flex_types.h:7: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/shared_plain.h:132:34: warning: ‘’ may be used uninitialized [-Wmaybe-uninitialized] 132 | std::uninitialized_fill_n(begin(), sz, ElementType()); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -17086,12 +17110,23 @@ from /usr/include/boost/python/make_function.hpp:10, from /usr/include/boost/python/def.hpp:11, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_wrapper.h:6: -/usr/include/c++/12/bits/stl_uninitialized.h:312:5: 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++/12/bits/stl_uninitialized.h:312:5: 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 312 | uninitialized_fill_n(_ForwardIterator __first, _Size __n, const _Tp& __x) | ^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/shared_plain.h:132:48: note: ‘’ declared here 132 | std::uninitialized_fill_n(begin(), sz, ElementType()); | ^~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/shared_plain.h:307: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/cubicle_neighbors.hpp:4: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ @@ -17108,15 +17143,7 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/fftpack/gridding.h:5, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/fftpack/boost_python/fftpack_ext.cpp:4: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/fftpack/factorization.h: In constructor ‘scitbx::fftpack::factorization::factorization(std::size_t, bool)’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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++) { - | ~~^~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/glmtbx/boost_python/ext.cc /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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()); @@ -17128,17 +17155,26 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/shared_plain.h:307: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/fftpack/gridding.h:5, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/fftpack/boost_python/fftpack_ext.cpp:4: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/fftpack/factorization.h: In constructor ‘scitbx::fftpack::factorization::factorization(std::size_t, bool)’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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++) { + | ~~^~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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++) { + | ~~^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -17160,10 +17196,10 @@ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ g++ -o lib/scitbx_cubicle_neighbors_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm -g++ -o scitbx/graphics_utils/ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/graphics_utils/ext.cpp 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-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/graphics_utils/ext.cpp g++ -o scitbx/iso_surface/iso_surface_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/iso_surface/iso_surface_ext.cpp g++ -o scitbx/lbfgs/ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DSCITBX_LBFGS_HAVE_LBFGS_FEM -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/lbfgs/ext.cpp g++ -o scitbx/lbfgs/lbfgs_fem.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable scitbx/lbfgs/lbfgs_fem.cpp @@ -17205,13 +17241,7 @@ 704 | while (pos < internal_file_len) { | ~~~~^~~~~~~~~~~~~~~~~~~ g++ -o scitbx/lbfgsb/boost_python/lbfgsb_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/lbfgsb/boost_python/lbfgsb_ext.cpp -g++ -o lib/scitbx_glmtbx_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm g++ -o scitbx/linalg/boost_python/linalg_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/linalg/boost_python/linalg_ext.cpp -g++ -o scitbx/linalg/boost_python/matrix.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/linalg/boost_python/matrix.cpp -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/cholesky.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/linalg/boost_python/cholesky.cpp In file included from /usr/include/boost/config/header_deprecated.hpp:18, from /usr/include/boost/timer.hpp:20, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/lbfgsb/raw.h:9, @@ -17220,8 +17250,7 @@ /usr/include/boost/timer.hpp:21:1: note: ‘#pragma message: This header is deprecated. Use the facilities in instead.’ 21 | BOOST_HEADER_DEPRECATED( "the facilities in " ) | ^~~~~~~~~~~~~~~~~~~~~~~ -g++ -o scitbx/linalg/boost_python/householder.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/linalg/boost_python/householder.cpp -g++ -o scitbx/linalg/boost_python/svd.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/linalg/boost_python/svd.cpp +g++ -o scitbx/linalg/boost_python/matrix.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/linalg/boost_python/matrix.cpp In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/error.h:16, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/serialization/base_256.h:2, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/math/floating_point_epsilon.h:4, @@ -17271,6 +17300,7 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/lbfgsb/raw.h:3675:5: note: in expansion of macro ‘SCITBX_ASSERT’ 3675 | SCITBX_ASSERT(g.size() == n); | ^~~~~~~~~~~~~ +g++ -o scitbx/linalg/boost_python/cholesky.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/linalg/boost_python/cholesky.cpp /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/lbfgsb/raw.h:974:19: required from ‘void scitbx::lbfgsb::raw::prn3lb(const int&, const ref1&, const FloatType&, const std::string&, const int&, const int&, const int&, const int&, const int&, const int&, const int&, const int&, const FloatType&, const FloatType&, const int&, const std::string&, const int&, const FloatType&, const FloatType&, const int&, const FloatType&, const FloatType&, const FloatType&) [with FloatType = double; std::string = std::__cxx11::basic_string]’ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/lbfgsb/raw.h:3786:15: required from ‘void scitbx::lbfgsb::raw::mainlb(const int&, const int&, const ref1&, const ref1&, const ref1&, const ref1&, FloatType&, const ref1&, const FloatType&, const FloatType&, const ref2&, const ref2&, const ref2&, const ref2&, const ref2&, const ref2&, const ref2&, const ref2&, const ref1&, const ref1&, const ref1&, const ref1&, const ref1&, const ref1&, const ref1&, const ref1&, const ref1&, const ref1&, const ref1&, const ref1&, std::string&, const int&, std::string&, const ref1&, const ref1&, const ref1&, bool) [with FloatType = double; std::string = std::__cxx11::basic_string]’ @@ -17284,7 +17314,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]’ /usr/include/boost/python/object/make_holder.hpp:94:18: required from ‘static void boost::python::objects::make_holder<9>::apply::execute(PyObject*, t0, t1, t2, t3, t4, t5, t6, t7, t8) [with Holder = boost::python::objects::value_holder >; ArgList = boost::mpl::vector9, scitbx::af::shared, scitbx::af::shared, bool, const double&, const double&, const int&>; PyObject = _object; t0 = const int&; t1 = const int&; t2 = scitbx::af::shared; t3 = scitbx::af::shared; t4 = scitbx::af::shared; t5 = bool; t6 = const double&; t7 = const double&; t8 = const int&]’ @@ -17321,21 +17350,32 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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/householder.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/linalg/boost_python/householder.cpp +g++ -o lib/scitbx_iso_surface_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm +g++ -o lib/scitbx_glmtbx_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm 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-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/linalg/boost_python/svd.cpp +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-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/linalg/boost_python/eigensystem.cpp -g++ -o lib/scitbx_fftpack_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lomptbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm g++ -o lib/scitbx_graphics_utils_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm -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/linalg/boost_python/lapack_fem_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/linalg/boost_python/lapack_fem_bpl.cpp Create symlinks for: 'lib/scitbx_graphics_utils_ext.so.0.0.1' 'lib/scitbx_graphics_utils_ext.so.0'->'lib/scitbx_graphics_utils_ext.so.0.0.1' 'lib/scitbx_graphics_utils_ext.so'->'lib/scitbx_graphics_utils_ext.so.0.0.1' +g++ -o scitbx/linalg/boost_python/lapack_fem_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/linalg/boost_python/lapack_fem_bpl.cpp g++ -o scitbx/lstbx/boost_python/lstbx_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/lstbx/boost_python/lstbx_ext.cpp g++ -o scitbx/lstbx/boost_python/normal_equations.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/lstbx/boost_python/normal_equations.cpp +g++ -o lib/scitbx_fftpack_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lomptbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm +g++ -o lib/scitbx_lbfgsb_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm +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/math_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/math/boost_python/math_ext.cpp g++ -o scitbx/math/boost_python/basic_statistics.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/math/boost_python/basic_statistics.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, @@ -17358,7 +17398,6 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -g++ -o lib/scitbx_lbfgsb_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/error.h:16, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/mat3.h:5, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/sym_mat3.h:4, @@ -17373,29 +17412,26 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/linalg/boost_python/lapack_fem_bpl.cpp:246:5: note: in expansion of macro ‘SCITBX_ASSERT’ 246 | SCITBX_ASSERT(w.size() == n); | ^~~~~~~~~~~~~ -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/gaussian.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/math/boost_python/gaussian.cpp g++ -o scitbx/math/boost_python/golay.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/math/boost_python/golay.cpp -g++ -o scitbx/math/boost_python/minimum_covering_sphere.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/math/boost_python/minimum_covering_sphere.cpp g++ -o lib/scitbx_lbfgs_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm -g++ -o scitbx/math/boost_python/principal_axes_of_inertia.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/math/boost_python/principal_axes_of_inertia.cpp -g++ -o lib/scitbx_linalg_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm +g++ -o scitbx/math/boost_python/minimum_covering_sphere.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/math/boost_python/minimum_covering_sphere.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' +g++ -o scitbx/math/boost_python/principal_axes_of_inertia.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/math/boost_python/principal_axes_of_inertia.cpp g++ -o scitbx/math/boost_python/row_echelon.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/math/boost_python/row_echelon.cpp +g++ -o scitbx/math/boost_python/tensor_rank_2.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/math/boost_python/tensor_rank_2.cpp +g++ -o lib/scitbx_linalg_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm 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/tensor_rank_2.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/math/boost_python/tensor_rank_2.cpp g++ -o scitbx/math/boost_python/chebyshev.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/math/boost_python/chebyshev.cpp -g++ -o scitbx/math/boost_python/icosahedron.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/math/boost_python/icosahedron.cpp g++ -o lib/scitbx_array_family_shared_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm -lboost_numpy311 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/icosahedron.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/math/boost_python/icosahedron.cpp g++ -o scitbx/math/boost_python/slatec.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/math/boost_python/slatec.cpp g++ -o scitbx/math/boost_python/line_search.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/math/boost_python/line_search.cpp g++ -o scitbx/math/boost_python/r3_rotation.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/math/boost_python/r3_rotation.cpp @@ -17404,11 +17440,11 @@ g++ -o scitbx/math/boost_python/unimodular_generator.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/math/boost_python/unimodular_generator.cpp g++ -o scitbx/math/boost_python/halton.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/math/boost_python/halton.cpp g++ -o scitbx/math/boost_python/least_squares_plane.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/math/boost_python/least_squares_plane.cpp +g++ -o scitbx/math/boost_python/continued_fraction.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/math/boost_python/continued_fraction.cpp g++ -o lib/scitbx_lstbx_normal_equations_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm 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/continued_fraction.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/math/boost_python/continued_fraction.cpp g++ -o scitbx/math/boost_python/numeric_limits.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/math/boost_python/numeric_limits.cpp g++ -o scitbx/math/boost_python/distributions.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/math/boost_python/distributions.cpp g++ -o scitbx/math/boost_python/exp_functions.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/math/boost_python/exp_functions.cpp @@ -17422,6 +17458,22 @@ g++ -o scitbx/math/boost_python/angle_derivative.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/math/boost_python/angle_derivative.cpp g++ -o scitbx/minpack/ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/minpack/ext.cpp g++ -o scitbx/r3_utils_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/r3_utils_ext.cpp +g++ -o scitbx/random/boost_python/random_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/random/boost_python/random_ext.cpp +g++ -o scitbx/random/boost_python/basic_distributions.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/random/boost_python/basic_distributions.cpp +In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/error.h:16, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/minpack/raw.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/minpack/levenberg_marquardt.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/minpack/ext.cpp:4: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/minpack/levenberg_marquardt.h: In member function ‘void scitbx::minpack::levenberg_marquardt::process_fvec(const scitbx::af::const_ref&)’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/minpack/levenberg_marquardt.h:80:35: warning: comparison of integer expressions of different signedness: ‘scitbx::af::const_ref::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 80 | SCITBX_ASSERT(fvec.size() == m); + | ~~~~~~~~~~~~^~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/minpack/levenberg_marquardt.h:80:9: note: in expansion of macro ‘SCITBX_ASSERT’ + 80 | SCITBX_ASSERT(fvec.size() == m); + | ^~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -17442,21 +17494,7 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/error.h:16, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/minpack/raw.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/minpack/levenberg_marquardt.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/minpack/ext.cpp:4: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/minpack/levenberg_marquardt.h: In member function ‘void scitbx::minpack::levenberg_marquardt::process_fvec(const scitbx::af::const_ref&)’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/minpack/levenberg_marquardt.h:80:35: warning: comparison of integer expressions of different signedness: ‘scitbx::af::const_ref::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 80 | SCITBX_ASSERT(fvec.size() == m); - | ~~~~~~~~~~~~^~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/random/boost_python/random_ext.cpp +g++ -o scitbx/rigid_body/ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/rigid_body/ext.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -17477,13 +17515,7 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -g++ -o scitbx/random/boost_python/basic_distributions.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/random/boost_python/basic_distributions.cpp -g++ -o scitbx/rigid_body/ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/rigid_body/ext.cpp g++ -o scitbx/sparse/boost_python/vector.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/sparse/boost_python/vector.cpp -g++ -o lib/scitbx_r3_utils_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm -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/matrix.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/sparse/boost_python/matrix.cpp In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny_plain.h:6, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny.h:4, @@ -17503,12 +17535,10 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/detail/tiny_helpers.h:148:20: note: in definition of macro ‘SCITBX_ARRAY_FAMILY_TINY_CONVENIENCE_CONSTRUCTORS’ 148 | if (last - first != this->size()) throw_range_error(); \ | ^~ -g++ -o scitbx/sparse/boost_python/approx_equal.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/sparse/boost_python/approx_equal.cpp -g++ -o lib/scitbx_minpack_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lscitbx_minpack -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm -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-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/sparse/boost_python/random.cpp +g++ -o lib/scitbx_r3_utils_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm +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' In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/small.h:4, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/accessors/flex_grid.h:5, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/versa_matrix.h:6, @@ -17521,6 +17551,7 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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/sparse/boost_python/approx_equal.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/sparse/boost_python/approx_equal.cpp In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/error.h:16, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/mat3.h:5: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]’: @@ -17543,6 +17574,10 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/rigid_body/tardy.h:163:9: note: in expansion of macro ‘SCITBX_ASSERT’ 163 | SCITBX_ASSERT(body->parent < nc); | ^~~~~~~~~~~~~ +g++ -o lib/scitbx_minpack_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lscitbx_minpack -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm +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' /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/rigid_body/joint_lib.h:643:5: required from here @@ -17552,6 +17587,7 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/detail/tiny_helpers.h:148:20: note: in definition of macro ‘SCITBX_ARRAY_FAMILY_TINY_CONVENIENCE_CONSTRUCTORS’ 148 | if (last - first != this->size()) throw_range_error(); \ | ^~ +g++ -o scitbx/sparse/boost_python/random.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/sparse/boost_python/random.cpp /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/rigid_body/joint_lib.h:279:21: required from ‘boost::shared_ptr > scitbx::rigid_body::joint_lib::six_dof::time_step_position(const scitbx::af::const_ref&, const ft&) const [with FloatType = double; ft = double]’ @@ -17579,12 +17615,15 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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_array_family_flex_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm -lboost_numpy311 g++ -o scitbx/sparse/boost_python/lu_factorization.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/sparse/boost_python/lu_factorization.cpp g++ -o scitbx/sparse/boost_python/sparse_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/sparse/boost_python/sparse_ext.cpp g++ -o scitbx/stl/map_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/stl/map_ext.cpp -g++ -o lib/scitbx_array_family_flex_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm -lboost_numpy311 g++ -o scitbx/stl/set_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/stl/set_ext.cpp g++ -o scitbx/stl/vector_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/stl/vector_ext.cpp +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/suffixtree/boost_python/suffixtree_shared_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/suffixtree/boost_python/suffixtree_shared_ext.cpp In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/stl/set_ext.cpp:1: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/stl/set_wrapper.h: In static member function ‘static void scitbx::stl::boost_python::set_wrapper::wrap(const std::string&)’: @@ -17622,6 +17661,7 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/stl/set_wrapper.h:68:52: required from ‘static void scitbx::stl::boost_python::set_wrapper::wrap(const std::string&) [with ElementType = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/stl/set_ext.cpp:10:35: required from here /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] +g++ -o scitbx/suffixtree/boost_python/suffixtree_single_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/suffixtree/boost_python/suffixtree_single_ext.cpp In file included from /usr/include/boost/assert.hpp:58, from /usr/include/boost/smart_ptr/shared_ptr.hpp:24, from /usr/include/boost/shared_ptr.hpp:17, @@ -17684,11 +17724,12 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/shared_plain.h:132:48: note: ‘’ declared here 132 | std::uninitialized_fill_n(begin(), sz, ElementType()); | ^~~~~~~~~~~~~ -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/suffixtree/boost_python/suffixtree_single_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/suffixtree/boost_python/suffixtree_single_ext.cpp +g++ -o lib/scitbx_random_ext.so.0.0.1 -shared -rdynamic -std=c++11 -Wl,-soname=scitbx_random_ext.so.0 scitbx/random/boost_python/random_ext.o scitbx/random/boost_python/basic_distributions.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm +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 scitbx/suffixtree/boost_python/object_extensions.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/suffixtree/boost_python/object_extensions.cpp +g++ -o scitbx/wigner/ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/wigner/ext.cpp In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/shared_plain.h:307: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/detail/push_back_etc.h:175:15: warning: ‘’ may be used uninitialized [-Wmaybe-uninitialized] @@ -17704,19 +17745,7 @@ 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/wigner/ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/wigner/ext.cpp -g++ -o lib/scitbx_random_ext.so.0.0.1 -shared -rdynamic -std=c++11 -Wl,-soname=scitbx_random_ext.so.0 scitbx/random/boost_python/random_ext.o scitbx/random/boost_python/basic_distributions.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm -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 smtbx/ab_initio/ab_initio_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/ab_initio/ab_initio_ext.cpp -g++ -o smtbx/array_family/af_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/array_family/af_ext.cpp -g++ -o smtbx/refinement/constraints/boost_python/affine.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/refinement/constraints/boost_python/affine.cpp -g++ -o lib/scitbx_stl_set_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm -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/constraints_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/refinement/constraints/boost_python/constraints_ext.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -17737,32 +17766,39 @@ /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 smtbx/array_family/af_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/array_family/af_ext.cpp +g++ -o smtbx/refinement/constraints/boost_python/affine.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/refinement/constraints/boost_python/affine.cpp +g++ -o lib/scitbx_stl_set_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm +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/constraints_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/refinement/constraints/boost_python/constraints_ext.cpp g++ -o smtbx/refinement/constraints/boost_python/direction.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/refinement/constraints/boost_python/direction.cpp -g++ -o lib/scitbx_sparse_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm -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/geometrical_hydrogens.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/refinement/constraints/boost_python/geometrical_hydrogens.cpp -g++ -o lib/smtbx_ab_initio_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lboost_thread -lboost_system -lboost_python311 -lm -g++ -o smtbx/refinement/constraints/boost_python/independent_scalar_parameters.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/refinement/constraints/boost_python/independent_scalar_parameters.cpp g++ -o lib/smtbx_array_family_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lboost_thread -lboost_system -lboost_python311 -lm +g++ -o lib/scitbx_math_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lscitbx_slatec -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm 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/occupancy.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/refinement/constraints/boost_python/occupancy.cpp +g++ -o smtbx/refinement/constraints/boost_python/geometrical_hydrogens.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/refinement/constraints/boost_python/geometrical_hydrogens.cpp +g++ -o lib/smtbx_ab_initio_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lboost_thread -lboost_system -lboost_python311 -lm 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' +g++ -o smtbx/refinement/constraints/boost_python/independent_scalar_parameters.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/refinement/constraints/boost_python/independent_scalar_parameters.cpp +g++ -o lib/scitbx_wigner_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm +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-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/refinement/constraints/boost_python/occupancy.cpp g++ -o smtbx/refinement/constraints/boost_python/reparametrisation.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/refinement/constraints/boost_python/reparametrisation.cpp -g++ -o lib/scitbx_math_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lscitbx_slatec -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm 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 lib/scitbx_wigner_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm +g++ -o lib/scitbx_sparse_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm g++ -o smtbx/refinement/constraints/boost_python/rigid.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/refinement/constraints/boost_python/rigid.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' +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/same_group.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/refinement/constraints/boost_python/same_group.cpp g++ -o lib/scitbx_rigid_body_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm Create symlinks for: 'lib/scitbx_rigid_body_ext.so.0.0.1' @@ -17777,19 +17813,19 @@ g++ -o smtbx/refinement/constraints/boost_python/shared.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/refinement/constraints/boost_python/shared.cpp g++ -o smtbx/refinement/constraints/boost_python/special_position.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/refinement/constraints/boost_python/special_position.cpp g++ -o smtbx/refinement/constraints/boost_python/symmetry_equivalent.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/refinement/constraints/boost_python/symmetry_equivalent.cpp +g++ -o smtbx/refinement/constraints/boost_python/u_eq_dependent_u_iso.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/refinement/constraints/boost_python/u_eq_dependent_u_iso.cpp +g++ -o lib/scitbx_suffixtree_single_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm +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-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/refinement/constraints/boost_python/u_iso_dependent_u_iso.cpp g++ -o lib/scitbx_stl_map_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm +g++ -o smtbx/refinement/boost_python/least_squares_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/refinement/boost_python/least_squares_ext.cpp 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-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/refinement/constraints/boost_python/u_eq_dependent_u_iso.cpp -g++ -o smtbx/refinement/constraints/boost_python/u_iso_dependent_u_iso.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/refinement/constraints/boost_python/u_iso_dependent_u_iso.cpp -g++ -o smtbx/refinement/boost_python/least_squares_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/refinement/boost_python/least_squares_ext.cpp g++ -o smtbx/refinement/boost_python/weighting_schemes.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/refinement/boost_python/weighting_schemes.cpp g++ -o smtbx/refinement/boost_python/least_squares.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/refinement/boost_python/least_squares.cpp -g++ -o lib/scitbx_suffixtree_single_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm -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/restraints/boost_python/origin_fixing.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/refinement/restraints/boost_python/origin_fixing.cpp g++ -o smtbx/refinement/restraints/boost_python/restraints_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/refinement/restraints/boost_python/restraints_ext.cpp g++ -o smtbx/stl/map_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/stl/map_ext.cpp @@ -17801,6 +17837,10 @@ g++ -o spotfinder/diffraction/geometry.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -I/usr/include/python3.11 -Ispotfinder/core_toolbox/boost_python/src -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/spotfinder/core_toolbox/boost_python/src -Ispotfinder/core_toolbox/boost_python/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/spotfinder/core_toolbox/boost_python/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/spotfinder/diffraction/geometry.cpp g++ -o spotfinder/dxtbx_toolbox/ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -I/usr/include/python3.11 -Ispotfinder/dxtbx_toolbox/src -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/spotfinder/dxtbx_toolbox/src -Ispotfinder/dxtbx_toolbox/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/spotfinder/dxtbx_toolbox/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/spotfinder/dxtbx_toolbox/ext.cpp g++ -o spotfinder/core_toolbox/boost_python/hough_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src -I/usr/include/python3.11 -Ispotfinder/core_toolbox/boost_python/src -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/spotfinder/core_toolbox/boost_python/src -Ispotfinder/core_toolbox/boost_python/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/spotfinder/core_toolbox/boost_python/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/spotfinder/core_toolbox/boost_python/hough_ext.cpp +g++ -o lib/std_pair_ext.so.0.0.1 -shared -rdynamic -std=c++11 -Wl,-soname=std_pair_ext.so.0 boost_adaptbx/std_pair_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lboost_thread -lboost_system -lboost_python311 -lm +Create symlinks for: 'lib/std_pair_ext.so.0.0.1' + 'lib/std_pair_ext.so.0'->'lib/std_pair_ext.so.0.0.1' + 'lib/std_pair_ext.so'->'lib/std_pair_ext.so.0.0.1' In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -17821,10 +17861,6 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -g++ -o lib/std_pair_ext.so.0.0.1 -shared -rdynamic -std=c++11 -Wl,-soname=std_pair_ext.so.0 boost_adaptbx/std_pair_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lboost_thread -lboost_system -lboost_python311 -lm -Create symlinks for: 'lib/std_pair_ext.so.0.0.1' - 'lib/std_pair_ext.so.0'->'lib/std_pair_ext.so.0.0.1' - '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-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/masks/tst_mask.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, @@ -17859,7 +17895,7 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/spotfinder/dxtbx_toolbox/ext.cpp:1: + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/spotfinder/core_toolbox/boost_python/hough_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( | ^~~~~~~~~~~~~~~~~~~~ @@ -17879,7 +17915,7 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/spotfinder/core_toolbox/boost_python/hough_ext.cpp:2: + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/spotfinder/dxtbx_toolbox/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( | ^~~~~~~~~~~~~~~~~~~~ @@ -17892,8 +17928,6 @@ '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/tst_accessors.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -Iscitbx/array_family -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_accessors.cpp -g++ -o scitbx/array_family/tst_af_1.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -Iscitbx/array_family -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_af_1.cpp -g++ -o lib/spotfinder_hough_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lspotfinder -lomptbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/ref.h:8, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny_plain.h:4, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny.h:4, @@ -17954,9 +17988,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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' /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/shared_plain.h: In member function ‘ElementType& scitbx::af::shared_plain::at(size_type)’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]; \ @@ -18009,7 +18040,68 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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_af_2.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -Iscitbx/array_family -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_af_2.cpp +In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_accessors.cpp:15: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_af_helpers.cpp: In instantiation of ‘void {anonymous}::verify(long int, const VectorType1&, const VectorType2&) [with VectorType1 = scitbx::af::small; VectorType2 = scitbx::af::c_grid<1>]’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_accessors.cpp:127:11: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]) { + | ~~~~~^~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_af_helpers.cpp: In instantiation of ‘void {anonymous}::verify(long int, const VectorType1&, const VectorType2&) [with VectorType1 = scitbx::af::small; VectorType2 = scitbx::af::c_grid<4>]’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_accessors.cpp:145:11: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_af_helpers.cpp: In instantiation of ‘void {anonymous}::verify(long int, const VectorType1&, const VectorType2&) [with VectorType1 = scitbx::af::small; VectorType2 = scitbx::af::c_grid<2>]’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_accessors.cpp:172:11: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_af_helpers.cpp: In instantiation of ‘void {anonymous}::verify(long int, const VectorType1&, const VectorType2&) [with VectorType1 = scitbx::af::small; VectorType2 = scitbx::af::c_grid<3>]’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_accessors.cpp:202:11: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_af_helpers.cpp: In instantiation of ‘void {anonymous}::verify(long int, const VectorType1&, const VectorType2&) [with VectorType1 = scitbx::af::small; VectorType2 = scitbx::af::tiny]’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_accessors.cpp:248:11: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_af_helpers.cpp: In instantiation of ‘void {anonymous}::verify(long int, const VectorType1&, const VectorType2&) [with VectorType1 = scitbx::af::small; VectorType2 = scitbx::af::tiny]’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_accessors.cpp:280:11: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_af_helpers.cpp: In instantiation of ‘void {anonymous}::verify(long int, const VectorType1&, const VectorType2&) [with VectorType1 = scitbx::af::small; VectorType2 = scitbx::af::tiny]’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_accessors.cpp:326:11: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_af_helpers.cpp: In instantiation of ‘void {anonymous}::verify(long int, const VectorType1&, const VectorType2&) [with VectorType1 = scitbx::af::small; VectorType2 = scitbx::af::tiny]’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_accessors.cpp:371:11: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] +g++ -o scitbx/array_family/tst_af_1.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -Iscitbx/array_family -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_af_1.cpp +In file included from /usr/include/boost/assert.hpp:58, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:24, + 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-2022.9+ds2+~3.11.2+ds1/scitbx/boost_python/container_conversions.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/regression_test_ext.cpp:7: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/regression_test_ext.cpp:156:78: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/regression_test_ext.cpp:160:72: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/regression_test_ext.cpp:164:71: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/regression_test_ext.cpp:168:71: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/regression_test_ext.cpp:172:75: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] +g++ -o lib/spotfinder_hough_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lspotfinder -lomptbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/ref.h:8, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny_plain.h:4, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include/scitbx/array_family/tiny_plain_apply.h:15, @@ -18066,15 +18158,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_accessors.cpp:15: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_af_helpers.cpp: In instantiation of ‘void {anonymous}::verify(long int, const VectorType1&, const VectorType2&) [with VectorType1 = scitbx::af::small; VectorType2 = scitbx::af::c_grid<1>]’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_accessors.cpp:127:11: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]) { - | ~~~~~^~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_af_helpers.cpp: In instantiation of ‘void {anonymous}::verify(long int, const VectorType1&, const VectorType2&) [with VectorType1 = scitbx::af::small; VectorType2 = scitbx::af::c_grid<4>]’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_accessors.cpp:145:11: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/shared_plain.h: In member function ‘ElementType& scitbx::af::shared_plain::at(size_type)’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]; \ @@ -18082,9 +18165,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_af_helpers.cpp: In instantiation of ‘void {anonymous}::verify(long int, const VectorType1&, const VectorType2&) [with VectorType1 = scitbx::af::small; VectorType2 = scitbx::af::c_grid<2>]’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_accessors.cpp:172:11: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]; \ | ^~~~~~ @@ -18104,9 +18184,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_af_helpers.cpp: In instantiation of ‘void {anonymous}::verify(long int, const VectorType1&, const VectorType2&) [with VectorType1 = scitbx::af::small; VectorType2 = scitbx::af::c_grid<3>]’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_accessors.cpp:202:11: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/versa_plain.h: In member function ‘ElementType& scitbx::af::versa_plain::at(size_type)’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]; \ @@ -18133,18 +18210,10 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_af_helpers.cpp: In instantiation of ‘void {anonymous}::verify(long int, const VectorType1&, const VectorType2&) [with VectorType1 = scitbx::af::small; VectorType2 = scitbx::af::tiny]’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_accessors.cpp:248:11: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_af_helpers.cpp: In instantiation of ‘void {anonymous}::verify(long int, const VectorType1&, const VectorType2&) [with VectorType1 = scitbx::af::small; VectorType2 = scitbx::af::tiny]’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_accessors.cpp:280:11: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_af_helpers.cpp: In instantiation of ‘void {anonymous}::verify(long int, const VectorType1&, const VectorType2&) [with VectorType1 = scitbx::af::small; VectorType2 = scitbx::af::tiny]’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_accessors.cpp:326:11: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_af_helpers.cpp: In instantiation of ‘void {anonymous}::verify(long int, const VectorType1&, const VectorType2&) [with VectorType1 = scitbx::af::small; VectorType2 = scitbx::af::tiny]’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_accessors.cpp:371:11: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] +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_2.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -Iscitbx/array_family -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_af_2.cpp In file included from /usr/include/boost/bind.hpp:30, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_af_1.cpp:15: /usr/include/boost/bind.hpp: At global scope: @@ -18214,7 +18283,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 mmtbx/masks/tst_mask -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -pthread mmtbx/masks/tst_mask.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lmmtbx_masks -liotbx_pdb -lcctbx -lomptbx -lcctbx_sgtbx_asu -lm In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/ref.h:8, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny_plain.h:4, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny.h:4, @@ -18248,6 +18316,7 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 mmtbx/masks/tst_mask -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -pthread mmtbx/masks/tst_mask.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lmmtbx_masks -liotbx_pdb -lcctbx -lomptbx -lcctbx_sgtbx_asu -lm /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/small_plain.h: In member function ‘ElementType& scitbx::af::small_plain::at(size_type)’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]; \ @@ -18327,39 +18396,6 @@ 161 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(versa_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -o scitbx/array_family/tst_af_3.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -Iscitbx/array_family -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_af_3.cpp -In file included from /usr/include/boost/assert.hpp:58, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:24, - 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-2022.9+ds2+~3.11.2+ds1/scitbx/boost_python/container_conversions.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/regression_test_ext.cpp:7: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/regression_test_ext.cpp:156:78: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/regression_test_ext.cpp:160:72: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/regression_test_ext.cpp:164:71: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/regression_test_ext.cpp:168:71: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/regression_test_ext.cpp:172:75: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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] In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/ref.h:8, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/simple_io.h:5, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_af_3.cpp:1: @@ -18468,7 +18504,9 @@ 161 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(versa_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -o scitbx/array_family/tst_af_2 -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lboost_thread -lboost_system +g++ -o scitbx/array_family/tst_accessors -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -Iscitbx/array_family -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_af_4.cpp +g++ -o scitbx/array_family/tst_af_5.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -Iscitbx/array_family -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_af_5.cpp In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/ref.h:8, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/simple_io.h:5, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_af_4.cpp:1: @@ -18576,10 +18614,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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_af_3 -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -Iscitbx/array_family -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_af_5.cpp -g++ -o scitbx/array_family/tst_accessors -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lboost_thread -lboost_system -g++ -o scitbx/array_family/tst_mat3.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -Iscitbx/array_family -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_mat3.cpp In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/ref.h:8, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/simple_io.h:5, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_af_5.cpp:1: @@ -18635,8 +18669,13 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 lib/smtbx_refinement_constraints_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lsmtbx_refinement_constraints -lscitbx_boost_python -lcctbx -lboost_thread -lboost_system -lboost_python311 -lm -g++ -o scitbx/array_family/tst_af_1 -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lboost_thread -lboost_system +g++ -o scitbx/array_family/tst_mat3.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -Iscitbx/array_family -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_mat3.cpp +g++ -o lib/spotfinder_dxtbx_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -ldxtbxspotfinder -lspotfinder -lomptbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm +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-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -Iscitbx/array_family -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_optional_copy.cpp In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/ref.h:8, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny_plain.h:4, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny.h:4, @@ -18669,12 +18708,16 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -Iscitbx/array_family -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_optional_copy.cpp -g++ -o lib/spotfinder_dxtbx_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -ldxtbxspotfinder -lspotfinder -lomptbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm -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_af_1 -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lboost_thread -lboost_system +g++ -o scitbx/array_family/boost_python/regression_test_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm -lboost_numpy311 g++ -o scitbx/array_family/tst_rectangular_full_packed.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -Iscitbx/array_family -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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_ref_matrix_facet.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -Iscitbx/array_family -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_ref_matrix_facet.cpp +g++ -o scitbx/array_family/tst_sym_mat3.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -Iscitbx/array_family -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_sym_mat3.cpp +g++ -o lib/smtbx_refinement_constraints_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lsmtbx_refinement_constraints -lscitbx_boost_python -lcctbx -lboost_thread -lboost_system -lboost_python311 -lm In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/ref.h:8, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny_plain.h:4, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny.h:4, @@ -18786,15 +18829,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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/boost_python/regression_test_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm -lboost_numpy311 -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' -g++ -o scitbx/array_family/tst_ref_matrix_facet.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -Iscitbx/array_family -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_ref_matrix_facet.cpp -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_sym_mat3.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -Iscitbx/array_family -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_sym_mat3.cpp In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/ref.h:8, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny_plain.h:4, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/accessors/rectangular_full_packed.h:3, @@ -18825,6 +18859,34 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/ref.h:8, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_ref_matrix_facet.cpp:1: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny_plain.h: In member function ‘ElementType& scitbx::af::tiny_plain::at(size_type)’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny_plain.h: In member function ‘const ElementType& scitbx::af::tiny_plain::at(size_type) const’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/small_plain.h: In member function ‘ElementType& scitbx::af::small_plain::at(size_type)’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]; \ @@ -18851,6 +18913,7 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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 lib/smtbx_refinement_restraints_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lboost_thread -lboost_system -lboost_python311 -lm /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/shared_plain.h: In member function ‘ElementType& scitbx::af::shared_plain::at(size_type)’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]; \ @@ -18910,73 +18973,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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::at(size_type)’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny_plain.h: In member function ‘const ElementType& scitbx::af::tiny_plain::at(size_type) const’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -Iscitbx/array_family -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_vec3.cpp -In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/ref.h:8, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny_plain.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/vec3.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/mat3.h:6, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/sym_mat3.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_sym_mat3.cpp:2: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny_plain.h: In member function ‘ElementType& scitbx::af::tiny_plain::at(size_type)’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny_plain.h: In member function ‘const ElementType& scitbx::af::tiny_plain::at(size_type) const’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/small_plain.h: In member function ‘ElementType& scitbx::af::small_plain::at(size_type)’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]; \ @@ -19003,7 +18999,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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/error/tst_error.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -Iscitbx/error -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/error /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/error/tst_error.cpp /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/shared_plain.h: In member function ‘ElementType& scitbx::af::shared_plain::at(size_type)’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]; \ @@ -19056,10 +19051,50 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/ref.h:8, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny_plain.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/vec3.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/mat3.h:6, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/sym_mat3.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_sym_mat3.cpp:2: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny_plain.h: In member function ‘ElementType& scitbx::af::tiny_plain::at(size_type)’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny_plain.h: In member function ‘const ElementType& scitbx::af::tiny_plain::at(size_type) const’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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: '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/fftpack_timer.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/fftpack/timing/fftpack_timer.cpp +g++ -o scitbx/array_family/tst_unsigned_float_arithmetic.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -Iscitbx/array_family -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_unsigned_float_arithmetic.cpp +g++ -o scitbx/array_family/tst_rectangular_full_packed -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lm +g++ -o scitbx/array_family/tst_vec3.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include -Iscitbx/array_family -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_vec3.cpp +g++ -o scitbx/error/tst_error.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -Iscitbx/error -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/error /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/error/tst_error.cpp +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' In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/ref.h:8, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny_plain.h:4, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny.h:4, @@ -19091,8 +19126,14 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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++11 -pthread scitbx/error/tst_error.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lboost_thread -lboost_system +g++ -o scitbx/fftpack/timing/fftpack_timer.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/fftpack/timing/fftpack_timer.cpp +g++ -o scitbx/array_family/tst_ref_matrix_facet -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lboost_thread -lboost_system g++ -o scitbx/array_family/tst_optional_copy -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lboost_thread -lboost_system +g++ -o scitbx/fftpack/timing/test0.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/fftpack/timing/test0.cpp +g++ -o scitbx/lbfgs/sdrive_fem.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable scitbx/lbfgs/sdrive_fem.cpp +g++ -o scitbx/array_family/tst_unsigned_float_arithmetic -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lboost_thread -lboost_system +g++ -o scitbx/error/tst_error -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -pthread scitbx/error/tst_error.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lboost_thread -lboost_system +g++ -o scitbx/lbfgs/tst_lbfgs.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/lbfgs/tst_lbfgs.cpp In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/ref.h:8, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny_plain.h:4, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny.h:4, @@ -19124,9 +19165,19 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/fftpack/timing/test0.cpp -g++ -o scitbx/lbfgs/sdrive_fem.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable scitbx/lbfgs/sdrive_fem.cpp -g++ -o scitbx/array_family/tst_unsigned_float_arithmetic -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lboost_thread -lboost_system +g++ -o scitbx/lbfgsb/dev/driver1.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/lbfgsb/dev/driver1.cpp +In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem/io.hpp:8, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem/close_chain.hpp:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem/common.hpp:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem/read.hpp:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem/major_types.hpp:6, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem.hpp:10, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include/scitbx/lbfgs_fem.hpp:1, + from scitbx/lbfgs/sdrive_fem.cpp:1: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/ref.h:8, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny_plain.h:4, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny.h:4, @@ -19160,6 +19211,41 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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_sym_mat3 -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lm +In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/ref.h:8, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny_plain.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny_types.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/fftpack/factorization.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/fftpack/complex_to_complex.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/fftpack/complex_to_complex_3d.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/fftpack/timing/test0.cpp:3: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny_plain.h: In member function ‘ElementType& scitbx::af::tiny_plain::at(size_type)’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny_plain.h: In member function ‘const ElementType& scitbx::af::tiny_plain::at(size_type) const’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/shared_plain.h: In member function ‘ElementType& scitbx::af::shared_plain::at(size_type)’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]; \ @@ -19186,28 +19272,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/fftpack/factorization.h: In constructor ‘scitbx::fftpack::factorization::factorization(std::size_t, bool)’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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++) { - | ~~^~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lboost_thread -lboost_system -g++ -o scitbx/lbfgs/tst_lbfgs.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/lbfgs/tst_lbfgs.cpp -g++ -o scitbx/lbfgsb/dev/driver1.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/lbfgsb/dev/driver1.cpp -In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem/io.hpp:8, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem/close_chain.hpp:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem/common.hpp:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem/read.hpp:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem/major_types.hpp:6, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem.hpp:10, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include/scitbx/lbfgs_fem.hpp:1, - from scitbx/lbfgs/sdrive_fem.cpp:1: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/fable/fem/common.hpp: In member function ‘void fem::common::getarg(int, fem::str_ref) const’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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()) { @@ -19218,6 +19282,13 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem/utils/string_to_double.hpp:115:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare] 115 | if (dexp <= ad_hoc_limits::max_digit_count) { | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/fftpack/factorization.h: In constructor ‘scitbx::fftpack::factorization::factorization(std::size_t, bool)’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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++) { + | ~~^~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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++) { + | ~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem/read.hpp: In member function ‘double fem::read_loop::read_fmt_double()’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable/fem/read.hpp:652:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 652 | if (iw+1 != ed.size()) { @@ -19233,42 +19304,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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/array_family/tst_vec3 -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lm -In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/ref.h:8, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny_plain.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny_types.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/fftpack/factorization.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/fftpack/complex_to_complex.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/fftpack/complex_to_complex_3d.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/fftpack/timing/test0.cpp:3: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny_plain.h: In member function ‘ElementType& scitbx::af::tiny_plain::at(size_type)’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny_plain.h: In member function ‘const ElementType& scitbx::af::tiny_plain::at(size_type) const’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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_sym_mat3 -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lm /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/shared_plain.h: In member function ‘ElementType& scitbx::af::shared_plain::at(size_type)’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]; \ @@ -19335,7 +19370,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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/lbfgsb/dev/driver2.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/lbfgsb/dev/driver2.cpp /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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]; \ | ^~~~~~ @@ -19355,7 +19389,7 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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/lbfgsb/dev/driver3.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/lbfgsb/dev/driver3.cpp +g++ -o scitbx/lbfgsb/dev/driver2.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -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 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/lbfgsb/dev/driver2.cpp In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/ref.h:8, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/lbfgsb/raw.h:6, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/lbfgsb/dev/driver1.cpp:1: @@ -19411,6 +19445,7 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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_vec3 -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lm In file included from /usr/include/boost/config/header_deprecated.hpp:18, from /usr/include/boost/timer.hpp:20, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/lbfgsb/raw.h:9: @@ -19502,39 +19537,11 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny_plain.h: In member function ‘const ElementType& scitbx::af::tiny_plain::at(size_type) const’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/ref.h:8, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/lbfgsb/raw.h:6, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/lbfgsb/dev/driver2.cpp:1: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny_plain.h: In member function ‘ElementType& scitbx::af::tiny_plain::at(size_type)’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] @@ -19622,34 +19629,8 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/small_plain.h: In member function ‘ElementType& scitbx::af::small_plain::at(size_type)’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/small_plain.h: In member function ‘const ElementType& scitbx::af::small_plain::at(size_type) const’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/lbfgsb/dev/driver3.cpp:82:19: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/lbfgsb/dev/driver2.cpp:102:19: required from here /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/lbfgsb/raw.h:184:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::const_ref::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 184 | for(int i=1;i<=a.size();i++) { | ~^~~~~~~~~~ @@ -19662,7 +19643,7 @@ from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/lbfgsb/raw.h:5: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/lbfgsb/raw.h: In instantiation of ‘void scitbx::lbfgsb::raw::mainlb(const int&, const int&, const ref1&, const ref1&, const ref1&, const ref1&, FloatType&, const ref1&, const FloatType&, const FloatType&, const ref2&, const ref2&, const ref2&, const ref2&, const ref2&, const ref2&, const ref2&, const ref2&, const ref1&, const ref1&, const ref1&, const ref1&, const ref1&, const ref1&, const ref1&, const ref1&, const ref1&, const ref1&, const ref1&, const ref1&, std::string&, const int&, std::string&, const ref1&, const ref1&, const ref1&, bool) [with FloatType = double; std::string = std::__cxx11::basic_string]’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/lbfgsb/raw.h:4433:11: required from ‘void scitbx::lbfgsb::raw::setulb(const int&, const int&, const ref1&, const ref1&, const ref1&, const ref1&, FloatType&, const ref1&, const FloatType&, const FloatType&, const ref1&, const ref1&, std::string&, const int&, std::string&, const ref1&, const ref1&, const ref1&, bool) [with FloatType = double; std::string = std::__cxx11::basic_string]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/lbfgsb/dev/driver3.cpp:72:11: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/lbfgsb/dev/driver2.cpp:70:11: required from here /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/lbfgsb/raw.h:3671:28: warning: comparison of integer expressions of different signedness: ‘scitbx::af::const_ref::size_type’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare] 3671 | SCITBX_ASSERT(x.size() == n); /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/error_utils.h:166:9: note: in definition of macro ‘SCITBX_ERROR_UTILS_ASSERT’ @@ -19671,6 +19652,7 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/lbfgsb/raw.h:3671:5: note: in expansion of macro ‘SCITBX_ASSERT’ 3671 | SCITBX_ASSERT(x.size() == n); | ^~~~~~~~~~~~~ +g++ -o scitbx/matrix/tests/tst_cholesky.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -Iscitbx/matrix/tests -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/matrix/tests /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/matrix/tests/tst_cholesky.cpp /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/lbfgsb/raw.h:3672:28: warning: comparison of integer expressions of different signedness: ‘scitbx::af::const_ref::size_type’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare] 3672 | SCITBX_ASSERT(l.size() == n); /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/error_utils.h:166:9: note: in definition of macro ‘SCITBX_ERROR_UTILS_ASSERT’ @@ -19703,6 +19685,61 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/lbfgsb/raw.h:3675:5: note: in expansion of macro ‘SCITBX_ASSERT’ 3675 | SCITBX_ASSERT(g.size() == n); | ^~~~~~~~~~~~~ +In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/ref.h:8, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/lbfgsb/raw.h:6, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/lbfgsb/dev/driver3.cpp:1: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny_plain.h: In member function ‘ElementType& scitbx::af::tiny_plain::at(size_type)’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tiny_plain.h: In member function ‘const ElementType& scitbx::af::tiny_plain::at(size_type) const’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/small_plain.h: In member function ‘ElementType& scitbx::af::small_plain::at(size_type)’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/small_plain.h: In member function ‘const ElementType& scitbx::af::small_plain::at(size_type) const’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+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/config/header_deprecated.hpp:18, from /usr/include/boost/timer.hpp:20, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/lbfgsb/raw.h:9: @@ -19736,9 +19773,8 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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/matrix/tests/tst_cholesky.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -Iscitbx/matrix/tests -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/matrix/tests /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/matrix/tests/tst_cholesky.cpp /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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-2022.9+ds2+~3.11.2+ds1/scitbx/lbfgsb/dev/driver2.cpp:102:19: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/lbfgsb/dev/driver3.cpp:82:19: required from here /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/lbfgsb/raw.h:184:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::const_ref::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 184 | for(int i=1;i<=a.size();i++) { | ~^~~~~~~~~~ @@ -19751,7 +19787,7 @@ from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/lbfgsb/raw.h:5: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/lbfgsb/raw.h: In instantiation of ‘void scitbx::lbfgsb::raw::mainlb(const int&, const int&, const ref1&, const ref1&, const ref1&, const ref1&, FloatType&, const ref1&, const FloatType&, const FloatType&, const ref2&, const ref2&, const ref2&, const ref2&, const ref2&, const ref2&, const ref2&, const ref2&, const ref1&, const ref1&, const ref1&, const ref1&, const ref1&, const ref1&, const ref1&, const ref1&, const ref1&, const ref1&, const ref1&, const ref1&, std::string&, const int&, std::string&, const ref1&, const ref1&, const ref1&, bool) [with FloatType = double; std::string = std::__cxx11::basic_string]’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/lbfgsb/raw.h:4433:11: required from ‘void scitbx::lbfgsb::raw::setulb(const int&, const int&, const ref1&, const ref1&, const ref1&, const ref1&, FloatType&, const ref1&, const FloatType&, const FloatType&, const ref1&, const ref1&, std::string&, const int&, std::string&, const ref1&, const ref1&, const ref1&, bool) [with FloatType = double; std::string = std::__cxx11::basic_string]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/lbfgsb/dev/driver2.cpp:70:11: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/lbfgsb/dev/driver3.cpp:72:11: required from here /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/lbfgsb/raw.h:3671:28: warning: comparison of integer expressions of different signedness: ‘scitbx::af::const_ref::size_type’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare] 3671 | SCITBX_ASSERT(x.size() == n); /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/error_utils.h:166:9: note: in definition of macro ‘SCITBX_ERROR_UTILS_ASSERT’ @@ -19808,33 +19844,33 @@ g++ -o smtbx/refinement/constraints/tests/tst_reparametrisation.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -Ismtbx/refinement/constraints -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/refinement/constraints /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/refinement/constraints/tests/tst_reparametrisation.cpp g++ -o scitbx/serialization/tst_base_256 -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lm g++ -o smtbx/refinement/constraints/tests/tst_special_position.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial -std=c++11 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -Ismtbx/refinement/constraints -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/refinement/constraints /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/smtbx/refinement/constraints/tests/tst_special_position.cpp +g++ -o scitbx/matrix/tests/tst_cholesky -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lboost_thread -lboost_system g++ -o lib/spotfinder_distltbx_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lspotfinder -lomptbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm 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/matrix/tests/tst_cholesky -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lboost_thread -lboost_system g++ -o scitbx/matrix/tests/tst_svd -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lboost_thread -lboost_system g++ -o scitbx/sparse/tests/tst_sparse -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lboost_thread -lboost_system +g++ -o lib/smtbx_refinement_least_squares_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lsmtbx_refinement_constraints -lscitbx_boost_python -lcctbx -lboost_thread -lboost_system -lboost_python311 -lm g++ -o lib/smtbx_structure_factors_direct_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lboost_thread -lboost_system -lboost_python311 -lm -g++ -o smtbx/refinement/constraints/tests/tst_geometrical_hydrogens -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lsmtbx_refinement_constraints -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_reparametrisation -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lsmtbx_refinement_constraints -lscitbx_boost_python -lcctbx -lboost_thread -lboost_system -lboost_python311 -lm 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++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lcctbx -lsmtbx_refinement_constraints -lboost_thread -lboost_system +g++ -o smtbx/refinement/constraints/tests/tst_geometrical_hydrogens -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lm g++ -o lib/spotfinder_array_family_flex_ext.so.0.0.1 -shared -rdynamic -std=c++11 -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-2022.9+ds2+~3.11.2+ds1/lib -Llib -L/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/lib -lspotfinder -lomptbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python311 -lm Create symlinks for: 'lib/spotfinder_array_family_flex_ext.so.0.0.1' '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: 32.53 seconds -wall clock time: 11 minutes 23.25 seconds (683.25 seconds total) +usr+sys time: 33.24 seconds +wall clock time: 7 minutes 18.62 seconds (438.62 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 @@ -34633,40 +34669,7 @@ {'_dispatcher_include_at_start': [], '_dispatcher_include_before_command': [], '_dispatcher_precall_commands': None, - '_dispatcher_registry': {relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/iotbx.pdb.join_fragment_files"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../iotbx/command_line/pdb.join_fragment_files.py"), - relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/iotbx.pdb.insert_scale_records"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../iotbx/command_line/pdb.insert_scale_records.py"), - relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/phenix.pdb.hierarchy"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../iotbx/command_line/pdb.hierarchy.py"), - relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/iotbx.pdb.box_around_molecule"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../iotbx/command_line/pdb.box_around_molecule.py"), - relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/phenix.pdb.b_factor_stats"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../iotbx/command_line/pdb.b_factor_stats.py"), - relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/iotbx.pdb.as_xray_structure"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../iotbx/command_line/pdb.as_xray_structure.py"), - relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/cctbx.patterson_map"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../iotbx/command_line/patterson_map.py"), - relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/phenix.mtz_as_cif"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../iotbx/command_line/mtz_as_cif.py"), - relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/phenix.mtz.dump"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../iotbx/command_line/mtz.dump.py"), - relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/iotbx.mtz.dump"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../iotbx/command_line/mtz.dump.py"), - relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/phenix.pdb.mtrix_reconstruction"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../iotbx/command_line/mtrix_reconstruction.py"), - relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/phenix.merging_statistics"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../iotbx/command_line/merging_statistics.py"), - relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/iotbx.merging_statistics"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../iotbx/command_line/merging_statistics.py"), - relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/iotbx.lattice_symmetry"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../iotbx/command_line/lattice_symmetry.py"), - relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/cctbx.isomorphous_difference_patterson"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../iotbx/command_line/isomorphous_difference_patterson.py"), - relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/iotbx.get_pubmed_citation"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../iotbx/command_line/get_pubmed_citation.py"), - relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/phenix.french_wilson"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../iotbx/command_line/french_wilson.py"), - relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/iotbx.french_wilson"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../iotbx/command_line/french_wilson.py"), - relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/iotbx.pdb.flip_symmetric_amino_acids"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../iotbx/command_line/flip_symmetric_amino_acids.py"), - relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/iotbx.file_reader"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../iotbx/command_line/file_reader.py"), - relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/iotbx.export_scalepack_unmerged"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../iotbx/command_line/export_scalepack_unmerged.py"), - relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/phenix.explore_metric_symmetry"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../iotbx/command_line/explore_metric_symmetry.py"), - relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/phenix.emma"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../iotbx/command_line/emma.py"), - relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/iotbx.emma"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../iotbx/command_line/emma.py"), - relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/phenix.resolution"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../iotbx/command_line/effective_resolution.py"), - relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/iotbx.dtrek.to_cns"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../iotbx/command_line/dtrek.to_cns.py"), - relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/iotbx.distance_least_squares"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../iotbx/command_line/distance_least_squares.py"), - relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/labelit.png"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../iotbx/command_line/detector_image_as_png.py"), - relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/iotbx.dano_as_amplitudes"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../iotbx/command_line/dano_as_amplitudes.py"), - relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/phenix.csv_as_mtz"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../iotbx/command_line/csv_as_mtz.py"), - relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/iotbx.crystal_symmetry_from_any"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../iotbx/command_line/crystal_symmetry_from_any.py"), - relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/phenix.cns_as_mtz"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../iotbx/command_line/cns_as_mtz.py"), - relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/iotbx.cns.transfer_crystal_symmetry"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../iotbx/command_line/cns.transfer_crystal_symmetry.py"), - relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/iotbx.cns.sdb_reader"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../iotbx/command_line/cns.sdb_reader.py"), + '_dispatcher_registry': {relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/iotbx.cns.sdb_reader"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../iotbx/command_line/cns.sdb_reader.py"), relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/iotbx.cns.reflection_reader"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../iotbx/command_line/cns.reflection_reader.py"), relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/phenix.cif_as_pdb"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../iotbx/command_line/cif_as_pdb.py"), relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/iotbx.cif_as_pdb"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../iotbx/command_line/cif_as_pdb.py"), @@ -34940,6 +34943,72 @@ relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/phenix.fake_f_obs"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../mmtbx/command_line/fake_f_obs.py"), relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/phenix.fab_elbow_angle"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../mmtbx/command_line/fab_elbow_angle.py"), relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/phenix.f000"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../mmtbx/command_line/f000.py"), + relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/iotbx.symmetry_search"): 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relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../iotbx/command_line/pdb.print_sequence.py"), - relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/iotbx.pdb.link_as_geometry_restraints_edits"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../iotbx/command_line/pdb.link_as_geometry_restraints_edits.py"), + relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/libtbx.add_from_future_import_division"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../libtbx/command_line/add_from_future_import_division.py"), relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/boost_adaptbx.show_platform_info"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../boost_adaptbx/command_line/show_platform_info.py"), relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/boost_adaptbx.show_environ_usage"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../boost_adaptbx/command_line/show_environ_usage.py"), relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/boost_adaptbx.segmentation_fault"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../boost_adaptbx/command_line/segmentation_fault.py"), @@ -35038,6 +35075,7 @@ relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/cctbx.structure_factor_timings"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../cctbx/command_line/structure_factor_timings.py"), relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/cctbx.space_group_info"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../cctbx/command_line/space_group_info.py"), relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/phenix.segment_and_split_map"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../cctbx/command_line/segment_and_split_map.py"), + relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/libtbx.find_unused_imports"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../libtbx/command_line/find_unused_imports.py"), relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/libtbx.find_untested"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../libtbx/command_line/find_untested.py"), relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/libtbx.find_under_build"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../libtbx/command_line/find_under_build.py"), relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/libtbx.find_reserved_names"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../libtbx/command_line/find_reserved_names.py"), @@ -35077,7 +35115,6 @@ relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/libtbx.assert_line_count"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../libtbx/command_line/assert_line_count.py"), relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/libtbx.any2unix"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../libtbx/command_line/any2unix.py"), relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/libtbx.analyse_code_comments"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../libtbx/command_line/analyse_code_comments.py"), - relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/libtbx.add_from_future_import_division"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../libtbx/command_line/add_from_future_import_division.py"), relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/libtbx.show_date_and_time"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../libtbx/command_line/show_date_and_time.py"), relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/libtbx.show_commands"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../libtbx/command_line/show_commands.py"), relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/libtbx.show_but_no_repr"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../libtbx/command_line/show_but_no_repr.py"), @@ -35119,7 +35156,6 @@ relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/libtbx.git_avoid_merges"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../libtbx/command_line/git_avoid_merges.py"), relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/libtbx.gdb"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../libtbx/command_line/gdb.sh"), relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/libtbx.find_unused_imports_crude"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../libtbx/command_line/find_unused_imports_crude.py"), - relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/libtbx.find_unused_imports"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../libtbx/command_line/find_unused_imports.py"), relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/libtbx.python"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="/usr/bin/python3.11"), relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/libtbx.wait_for_file"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../libtbx/command_line/wait_for_file.py"), relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/libtbx.valgrind"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../libtbx/command_line/valgrind.sh"), @@ -35147,7 +35183,7 @@ relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/libtbx.show_dist_paths"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../libtbx/command_line/show_dist_paths.py")}, 'bin_path': relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin"), 'boost_version': 107400, - 'build_options': , + 'build_options': , 'build_path': absolute_path("/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11"), 'command_line_redirections': {}, 'command_version_suffix': None, @@ -35183,29 +35219,29 @@ 'lib_path': relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="lib"), 'missing_for_build': set(), 'missing_for_use': set(), - 'missing_optional': {'reduce', 'king', 'cbflib', 'docutils', 'probe'}, - 'module_dict': {'annlib': , - 'boost': , - 'cbflib': , - 'ccp4io': , - 'cctbx': , - 'chiltbx': , - 'cma_es': , - 'crys3d': , - 'dxtbx': , - 'fable': , - 'gltbx': , - 'iotbx': , - 'libtbx': , - 'mmtbx': , - 'omptbx': , - 'rstbx': , - 'scitbx': , - 'smtbx': , - 'spotfinder': , - 'tbxx': , - 'ucif': , - 'wxtbx': }, + 'missing_optional': {'king', 'docutils', 'cbflib', 'probe', 'reduce'}, + 'module_dict': {'annlib': , + 'boost': , + 'cbflib': , + 'ccp4io': , + 'cctbx': , + 'chiltbx': , + 'cma_es': , + 'crys3d': , + 'dxtbx': , + 'fable': , + 'gltbx': , + 'iotbx': , + 'libtbx': , + 'mmtbx': , + 'omptbx': , + 'rstbx': , + 'scitbx': , + 'smtbx': , + 'spotfinder': , + 'tbxx': , + 'ucif': , + 'wxtbx': }, 'module_dist_paths': {'annlib': relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../annlib"), 'annlib_adaptbx': relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../annlib_adaptbx"), 'boost': relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../boost"), @@ -35231,28 +35267,28 @@ 'tbxx': relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../tbxx"), 'ucif': relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../ucif"), 'wxtbx': relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../wxtbx")}, - 'module_list': [, - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - ], + 'module_list': [, + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + ], 'no_bin_python': False, 'path_utility': relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../libtbx/command_line/path_utility.py"), 'python_exe': relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="/usr/bin/python3.11"), @@ -35273,35 +35309,7 @@ '_dispatcher_include_before_command': [], '_dispatcher_precall_commands': None, '_dispatcher_registry': {relocatable_path(anchor="/usr", relocatable="bin/libtbx.python"): relocatable_path(anchor="/usr", relocatable="bin/python3.11"), - relocatable_path(anchor="/usr", relocatable="bin/libtbx.valgrind"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/valgrind.sh"), relocatable_path(anchor="/usr", relocatable="bin/libtbx.wait_for_file"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/wait_for_file.py"), - relocatable_path(anchor="/usr", relocatable="bin/iotbx.cns.reflection_reader"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/cns.reflection_reader.py"), - relocatable_path(anchor="/usr", relocatable="bin/phenix.cif_as_pdb"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/cif_as_pdb.py"), - relocatable_path(anchor="/usr", relocatable="bin/iotbx.cif_as_pdb"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/cif_as_pdb.py"), - relocatable_path(anchor="/usr", relocatable="bin/iotbx.cif.validate"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/cif.validate.py"), - relocatable_path(anchor="/usr", relocatable="bin/iotbx.cif.as_xray_structure"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/cif.as_xray_structure.py"), - relocatable_path(anchor="/usr", relocatable="bin/iotbx.cif.as_miller_arrays"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/cif.as_miller_arrays.py"), - relocatable_path(anchor="/usr", relocatable="bin/iotbx.cbf_read"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/cbf_read.py"), - relocatable_path(anchor="/usr", relocatable="bin/iotbx.build_phil_cache"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/build_phil_cache.py"), - relocatable_path(anchor="/usr", relocatable="bin/iotbx.blast_pdb"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/blast_pdb.py"), - relocatable_path(anchor="/usr", relocatable="bin/phenix.pdb.biomt_reconstruction"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/biomt_reconstruction.py"), - relocatable_path(anchor="/usr", relocatable="bin/gltbx.try_imports"): relocatable_path(anchor="/usr", 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relocatable="bin/omptbx.show_build_path"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/show_build_path.py"), + relocatable_path(anchor="/usr", relocatable="bin/boost.show_build_path"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/show_build_path.py"), relocatable_path(anchor="/usr", relocatable="bin/fable.show_build_path"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/show_build_path.py"), relocatable_path(anchor="/usr", relocatable="bin/scitbx.show_build_path"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/show_build_path.py"), relocatable_path(anchor="/usr", relocatable="bin/annlib.show_build_path"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/show_build_path.py"), @@ -35435,7 +35441,12 @@ relocatable_path(anchor="/usr", relocatable="bin/spotfinder.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/rstbx.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/wxtbx.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/omptbx.show_build_path"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/show_build_path.py"), + relocatable_path(anchor="/usr", relocatable="bin/rstbx.python"): relocatable_path(anchor="/usr", relocatable="bin/python3.11"), + relocatable_path(anchor="/usr", relocatable="bin/dxtbx.depends_on"): relocatable_path(anchor="/usr", 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relocatable_path(anchor="/usr", relocatable="bin/python3.11"), @@ -35448,10 +35459,11 @@ relocatable_path(anchor="/usr", relocatable="bin/iotbx.python"): relocatable_path(anchor="/usr", relocatable="bin/python3.11"), relocatable_path(anchor="/usr", relocatable="bin/dxtbx.python"): relocatable_path(anchor="/usr", relocatable="bin/python3.11"), relocatable_path(anchor="/usr", relocatable="bin/gltbx.python"): relocatable_path(anchor="/usr", relocatable="bin/python3.11"), - relocatable_path(anchor="/usr", relocatable="bin/mmtbx.python"): relocatable_path(anchor="/usr", relocatable="bin/python3.11"), - relocatable_path(anchor="/usr", relocatable="bin/spotfinder.python"): relocatable_path(anchor="/usr", relocatable="bin/python3.11"), - relocatable_path(anchor="/usr", relocatable="bin/rstbx.python"): relocatable_path(anchor="/usr", relocatable="bin/python3.11"), - relocatable_path(anchor="/usr", relocatable="bin/wxtbx.python"): relocatable_path(anchor="/usr", relocatable="bin/python3.11"), + relocatable_path(anchor="/usr", relocatable="bin/dxtbx.detector_superpose"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/dxtbx/src/dxtbx/command_line/detector_superpose.py"), + relocatable_path(anchor="/usr", relocatable="bin/rstbx.index"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/rstbx/command_line/index.py"), + relocatable_path(anchor="/usr", relocatable="bin/phenix.example_viewer"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/rstbx/command_line/example_viewer.py"), + relocatable_path(anchor="/usr", relocatable="bin/wxtbx.xtriage"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/wxtbx/command_line/xtriage.py"), + relocatable_path(anchor="/usr", relocatable="bin/mmtbx.xtriage_gui"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/wxtbx/command_line/xtriage.py"), relocatable_path(anchor="/usr", relocatable="bin/cctbx.wxpython"): 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relocatable="lib/python3/dist-packages/libtbx/command_line/phil.py"), relocatable_path(anchor="/usr", relocatable="bin/libtbx.pdflatex"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/pdflatex.sh"), relocatable_path(anchor="/usr", relocatable="bin/libtbx.path_utility"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/path_utility.py"), @@ -35751,42 +35793,36 @@ relocatable_path(anchor="/usr", relocatable="bin/libtbx.list_files"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/list_files.py"), relocatable_path(anchor="/usr", relocatable="bin/libtbx.line_count"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/line_count.py"), relocatable_path(anchor="/usr", relocatable="bin/libtbx.latex"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/latex.sh"), - 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relocatable="lib/python3/dist-packages/libtbx/command_line/valgrind.sh"), + relocatable_path(anchor="/usr", relocatable="bin/libtbx.unpack_in_sources"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/unpack_in_sources.csh"), + relocatable_path(anchor="/usr", relocatable="bin/libtbx.tcsh"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/tcsh.sh"), + relocatable_path(anchor="/usr", relocatable="bin/libtbx.start_process"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/start_process.py"), + relocatable_path(anchor="/usr", relocatable="bin/libtbx.start_binary_bundle"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/start_binary_bundle.py"), + relocatable_path(anchor="/usr", relocatable="bin/wxtbx.python"): relocatable_path(anchor="/usr", relocatable="bin/python3.11"), + relocatable_path(anchor="/usr", relocatable="bin/spotfinder.python"): relocatable_path(anchor="/usr", relocatable="bin/python3.11")}, 'bin_path': relocatable_path(anchor="/usr", relocatable="bin"), 'boost_version': 107400, - 'build_options': , + 'build_options': , 'build_path': absolute_path("/usr/lib/cctbx/python3.11"), 'command_line_redirections': {}, 'command_version_suffix': None, @@ -35822,29 +35858,29 @@ 'lib_path': relocatable_path(anchor="/usr", relocatable="lib"), 'missing_for_build': set(), 'missing_for_use': set(), - 'missing_optional': {'reduce', 'king', 'cbflib', 'docutils', 'probe'}, - 'module_dict': {'annlib': , - 'boost': , - 'cbflib': , - 'ccp4io': , - 'cctbx': , - 'chiltbx': , - 'cma_es': , - 'crys3d': , - 'dxtbx': , - 'fable': , - 'gltbx': , - 'iotbx': , - 'libtbx': , - 'mmtbx': , - 'omptbx': , - 'rstbx': , - 'scitbx': , - 'smtbx': , - 'spotfinder': , - 'tbxx': , - 'ucif': , - 'wxtbx': }, + 'missing_optional': {'king', 'docutils', 'cbflib', 'probe', 'reduce'}, + 'module_dict': {'annlib': , + 'boost': , + 'cbflib': , + 'ccp4io': , + 'cctbx': , + 'chiltbx': , + 'cma_es': , + 'crys3d': , + 'dxtbx': , + 'fable': , + 'gltbx': , + 'iotbx': , + 'libtbx': , + 'mmtbx': , + 'omptbx': , + 'rstbx': , + 'scitbx': , + '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"), @@ -35870,28 +35906,28 @@ '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/python3.11"), @@ -35946,7 +35982,7 @@ smtbx/refinement/constraints/tests/tst_reparametrisation smtbx/refinement/constraints/tests/tst_special_position -sent 16,586,925 bytes received 568 bytes 33,174,986.00 bytes/sec +sent 16,586,908 bytes received 568 bytes 33,174,952.00 bytes/sec total size is 16,575,272 speedup is 1.00 building file list ... done ./ @@ -36008,7 +36044,7 @@ libspotfinder.so.0 -> libspotfinder.so.0.0.1 libspotfinder.so.0.0.1 -sent 57,914,175 bytes received 494 bytes 115,829,338.00 bytes/sec +sent 57,914,213 bytes received 494 bytes 115,829,414.00 bytes/sec total size is 57,897,770 speedup is 1.00 building file list ... done annlib_adaptbx/ @@ -36040,7 +36076,7 @@ boost_adaptbx/tests/ boost_adaptbx/tests/tst_optional_copy.h -sent 73,848 bytes received 386 bytes 148,468.00 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/ @@ -36054,7 +36090,7 @@ cbflib_adaptbx/detectors/boost_python/cbf_binary_adaptor.h cbflib_adaptbx/detectors/boost_python/general_cbf_write.h -sent 22,341 bytes received 158 bytes 44,998.00 bytes/sec +sent 22,342 bytes received 158 bytes 45,000.00 bytes/sec total size is 21,656 speedup is 0.96 building file list ... done ccp4io_adaptbx/ @@ -36076,7 +36112,7 @@ ccp4io_adaptbx/dev/ ccp4io_adaptbx/dev/fftlib.hpp -sent 87,936 bytes received 326 bytes 176,524.00 bytes/sec +sent 87,938 bytes received 326 bytes 176,528.00 bytes/sec total size is 86,683 speedup is 0.98 building file list ... done cctbx/ @@ -36335,7 +36371,7 @@ cctbx/xray/targets/mli.h cctbx/xray/targets/shelxl_wght_ls.hpp -sent 1,895,070 bytes received 4,401 bytes 3,798,942.00 bytes/sec +sent 1,895,097 bytes received 4,401 bytes 3,798,996.00 bytes/sec total size is 1,878,555 speedup is 0.99 building file list ... done cma_es/ @@ -36343,7 +36379,7 @@ cma_es/cma/cmaes.h cma_es/cma/cmaes_interface.h -sent 6,888 bytes received 60 bytes 13,896.00 bytes/sec +sent 6,892 bytes received 60 bytes 13,904.00 bytes/sec total size is 6,671 speedup is 0.96 building file list ... done @@ -36442,7 +36478,7 @@ fem/utils/string_to_double_fmt.hpp fem/utils/token.hpp -sent 203,741 bytes received 918 bytes 409,318.00 bytes/sec +sent 203,753 bytes received 918 bytes 409,342.00 bytes/sec total size is 200,565 speedup is 0.98 building file list ... done gltbx/ @@ -36456,7 +36492,7 @@ gltbx/special_wrapper_support.h gltbx/util.h -sent 598,764 bytes received 190 bytes 1,197,908.00 bytes/sec +sent 598,774 bytes received 190 bytes 1,197,928.00 bytes/sec total size is 597,938 speedup is 1.00 building file list ... done iotbx/ @@ -36503,7 +36539,7 @@ total size is 265,547 speedup is 0.99 building file list ... done -sent 471 bytes received 12 bytes 322.00 bytes/sec +sent 496 bytes received 12 bytes 1,016.00 bytes/sec total size is 0 speedup is 0.00 building file list ... done mmtbx/ @@ -36594,7 +36630,7 @@ mmtbx/validation/ramachandran/rama8000_tables.h mmtbx/validation/ramachandran/rama_eval.h -sent 2,019,264 bytes received 1,253 bytes 4,041,034.00 bytes/sec +sent 2,019,268 bytes received 1,253 bytes 4,041,042.00 bytes/sec total size is 2,013,143 speedup is 1.00 building file list ... done omptbx/ @@ -36602,8 +36638,8 @@ omptbx/omp_or_stubs.h omptbx/stubs.h -sent 2,111 bytes received 76 bytes 4,374.00 bytes/sec -total size is 1,850 speedup is 0.85 +sent 2,115 bytes received 76 bytes 4,382.00 bytes/sec +total size is 1,850 speedup is 0.84 building file list ... done rstbx/ rstbx/backplane.h @@ -36638,7 +36674,7 @@ 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/ @@ -36961,7 +36997,7 @@ scitbx/wigner/ scitbx/wigner/wigner3j.h -sent 1,904,484 bytes received 5,521 bytes 3,820,010.00 bytes/sec +sent 1,904,500 bytes received 5,521 bytes 3,820,042.00 bytes/sec total size is 1,884,752 speedup is 0.99 building file list ... done smtbx/ @@ -36997,7 +37033,7 @@ smtbx/structure_factors/direct/standard_xray.h smtbx/structure_factors/direct/table_based.h -sent 182,117 bytes received 512 bytes 365,258.00 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/ @@ -37016,7 +37052,7 @@ spotfinder/dxtbx_toolbox/distl.h spotfinder/dxtbx_toolbox/libdistl.h -sent 42,926 bytes received 221 bytes 86,294.00 bytes/sec +sent 42,925 bytes received 221 bytes 86,292.00 bytes/sec total size is 41,955 speedup is 0.97 building file list ... done tbxx/ @@ -37027,7 +37063,7 @@ tbxx/pretty_type_name.hpp tbxx/time_accu.hpp -sent 12,027 bytes received 133 bytes 24,320.00 bytes/sec +sent 12,031 bytes received 133 bytes 24,328.00 bytes/sec total size is 11,532 speedup is 0.95 building file list ... done @@ -37037,6 +37073,7 @@ ./ boost_adaptbx/ boost_adaptbx/type_id_eq.h +cctbx/ cctbx/boost_python/ cctbx/boost_python/flex_fwd.h scitbx/ @@ -37066,27 +37103,28 @@ 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 347,301 bytes received 534 bytes 695,670.00 bytes/sec +sent 347,308 bytes received 540 bytes 695,696.00 bytes/sec total size is 345,070 speedup is 0.99 building file list ... done -sent 248 bytes received 12 bytes 173.33 bytes/sec +sent 248 bytes received 12 bytes 520.00 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 558 bytes received 55 bytes 408.67 bytes/sec +total size is 6,883 speedup is 11.23 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 149 bytes received 12 bytes 322.00 bytes/sec @@ -37096,8 +37134,8 @@ cctbx/command_line/ cctbx/command_line/web.install.csh -sent 2,938 bytes received 41 bytes 5,958.00 bytes/sec -total size is 39,547 speedup is 13.28 +sent 3,025 bytes received 101 bytes 6,252.00 bytes/sec +total size is 39,547 speedup is 12.65 building file list ... done sent 87 bytes received 12 bytes 198.00 bytes/sec @@ -37106,32 +37144,32 @@ crys3d/ crys3d/command_line/ -sent 464 bytes received 22 bytes 972.00 bytes/sec -total size is 31,551 speedup is 64.92 +sent 498 bytes received 52 bytes 1,100.00 bytes/sec +total size is 31,551 speedup is 57.37 building file list ... done dxtbx/ dxtbx/command_line/ -sent 825 bytes received 22 bytes 1,694.00 bytes/sec -total size is 79,884 speedup is 94.31 +sent 882 bytes received 79 bytes 1,922.00 bytes/sec +total size is 79,884 speedup is 83.13 building file list ... done fable/ fable/command_line/ -sent 448 bytes received 22 bytes 940.00 bytes/sec -total size is 15,542 speedup is 33.07 +sent 481 bytes received 43 bytes 1,048.00 bytes/sec +total size is 15,542 speedup is 29.66 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 2,632 bytes received 22 bytes 1,769.33 bytes/sec -total size is 216,768 speedup is 81.68 +sent 2,854 bytes received 244 bytes 6,196.00 bytes/sec +total size is 216,768 speedup is 69.97 building file list ... done libtbx/ libtbx/command_line/ @@ -37152,8 +37190,8 @@ libtbx/command_line/unpack_in_sources.csh libtbx/command_line/valgrind.sh -sent 6,813 bytes received 326 bytes 14,278.00 bytes/sec -total size is 155,965 speedup is 21.85 +sent 7,117 bytes received 605 bytes 15,444.00 bytes/sec +total size is 155,965 speedup is 20.20 building file list ... done mmtbx/ mmtbx/command_line/ @@ -37161,8 +37199,8 @@ mmtbx/regression/command_line/ mmtbx/regression/command_line/tst_find_residue_in_pdb.py -sent 5,209 bytes received 47 bytes 10,512.00 bytes/sec -total size is 822,860 speedup is 156.56 +sent 5,639 bytes received 473 bytes 12,224.00 bytes/sec +total size is 822,860 speedup is 134.63 building file list ... done sent 76 bytes received 12 bytes 176.00 bytes/sec @@ -37171,8 +37209,8 @@ rstbx/ rstbx/command_line/ -sent 751 bytes received 22 bytes 1,546.00 bytes/sec -total size is 11,092 speedup is 14.35 +sent 779 bytes received 49 bytes 1,656.00 bytes/sec +total size is 11,092 speedup is 13.40 building file list ... done scitbx/ scitbx/command_line/ @@ -37183,20 +37221,20 @@ 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 11,703 bytes received 136 bytes 23,678.00 bytes/sec total size is 9,958 speedup is 0.84 building file list ... done 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 @@ -37205,11 +37243,11 @@ wxtbx/ wxtbx/command_line/ -sent 449 bytes received 22 bytes 942.00 bytes/sec -total size is 16,078 speedup is 34.14 +sent 489 bytes received 58 bytes 1,094.00 bytes/sec +total size is 16,078 speedup is 29.39 building file list ... done -sent 248 bytes received 12 bytes 173.33 bytes/sec +sent 248 bytes received 12 bytes 520.00 bytes/sec total size is 0 speedup is 0.00 building file list ... done boost_adaptbx/graph/ @@ -37242,20 +37280,20 @@ 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 7,596 bytes received 44 bytes 15,280.00 bytes/sec +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/ @@ -37339,21 +37377,21 @@ cctbx/xray/observations/ cctbx/xray/targets/ -sent 417,462 bytes received 816 bytes 836,556.00 bytes/sec -total size is 1,932,392 speedup is 4.62 +sent 417,850 bytes received 1,185 bytes 838,070.00 bytes/sec +total size is 1,932,392 speedup is 4.61 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 241 bytes received 15 bytes 512.00 bytes/sec -total size is 29,755 speedup is 116.23 +sent 244 bytes received 18 bytes 524.00 bytes/sec +total size is 29,755 speedup is 113.57 building file list ... done -sent 633 bytes received 12 bytes 1,290.00 bytes/sec +sent 644 bytes received 12 bytes 1,312.00 bytes/sec total size is 0 speedup is 0.00 building file list ... done fable/test/ @@ -37362,12 +37400,12 @@ fable/test/tst_separate_files.py fable/test/tst_show_calls.py -sent 12,826 bytes received 91 bytes 25,834.00 bytes/sec -total size is 151,835 speedup is 11.75 +sent 12,845 bytes received 106 bytes 25,902.00 bytes/sec +total size is 151,835 speedup is 11.72 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/ @@ -37415,14 +37453,14 @@ iotbx/xds/tests/tst_xparm.py iotbx/xplor/ -sent 240,529 bytes received 499 bytes 482,056.00 bytes/sec -total size is 2,112,818 speedup is 8.77 +sent 240,855 bytes received 829 bytes 483,368.00 bytes/sec +total size is 2,112,818 speedup is 8.74 building file list ... done libtbx/phil/ libtbx/queuing_system_utils/ -sent 1,106 bytes received 18 bytes 2,248.00 bytes/sec -total size is 242,792 speedup is 216.01 +sent 1,206 bytes received 105 bytes 2,622.00 bytes/sec +total size is 242,792 speedup is 185.20 building file list ... done mmtbx/atomic_environment_vectors/ mmtbx/building/ @@ -37511,13 +37549,13 @@ mmtbx/validation/regression/ mmtbx/wwpdb/ -sent 747,030 bytes received 854 bytes 1,495,768.00 bytes/sec -total size is 6,362,461 speedup is 8.51 +sent 748,065 bytes received 1,889 bytes 1,499,908.00 bytes/sec +total size is 6,362,461 speedup is 8.48 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/ @@ -37531,8 +37569,8 @@ 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 @@ -37638,7 +37676,7 @@ scitbx/tests/tst_smoothing.py scitbx/wigner/ -sent 674,728 bytes received 1,349 bytes 1,352,154.00 bytes/sec +sent 674,942 bytes received 1,547 bytes 1,352,978.00 bytes/sec total size is 1,108,176 speedup is 1.64 building file list ... done smtbx/ab_initio/ @@ -37667,21 +37705,21 @@ smtbx/structure_factors/direct/tests/ smtbx/structure_factors/direct/tests/tst_standard_xray.py -sent 130,371 bytes received 231 bytes 261,204.00 bytes/sec +sent 130,399 bytes received 252 bytes 261,302.00 bytes/sec total size is 208,160 speedup is 1.59 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 3,674.00 bytes/sec total size is 5,074 speedup is 0.92 building file list ... done tbxx/ tbxx/tests/ tbxx/tests/tst_pretty_type_name.cpp -sent 495 bytes received 41 bytes 1,072.00 bytes/sec +sent 499 bytes received 41 bytes 1,080.00 bytes/sec total size is 323 speedup is 0.60 building file list ... done wxtbx/regression/ @@ -38155,7 +38193,7 @@ smtbx/regression/test_data/thpp.hkl smtbx/regression/test_data/thpp.ins -sent 4,044,938 bytes received 8,672 bytes 8,107,220.00 bytes/sec +sent 4,045,947 bytes received 8,672 bytes 8,109,238.00 bytes/sec total size is 3,985,674 speedup is 0.98 make[1]: Leaving directory '/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1' dh_install -O--buildsystem=pybuild @@ -38177,15 +38215,15 @@ 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/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 + 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 dh_python3 -O--buildsystem=pybuild D: dh_python3 dh_python3:179: version: 5.20230130+deb12u1 D: dh_python3 dh_python3:180: argv: ['/usr/bin/dh_python3', '-O--buildsystem=pybuild'] @@ -38926,7 +38964,7 @@ D: dh_python3 pydist:173: trying to find dependency for wxPython (python=None) D: dh_python3 pydist:207: dependency: module seems to be installed D: dh_python3 pydist:270: dependency: included in build-deps -D: dh_python3 depends:281: D={'python3-numpy', 'python3-pil', 'python3 (<< 3.12)', 'python3-mrcfile', 'python3-requests', 'python3-pint', 'python3-tqdm', 'python3-procrunner', 'python3-h5py (>= 3)', 'python3-wxgtk4.0', 'python3 (>= 3.11~)', 'python3:any', 'python3-six', 'python3-matplotlib', 'python3-scipy', 'python3-pymol'}; R=[]; S=[]; E=[], B=[]; RT=[] +D: dh_python3 depends:281: D={'python3-h5py (>= 3)', 'python3-pymol', 'python3-mrcfile', 'python3-requests', 'python3:any', 'python3-wxgtk4.0', 'python3-procrunner', 'python3-pil', 'python3 (<< 3.12)', 'python3-matplotlib', 'python3-pint', 'python3 (>= 3.11~)', 'python3-six', 'python3-tqdm', 'python3-scipy', 'python3-numpy'}; 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 @@ -38982,38 +39020,38 @@ make[1]: Leaving directory '/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1' dh_strip_nondeterminism -O--buildsystem=pybuild Using 1673188013 as canonical time - 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 + Normalizing debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx/bioinformatics/test/ncbi_blast.xml.gz using File::StripNondeterminism::handlers::gzip dh_compress -O--buildsystem=pybuild cd debian/libcctbx0 cd debian/libcctbx-dev cd debian/python3-cctbx 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/libcctbx0/changelog usr/share/doc/libcctbx0/changelog.Debian + chmod a-x usr/share/doc/libcctbx-dev/changelog usr/share/doc/libcctbx-dev/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 gzip -9nf usr/share/doc/python3-cctbx/changelog usr/share/doc/python3-cctbx/changelog.Debian cd '/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1' cd '/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1' cd '/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1' dh_fixperms -O--buildsystem=pybuild find debian/libcctbx0 ! -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/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/python3-cctbx/usr/share/doc -type f -a -true -a ! -regex 'debian/python3-cctbx/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 -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/include -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 - find debian/python3-cctbx/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/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 + find debian/python3-cctbx/usr/share/doc -type f -a -true -a ! -regex 'debian/python3-cctbx/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 + find debian/libcctbx-dev/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w + find debian/python3-cctbx/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/python3-cctbx/usr/share/lintian/overrides -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/python3-cctbx -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/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w find debian/python3-cctbx/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x find debian/python3-cctbx/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w dh_missing -O--buildsystem=pybuild @@ -39027,18 +39065,18 @@ objcopy --compress-debug-sections debian/python3-cctbx/usr/lib/debug/.dwz/aarch64-linux-gnu/python3-cctbx.debug chmod 0644 -- debian/python3-cctbx/usr/lib/debug/.dwz/aarch64-linux-gnu/python3-cctbx.debug dh_strip -a -O--buildsystem=pybuild - install -m0755 -d debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/04 - 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/04/2e81a352fbc5c7dc7062b72308b409b18ec9e8.debug - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1a - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_array_family_flex_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1a/acc25a7e755e7dbac8067f3bf54a88d847e8fa.debug - chmod 0644 -- debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/04/2e81a352fbc5c7dc7062b72308b409b18ec9e8.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/04/2e81a352fbc5c7dc7062b72308b409b18ec9e8.debug debian/libcctbx0/usr/lib/aarch64-linux-gnu/libiotbx_pdb.so.0.0.1 install -m0755 -d debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/44 objcopy --only-keep-debug --compress-debug-sections debian/libcctbx0/usr/lib/aarch64-linux-gnu/libsmtbx_refinement_constraints.so.0.0.1 debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/44/c127add3b44a8d154807700aaad81982a5b0cf.debug + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1a + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_array_family_flex_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1a/acc25a7e755e7dbac8067f3bf54a88d847e8fa.debug chmod 0644 -- debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/44/c127add3b44a8d154807700aaad81982a5b0cf.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libcctbx0/usr/lib/aarch64-linux-gnu/libsmtbx_refinement_constraints.so.0.0.1 objcopy --add-gnu-debuglink debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/44/c127add3b44a8d154807700aaad81982a5b0cf.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/04 + 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/04/2e81a352fbc5c7dc7062b72308b409b18ec9e8.debug + chmod 0644 -- debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/04/2e81a352fbc5c7dc7062b72308b409b18ec9e8.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/04/2e81a352fbc5c7dc7062b72308b409b18ec9e8.debug debian/libcctbx0/usr/lib/aarch64-linux-gnu/libiotbx_pdb.so.0.0.1 install -m0755 -d debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/3f objcopy --only-keep-debug --compress-debug-sections debian/libcctbx0/usr/lib/aarch64-linux-gnu/libcctbx.so.0.0.1 debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/3f/865da9b95f0486d3e2ca639024732ac4936c40.debug chmod 0644 -- debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/3f/865da9b95f0486d3e2ca639024732ac4936c40.debug @@ -39049,11 +39087,6 @@ chmod 0644 -- debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/da/ff85a500f292d478a5ac35bb663e2089fe1ead.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libcctbx0/usr/lib/aarch64-linux-gnu/libspotfinder.so.0.0.1 objcopy --add-gnu-debuglink debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/da/ff85a500f292d478a5ac35bb663e2089fe1ead.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/28 - objcopy --only-keep-debug --compress-debug-sections debian/libcctbx0/usr/lib/aarch64-linux-gnu/librstbx.so.0.0.1 debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/28/f0248ac20362c734c2a58397ab14b08c6058cb.debug - chmod 0644 -- debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/28/f0248ac20362c734c2a58397ab14b08c6058cb.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/28/f0248ac20362c734c2a58397ab14b08c6058cb.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/57 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/57/cccca638c62e40ac6cc9fce590edbe136ae180.debug chmod 0644 -- debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/57/cccca638c62e40ac6cc9fce590edbe136ae180.debug @@ -39064,6 +39097,11 @@ chmod 0644 -- debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/36/f8de703d6c7322d08d8c6323520d14a26d2fb7.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/36/f8de703d6c7322d08d8c6323520d14a26d2fb7.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/28 + objcopy --only-keep-debug --compress-debug-sections debian/libcctbx0/usr/lib/aarch64-linux-gnu/librstbx.so.0.0.1 debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/28/f0248ac20362c734c2a58397ab14b08c6058cb.debug + chmod 0644 -- debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/28/f0248ac20362c734c2a58397ab14b08c6058cb.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/28/f0248ac20362c734c2a58397ab14b08c6058cb.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/36 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/36/5741d4f7a91f33f9aa4af7a30202f2bdab41d9.debug chmod 0644 -- debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/36/5741d4f7a91f33f9aa4af7a30202f2bdab41d9.debug @@ -39079,21 +39117,23 @@ chmod 0644 -- debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/16/deae830931529852bcdc306d3920e1137ed7cc.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libcctbx0/usr/lib/aarch64-linux-gnu/libscitbx_boost_python.so.0.0.1 objcopy --add-gnu-debuglink debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/16/deae830931529852bcdc306d3920e1137ed7cc.debug debian/libcctbx0/usr/lib/aarch64-linux-gnu/libscitbx_boost_python.so.0.0.1 - install -m0755 -d debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/d1 - objcopy --only-keep-debug --compress-debug-sections debian/libcctbx0/usr/lib/aarch64-linux-gnu/libmmtbx_tls.so.0.0.1 debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/d1/9e9d462c0c49580bf0f8c849d9c29c75d2f1dd.debug - chmod 0644 -- debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/d1/9e9d462c0c49580bf0f8c849d9c29c75d2f1dd.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libcctbx0/usr/lib/aarch64-linux-gnu/libmmtbx_tls.so.0.0.1 - objcopy --add-gnu-debuglink debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/d1/9e9d462c0c49580bf0f8c849d9c29c75d2f1dd.debug debian/libcctbx0/usr/lib/aarch64-linux-gnu/libmmtbx_tls.so.0.0.1 install -m0755 -d debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/ff objcopy --only-keep-debug --compress-debug-sections debian/libcctbx0/usr/lib/aarch64-linux-gnu/libomptbx.so.0.0.1 debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/ff/817ee9203f571900e793dad487d2ed4d8b5249.debug chmod 0644 -- debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/ff/817ee9203f571900e793dad487d2ed4d8b5249.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libcctbx0/usr/lib/aarch64-linux-gnu/libomptbx.so.0.0.1 objcopy --add-gnu-debuglink debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/ff/817ee9203f571900e793dad487d2ed4d8b5249.debug debian/libcctbx0/usr/lib/aarch64-linux-gnu/libomptbx.so.0.0.1 + install -m0755 -d debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/d1 + objcopy --only-keep-debug --compress-debug-sections debian/libcctbx0/usr/lib/aarch64-linux-gnu/libmmtbx_tls.so.0.0.1 debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/d1/9e9d462c0c49580bf0f8c849d9c29c75d2f1dd.debug + chmod 0644 -- debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/d1/9e9d462c0c49580bf0f8c849d9c29c75d2f1dd.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libcctbx0/usr/lib/aarch64-linux-gnu/libmmtbx_tls.so.0.0.1 + objcopy --add-gnu-debuglink debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/d1/9e9d462c0c49580bf0f8c849d9c29c75d2f1dd.debug debian/libcctbx0/usr/lib/aarch64-linux-gnu/libmmtbx_tls.so.0.0.1 install -m0755 -d debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/17 objcopy --only-keep-debug --compress-debug-sections debian/libcctbx0/usr/lib/aarch64-linux-gnu/libasymmetric_map.so.0.0.1 debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/17/edc81da0974e8c32a54e081034bd84d4a2d0b1.debug chmod 0644 -- debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/17/edc81da0974e8c32a54e081034bd84d4a2d0b1.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libcctbx0/usr/lib/aarch64-linux-gnu/libasymmetric_map.so.0.0.1 objcopy --add-gnu-debuglink debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/17/edc81da0974e8c32a54e081034bd84d4a2d0b1.debug debian/libcctbx0/usr/lib/aarch64-linux-gnu/libasymmetric_map.so.0.0.1 + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1a/acc25a7e755e7dbac8067f3bf54a88d847e8fa.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_array_family_flex_ext.cpython-311-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/1e objcopy --only-keep-debug --compress-debug-sections debian/libcctbx0/usr/lib/aarch64-linux-gnu/libiotbx_mtz.so.0.0.1 debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/1e/d7e77734440d47db893f0398343aaa9212fecd.debug chmod 0644 -- debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/1e/d7e77734440d47db893f0398343aaa9212fecd.debug @@ -39101,6 +39141,7 @@ objcopy --add-gnu-debuglink debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/1e/d7e77734440d47db893f0398343aaa9212fecd.debug debian/libcctbx0/usr/lib/aarch64-linux-gnu/libiotbx_mtz.so.0.0.1 install -m0755 -d debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/42 objcopy --only-keep-debug --compress-debug-sections debian/libcctbx0/usr/lib/aarch64-linux-gnu/libiotbx_xplor.so.0.0.1 debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/42/ef424e6518bc8d664d6d5a6fe86462510ad224.debug + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1a/acc25a7e755e7dbac8067f3bf54a88d847e8fa.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_array_family_flex_ext.cpython-311-aarch64-linux-gnu.so chmod 0644 -- debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/42/ef424e6518bc8d664d6d5a6fe86462510ad224.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libcctbx0/usr/lib/aarch64-linux-gnu/libiotbx_xplor.so.0.0.1 objcopy --add-gnu-debuglink debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/42/ef424e6518bc8d664d6d5a6fe86462510ad224.debug debian/libcctbx0/usr/lib/aarch64-linux-gnu/libiotbx_xplor.so.0.0.1 @@ -39116,6 +39157,8 @@ objcopy --add-gnu-debuglink debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/9c/8260ba65779a62a9631ae90f582bb6720560a5.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/fc 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/fc/89708ef85735776428d20bd5e023dbf007bcd1.debug + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/fd + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_refinement_constraints_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/fd/62a1c010959e6e7369a98a8b20364f616bbbeb.debug chmod 0644 -- debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/fc/89708ef85735776428d20bd5e023dbf007bcd1.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/fc/89708ef85735776428d20bd5e023dbf007bcd1.debug debian/libcctbx0/usr/lib/aarch64-linux-gnu/libann_adaptor.so.0.0.1 @@ -39131,11 +39174,6 @@ install -m0755 -d debian/.debhelper/libcctbx0/dbgsym-root/usr/share/doc ln -s libcctbx0 debian/.debhelper/libcctbx0/dbgsym-root/usr/share/doc/libcctbx0-dbgsym install -m0755 -d debian/.debhelper/libcctbx0 - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1a/acc25a7e755e7dbac8067f3bf54a88d847e8fa.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_array_family_flex_ext.cpython-311-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1a/acc25a7e755e7dbac8067f3bf54a88d847e8fa.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_array_family_flex_ext.cpython-311-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/fd - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_refinement_constraints_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/fd/62a1c010959e6e7369a98a8b20364f616bbbeb.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/fd/62a1c010959e6e7369a98a8b20364f616bbbeb.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_refinement_constraints_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/fd/62a1c010959e6e7369a98a8b20364f616bbbeb.debug debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_refinement_constraints_ext.cpython-311-aarch64-linux-gnu.so @@ -39144,26 +39182,26 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7d/8850c3090134ed64afd8c56b8defb3838c4b0f.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_math_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7d/8850c3090134ed64afd8c56b8defb3838c4b0f.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_math_ext.cpython-311-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/bb - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_array_family_flex_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/bb/2f946d48efc2f3a925f58f75c014fe9021c3dc.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/bb/2f946d48efc2f3a925f58f75c014fe9021c3dc.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_array_family_flex_ext.cpython-311-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/bb/2f946d48efc2f3a925f58f75c014fe9021c3dc.debug debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_array_family_flex_ext.cpython-311-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/std_pair_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/2a/1472401d2d42bbee444b8c5dee6052997f5869.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/2a/1472401d2d42bbee444b8c5dee6052997f5869.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/std_pair_ext.cpython-311-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/2a/1472401d2d42bbee444b8c5dee6052997f5869.debug debian/python3-cctbx/usr/lib/python3/dist-packages/std_pair_ext.cpython-311-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/spotfinder_distltbx_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/35/5f15fb62d75416bbd8e83875d27e3ae4d5a0a3.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/35/5f15fb62d75416bbd8e83875d27e3ae4d5a0a3.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_distltbx_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/35/5f15fb62d75416bbd8e83875d27e3ae4d5a0a3.debug debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_distltbx_ext.cpython-311-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/std_pair_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/2a/1472401d2d42bbee444b8c5dee6052997f5869.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/2a/1472401d2d42bbee444b8c5dee6052997f5869.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/std_pair_ext.cpython-311-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/2a/1472401d2d42bbee444b8c5dee6052997f5869.debug debian/python3-cctbx/usr/lib/python3/dist-packages/std_pair_ext.cpython-311-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/spotfinder_hough_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a0/6b43e16a5f4127ccc41dce5fb5057daaece982.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a0/6b43e16a5f4127ccc41dce5fb5057daaece982.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_hough_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a0/6b43e16a5f4127ccc41dce5fb5057daaece982.debug debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_hough_ext.cpython-311-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/bb + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_array_family_flex_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/bb/2f946d48efc2f3a925f58f75c014fe9021c3dc.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/bb/2f946d48efc2f3a925f58f75c014fe9021c3dc.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_array_family_flex_ext.cpython-311-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/bb/2f946d48efc2f3a925f58f75c014fe9021c3dc.debug debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_array_family_flex_ext.cpython-311-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/33 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_dxtbx_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/33/df84a2f6c4f86f917a249b628b216a7a3d8770.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/33/df84a2f6c4f86f917a249b628b216a7a3d8770.debug @@ -39189,11 +39227,6 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8a/80f0b9c7857d2be201fe9af4611a18115e27d5.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_stl_map_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8a/80f0b9c7857d2be201fe9af4611a18115e27d5.debug debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_stl_map_ext.cpython-311-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a1 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_sparse_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a1/59b1966a3f7a862efd2d63e713c75477b524d1.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a1/59b1966a3f7a862efd2d63e713c75477b524d1.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_sparse_ext.cpython-311-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a1/59b1966a3f7a862efd2d63e713c75477b524d1.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_sparse_ext.cpython-311-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/scitbx_suffixtree_single_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b4/f1c61836dbf219d9773ce3bcf8dc3b8ae8fb1d.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b4/f1c61836dbf219d9773ce3bcf8dc3b8ae8fb1d.debug @@ -39204,6 +39237,11 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/09/a98d913fff377dc2a7a19f4ab3dbfd0deeb17e.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_array_family_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/09/a98d913fff377dc2a7a19f4ab3dbfd0deeb17e.debug debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_array_family_ext.cpython-311-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a1 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_sparse_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a1/59b1966a3f7a862efd2d63e713c75477b524d1.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a1/59b1966a3f7a862efd2d63e713c75477b524d1.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_sparse_ext.cpython-311-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a1/59b1966a3f7a862efd2d63e713c75477b524d1.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_sparse_ext.cpython-311-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/scitbx_wigner_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/26/808524f5643f4cb9dd8958acfa8191185f3f7a.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/26/808524f5643f4cb9dd8958acfa8191185f3f7a.debug @@ -39214,31 +39252,31 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7c/5ff35140c69d9e7cbb536ae4c697f8fd7ba243.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_ab_initio_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7c/5ff35140c69d9e7cbb536ae4c697f8fd7ba243.debug debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_ab_initio_ext.cpython-311-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/21 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_stl_map_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/21/3d417bfc941663f72c6fc54370d609306d8f40.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/21/3d417bfc941663f72c6fc54370d609306d8f40.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_stl_map_ext.cpython-311-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/21/3d417bfc941663f72c6fc54370d609306d8f40.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_stl_map_ext.cpython-311-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/6d objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_stl_vector_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/6d/e366f183f892027d559d1c50b823dade73317a.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/6d/e366f183f892027d559d1c50b823dade73317a.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_stl_vector_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/6d/e366f183f892027d559d1c50b823dade73317a.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_stl_vector_ext.cpython-311-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/21 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_stl_map_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/21/3d417bfc941663f72c6fc54370d609306d8f40.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/21/3d417bfc941663f72c6fc54370d609306d8f40.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_stl_map_ext.cpython-311-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/21/3d417bfc941663f72c6fc54370d609306d8f40.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_stl_map_ext.cpython-311-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/5f objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_suffixtree_shared_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/5f/439873d2976f3c712ff4da2e43770b049edcb2.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/5f/439873d2976f3c712ff4da2e43770b049edcb2.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_suffixtree_shared_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/5f/439873d2976f3c712ff4da2e43770b049edcb2.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_suffixtree_shared_ext.cpython-311-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/scitbx_stl_set_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d2/1d92bbd803927e4bfb983adb51fbf1bc85e055.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d2/1d92bbd803927e4bfb983adb51fbf1bc85e055.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_stl_set_ext.cpython-311-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d2/1d92bbd803927e4bfb983adb51fbf1bc85e055.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_stl_set_ext.cpython-311-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/50 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_rigid_body_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/50/136ee8854099a165bf3a8a9eb5a20e15f10b9f.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/50/136ee8854099a165bf3a8a9eb5a20e15f10b9f.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_rigid_body_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/50/136ee8854099a165bf3a8a9eb5a20e15f10b9f.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_rigid_body_ext.cpython-311-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/scitbx_stl_set_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d2/1d92bbd803927e4bfb983adb51fbf1bc85e055.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d2/1d92bbd803927e4bfb983adb51fbf1bc85e055.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_stl_set_ext.cpython-311-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d2/1d92bbd803927e4bfb983adb51fbf1bc85e055.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_stl_set_ext.cpython-311-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/scitbx_random_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b9/0be8e528f8fc8711790a52166e392d211d9c03.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b9/0be8e528f8fc8711790a52166e392d211d9c03.debug @@ -39254,36 +39292,41 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ca/b08f06b8596836c419a73e8874ae3988e703a4.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_r3_utils_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ca/b08f06b8596836c419a73e8874ae3988e703a4.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_r3_utils_ext.cpython-311-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/scitbx_minpack_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/3a/1780d64cdc3d43f19cad90cbcc3e63a8ee6a00.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/3a/1780d64cdc3d43f19cad90cbcc3e63a8ee6a00.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_minpack_ext.cpython-311-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/3a/1780d64cdc3d43f19cad90cbcc3e63a8ee6a00.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_minpack_ext.cpython-311-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/scitbx_lstbx_normal_equations_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b8/7af7f6eeaf2f2aed133ba29f91e0293a1fdf9e.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b8/7af7f6eeaf2f2aed133ba29f91e0293a1fdf9e.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_lstbx_normal_equations_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b8/7af7f6eeaf2f2aed133ba29f91e0293a1fdf9e.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_lstbx_normal_equations_ext.cpython-311-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/scitbx_minpack_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/3a/1780d64cdc3d43f19cad90cbcc3e63a8ee6a00.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/3a/1780d64cdc3d43f19cad90cbcc3e63a8ee6a00.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_minpack_ext.cpython-311-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/3a/1780d64cdc3d43f19cad90cbcc3e63a8ee6a00.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_minpack_ext.cpython-311-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/scitbx_lbfgs_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/02/2341c863b050645e18ac6b374f9b972874c396.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/02/2341c863b050645e18ac6b374f9b972874c396.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_lbfgs_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/02/2341c863b050645e18ac6b374f9b972874c396.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_lbfgs_ext.cpython-311-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_array_family_shared_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/5a/345cae345ca8e49bbf7722aa7c3f9f6609da65.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/5a/345cae345ca8e49bbf7722aa7c3f9f6609da65.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_array_family_shared_ext.cpython-311-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/5a/345cae345ca8e49bbf7722aa7c3f9f6609da65.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_array_family_shared_ext.cpython-311-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d3 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_lbfgsb_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d3/af4b10a3fd400e10636f85e770a1d9e5934aa0.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d3/af4b10a3fd400e10636f85e770a1d9e5934aa0.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_lbfgsb_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d3/af4b10a3fd400e10636f85e770a1d9e5934aa0.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_lbfgsb_ext.cpython-311-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_array_family_shared_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/5a/345cae345ca8e49bbf7722aa7c3f9f6609da65.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/5a/345cae345ca8e49bbf7722aa7c3f9f6609da65.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_array_family_shared_ext.cpython-311-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/5a/345cae345ca8e49bbf7722aa7c3f9f6609da65.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_array_family_shared_ext.cpython-311-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a7 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_fftpack_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a7/0c930ee275d5214edc4ae2556aa0bd1add9faf.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a7/0c930ee275d5214edc4ae2556aa0bd1add9faf.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_fftpack_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a7/0c930ee275d5214edc4ae2556aa0bd1add9faf.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_fftpack_ext.cpython-311-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/cf + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_glmtbx_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/cf/15705745b3b4a534cfacd4ef8a129e70bb3718.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/cf/15705745b3b4a534cfacd4ef8a129e70bb3718.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_glmtbx_ext.cpython-311-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/cf/15705745b3b4a534cfacd4ef8a129e70bb3718.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_glmtbx_ext.cpython-311-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d3 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_iso_surface_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d3/53c9a67813645a8e29c591f1788d402a49b7e2.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d3/53c9a67813645a8e29c591f1788d402a49b7e2.debug @@ -39294,41 +39337,26 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/24/45ecc3d04562508a550dbf605e587befb6478f.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_graphics_utils_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/24/45ecc3d04562508a550dbf605e587befb6478f.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_graphics_utils_ext.cpython-311-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/cf - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_glmtbx_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/cf/15705745b3b4a534cfacd4ef8a129e70bb3718.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/cf/15705745b3b4a534cfacd4ef8a129e70bb3718.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_glmtbx_ext.cpython-311-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/cf/15705745b3b4a534cfacd4ef8a129e70bb3718.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_glmtbx_ext.cpython-311-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/scitbx_cubicle_neighbors_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/fc/7af677f38da8f4389e26c19143ba0754669fa2.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/fc/7af677f38da8f4389e26c19143ba0754669fa2.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_cubicle_neighbors_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/fc/7af677f38da8f4389e26c19143ba0754669fa2.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_cubicle_neighbors_ext.cpython-311-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/c4 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_symmetry_constraints_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/c4/1a22932ad52a102f59a47d148076ffcd080c73.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/c4/1a22932ad52a102f59a47d148076ffcd080c73.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_symmetry_constraints_ext.cpython-311-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/c4/1a22932ad52a102f59a47d148076ffcd080c73.debug debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_symmetry_constraints_ext.cpython-311-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/rstbx_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/13/3719f8c8f0f1538629d9e090fdf4f5cdac9a6e.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/13/3719f8c8f0f1538629d9e090fdf4f5cdac9a6e.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/13/3719f8c8f0f1538629d9e090fdf4f5cdac9a6e.debug debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_ext.cpython-311-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/rstbx_simulation_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/82/77ec5aaa99cc73ec2a41ce2a0da0bdd93c85c3.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/82/77ec5aaa99cc73ec2a41ce2a0da0bdd93c85c3.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_simulation_ext.cpython-311-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/82/77ec5aaa99cc73ec2a41ce2a0da0bdd93c85c3.debug debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_simulation_ext.cpython-311-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/c4 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_symmetry_constraints_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/c4/1a22932ad52a102f59a47d148076ffcd080c73.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/c4/1a22932ad52a102f59a47d148076ffcd080c73.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_symmetry_constraints_ext.cpython-311-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/c4/1a22932ad52a102f59a47d148076ffcd080c73.debug debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_symmetry_constraints_ext.cpython-311-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e1 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_integration_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e1/58920b9b6bb7a511e6e88355a33d7d2a98070b.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e1/58920b9b6bb7a511e6e88355a33d7d2a98070b.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_integration_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e1/58920b9b6bb7a511e6e88355a33d7d2a98070b.debug debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_integration_ext.cpython-311-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d8 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_array_family_flex_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d8/10c53638136b2c2b9050241571306456cd6ce5.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d8/10c53638136b2c2b9050241571306456cd6ce5.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_array_family_flex_ext.cpython-311-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d8/10c53638136b2c2b9050241571306456cd6ce5.debug debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_array_family_flex_ext.cpython-311-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/4b objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_simage_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/4b/9ed6f2250980c6dfb2828145240801a39219dd.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/4b/9ed6f2250980c6dfb2828145240801a39219dd.debug @@ -39339,26 +39367,36 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/aa/e6cc34ffd620524d2e1df5bd945c31ef52cb9c.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_indexing_api_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/aa/e6cc34ffd620524d2e1df5bd945c31ef52cb9c.debug debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_indexing_api_ext.cpython-311-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/mmtbx_tls_utils_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a0/383641f2e0a0cd933b89183fa570ea88617da1.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a0/383641f2e0a0cd933b89183fa570ea88617da1.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_utils_ext.cpython-311-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a0/383641f2e0a0cd933b89183fa570ea88617da1.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_utils_ext.cpython-311-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/rstbx_simulation_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/82/77ec5aaa99cc73ec2a41ce2a0da0bdd93c85c3.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/82/77ec5aaa99cc73ec2a41ce2a0da0bdd93c85c3.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_simulation_ext.cpython-311-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/82/77ec5aaa99cc73ec2a41ce2a0da0bdd93c85c3.debug debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_simulation_ext.cpython-311-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d8 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_array_family_flex_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d8/10c53638136b2c2b9050241571306456cd6ce5.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d8/10c53638136b2c2b9050241571306456cd6ce5.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_array_family_flex_ext.cpython-311-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d8/10c53638136b2c2b9050241571306456cd6ce5.debug debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_array_family_flex_ext.cpython-311-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/84 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_diffraction_fastbragg_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/84/42eeb7450cbef7cc05119b62f0f00852446b6c.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/84/42eeb7450cbef7cc05119b62f0f00852446b6c.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_diffraction_fastbragg_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/84/42eeb7450cbef7cc05119b62f0f00852446b6c.debug debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_diffraction_fastbragg_ext.cpython-311-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b3 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_scaling_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b3/68d142134dcc2ed6fddf53807b03c0c44e58b8.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b3/68d142134dcc2ed6fddf53807b03c0c44e58b8.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_scaling_ext.cpython-311-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b3/68d142134dcc2ed6fddf53807b03c0c44e58b8.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_scaling_ext.cpython-311-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/92 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_bandpass_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/92/6861078edd7f57da127abe27a779bf01b480fc.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/92/6861078edd7f57da127abe27a779bf01b480fc.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_bandpass_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/92/6861078edd7f57da127abe27a779bf01b480fc.debug debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_bandpass_ext.cpython-311-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b3 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_scaling_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b3/68d142134dcc2ed6fddf53807b03c0c44e58b8.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b3/68d142134dcc2ed6fddf53807b03c0c44e58b8.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_scaling_ext.cpython-311-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b3/68d142134dcc2ed6fddf53807b03c0c44e58b8.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_scaling_ext.cpython-311-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/mmtbx_tls_utils_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a0/383641f2e0a0cd933b89183fa570ea88617da1.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a0/383641f2e0a0cd933b89183fa570ea88617da1.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_utils_ext.cpython-311-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a0/383641f2e0a0cd933b89183fa570ea88617da1.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_utils_ext.cpython-311-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ce objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_bpcx_detector_model_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ce/105bb8473663c5d547757f6dd635859f0df557.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ce/105bb8473663c5d547757f6dd635859f0df557.debug @@ -39369,16 +39407,16 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/51/b25b5f8729db89b14b057d4908f03572f65edf.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/regression_test_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/51/b25b5f8729db89b14b057d4908f03572f65edf.debug debian/python3-cctbx/usr/lib/python3/dist-packages/regression_test_ext.cpython-311-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/mmtbx_tls_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/02/208e0fb3e5e3514d2268b88a5e87b452e183fe.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/02/208e0fb3e5e3514d2268b88a5e87b452e183fe.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_ext.cpython-311-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/02/208e0fb3e5e3514d2268b88a5e87b452e183fe.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_ext.cpython-311-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f2 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_validation_ramachandran_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f2/4c8fd0f92f3464e4afbcff6bbce759def2911f.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f2/4c8fd0f92f3464e4afbcff6bbce759def2911f.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_validation_ramachandran_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f2/4c8fd0f92f3464e4afbcff6bbce759def2911f.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_validation_ramachandran_ext.cpython-311-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/mmtbx_tls_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/02/208e0fb3e5e3514d2268b88a5e87b452e183fe.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/02/208e0fb3e5e3514d2268b88a5e87b452e183fe.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_ext.cpython-311-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/02/208e0fb3e5e3514d2268b88a5e87b452e183fe.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_ext.cpython-311-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/70 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/omptbx_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/70/df183a6c7dc116f2e72f88a79e2b70e3bcafe0.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/70/df183a6c7dc116f2e72f88a79e2b70e3bcafe0.debug @@ -39389,41 +39427,41 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8f/9add36df716432c07202cf759a420167a2187b.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_utils_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8f/9add36df716432c07202cf759a420167a2187b.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_utils_ext.cpython-311-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_probe_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/79/0b7c3d5fce37080014c28f39aa3a87cc140fea.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/79/0b7c3d5fce37080014c28f39aa3a87cc140fea.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_probe_ext.cpython-311-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/79/0b7c3d5fce37080014c28f39aa3a87cc140fea.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_probe_ext.cpython-311-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a2 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_optimise_amplitudes_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a2/971e36d5adcbdd4fa741a262037c16a59a6578.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a2/971e36d5adcbdd4fa741a262037c16a59a6578.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_optimise_amplitudes_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a2/971e36d5adcbdd4fa741a262037c16a59a6578.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_optimise_amplitudes_ext.cpython-311-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_probe_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/79/0b7c3d5fce37080014c28f39aa3a87cc140fea.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/79/0b7c3d5fce37080014c28f39aa3a87cc140fea.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_probe_ext.cpython-311-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/79/0b7c3d5fce37080014c28f39aa3a87cc140fea.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_probe_ext.cpython-311-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/mmtbx_tls_decompose_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/31/32ffa0ba0d295464ffc23ca532f09a4d56e2f4.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/31/32ffa0ba0d295464ffc23ca532f09a4d56e2f4.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_decompose_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/31/32ffa0ba0d295464ffc23ca532f09a4d56e2f4.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_decompose_ext.cpython-311-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/6b - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_ramachandran_restraints_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/6b/ab3cc0cb8eaebde407d51158c6ee3008dffd94.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/6b/ab3cc0cb8eaebde407d51158c6ee3008dffd94.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_ramachandran_restraints_ext.cpython-311-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/6b/ab3cc0cb8eaebde407d51158c6ee3008dffd94.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_ramachandran_restraints_ext.cpython-311-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e0 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_secondary_structure_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e0/eea947d3ae45aba28a4ae2c68fdf44d8f752e7.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e0/eea947d3ae45aba28a4ae2c68fdf44d8f752e7.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_secondary_structure_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e0/eea947d3ae45aba28a4ae2c68fdf44d8f752e7.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_secondary_structure_ext.cpython-311-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a9 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_rsr_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a9/8fc227799c65ebf6055bc35da568d48bff4e3a.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a9/8fc227799c65ebf6055bc35da568d48bff4e3a.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_rsr_ext.cpython-311-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a9/8fc227799c65ebf6055bc35da568d48bff4e3a.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_rsr_ext.cpython-311-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/mmtbx_rotamer_fit_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/31/6f2ee334ce4be9ab34b2dac5ecbf9898fd80a0.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/31/6f2ee334ce4be9ab34b2dac5ecbf9898fd80a0.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_rotamer_fit_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/31/6f2ee334ce4be9ab34b2dac5ecbf9898fd80a0.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_rotamer_fit_ext.cpython-311-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/6b + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_ramachandran_restraints_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/6b/ab3cc0cb8eaebde407d51158c6ee3008dffd94.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/6b/ab3cc0cb8eaebde407d51158c6ee3008dffd94.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_ramachandran_restraints_ext.cpython-311-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/6b/ab3cc0cb8eaebde407d51158c6ee3008dffd94.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_ramachandran_restraints_ext.cpython-311-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a9 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_rsr_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a9/8fc227799c65ebf6055bc35da568d48bff4e3a.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a9/8fc227799c65ebf6055bc35da568d48bff4e3a.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_rsr_ext.cpython-311-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a9/8fc227799c65ebf6055bc35da568d48bff4e3a.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_rsr_ext.cpython-311-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a7 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_reference_coordinate_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a7/a1ee3b2050590e6630d14fb4e4fc9f89cc1da1.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a7/a1ee3b2050590e6630d14fb4e4fc9f89cc1da1.debug @@ -39434,16 +39472,21 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/51/bb3b2c0d5ff634cb9115417f3cacf807ca3232.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_pair_interaction_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/51/bb3b2c0d5ff634cb9115417f3cacf807ca3232.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_pair_interaction_ext.cpython-311-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/81 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_max_lik_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/81/d30cfdae541e0c90573d28e02c8486c5b28987.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/81/d30cfdae541e0c90573d28e02c8486c5b28987.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_max_lik_ext.cpython-311-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/81/d30cfdae541e0c90573d28e02c8486c5b28987.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_max_lik_ext.cpython-311-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e0 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_ncs_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e0/105d2cffa4579e5404872f8a51ca2ad2dc7854.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e0/105d2cffa4579e5404872f8a51ca2ad2dc7854.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_ncs_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e0/105d2cffa4579e5404872f8a51ca2ad2dc7854.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_ncs_ext.cpython-311-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/mmtbx_ncs_cartesian_restraints_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/45/0016efb7859dffc74b935476bc4bd8174bf53b.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/45/0016efb7859dffc74b935476bc4bd8174bf53b.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_ncs_cartesian_restraints_ext.cpython-311-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/45/0016efb7859dffc74b935476bc4bd8174bf53b.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_ncs_cartesian_restraints_ext.cpython-311-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/81 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_max_lik_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/81/d30cfdae541e0c90573d28e02c8486c5b28987.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/81/d30cfdae541e0c90573d28e02c8486c5b28987.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_max_lik_ext.cpython-311-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/81/d30cfdae541e0c90573d28e02c8486c5b28987.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_max_lik_ext.cpython-311-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/mmtbx_masks_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ca/552ac0104fc9126e93307d7b1e7bdeac9f6051.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ca/552ac0104fc9126e93307d7b1e7bdeac9f6051.debug @@ -39454,11 +39497,6 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7f/793ed1c03b5c8b126ea4588aec3fa94ffa97dd.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_asa_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7f/793ed1c03b5c8b126ea4588aec3fa94ffa97dd.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_asa_ext.cpython-311-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/mmtbx_ncs_cartesian_restraints_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/45/0016efb7859dffc74b935476bc4bd8174bf53b.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/45/0016efb7859dffc74b935476bc4bd8174bf53b.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_ncs_cartesian_restraints_ext.cpython-311-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/45/0016efb7859dffc74b935476bc4bd8174bf53b.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_ncs_cartesian_restraints_ext.cpython-311-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/mmtbx_mosaic_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d2/ac66d87896237b6c3b7f6deeb7fcaecf444a52.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d2/ac66d87896237b6c3b7f6deeb7fcaecf444a52.debug @@ -39469,31 +39507,16 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/c5/b3c0c2006c353710c831b383fdb79c9c49d5ca.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_hydrogens_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/c5/b3c0c2006c353710c831b383fdb79c9c49d5ca.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_hydrogens_ext.cpython-311-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/mmtbx_geometry_sphere_surface_sampling_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/15/79d60e4f5499192e93bcda23a687c7edefedff.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/15/79d60e4f5499192e93bcda23a687c7edefedff.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-311-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/15/79d60e4f5499192e93bcda23a687c7edefedff.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_sphere_surface_sampling_ext.cpython-311-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/dxtbx_model_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e7/72e96854cc81f37277fd8f6b633fd4cb953293.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e7/72e96854cc81f37277fd8f6b633fd4cb953293.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_model_ext.cpython-311-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e7/72e96854cc81f37277fd8f6b633fd4cb953293.debug debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_model_ext.cpython-311-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/mmtbx_geometry_clash_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/45/158799d3890f6069689b8f78013f384e286433.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/45/158799d3890f6069689b8f78013f384e286433.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_clash_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/45/158799d3890f6069689b8f78013f384e286433.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_clash_ext.cpython-311-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/19 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_pdb_hierarchy_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/19/55f7de8ad1420e0bb44ed4ecd3e319e9151905.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/19/55f7de8ad1420e0bb44ed4ecd3e319e9151905.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_pdb_hierarchy_ext.cpython-311-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/19/55f7de8ad1420e0bb44ed4ecd3e319e9151905.debug debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_pdb_hierarchy_ext.cpython-311-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/da - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_shared_types_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/da/1e23a8554c6b17b0262014c245dc786a8f47b6.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/da/1e23a8554c6b17b0262014c245dc786a8f47b6.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_shared_types_ext.cpython-311-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/da/1e23a8554c6b17b0262014c245dc786a8f47b6.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_shared_types_ext.cpython-311-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/mmtbx_geometry_sphere_surface_sampling_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/15/79d60e4f5499192e93bcda23a687c7edefedff.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/15/79d60e4f5499192e93bcda23a687c7edefedff.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-311-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/15/79d60e4f5499192e93bcda23a687c7edefedff.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_sphere_surface_sampling_ext.cpython-311-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/03 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_indexing_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/03/1b2def01cec89d7af98fdd8f6e5f320da3940e.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/03/1b2def01cec89d7af98fdd8f6e5f320da3940e.debug @@ -39504,96 +39527,111 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e1/6cbcad0a521e1438a72804a8b917ddb9fbf139.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_primitive_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e1/6cbcad0a521e1438a72804a8b917ddb9fbf139.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_primitive_ext.cpython-311-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/dxtbx_model_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e7/72e96854cc81f37277fd8f6b633fd4cb953293.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e7/72e96854cc81f37277fd8f6b633fd4cb953293.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_model_ext.cpython-311-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e7/72e96854cc81f37277fd8f6b633fd4cb953293.debug debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_model_ext.cpython-311-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/da + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_shared_types_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/da/1e23a8554c6b17b0262014c245dc786a8f47b6.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/da/1e23a8554c6b17b0262014c245dc786a8f47b6.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_shared_types_ext.cpython-311-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/da/1e23a8554c6b17b0262014c245dc786a8f47b6.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_shared_types_ext.cpython-311-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/19 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_pdb_hierarchy_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/19/55f7de8ad1420e0bb44ed4ecd3e319e9151905.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/19/55f7de8ad1420e0bb44ed4ecd3e319e9151905.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_pdb_hierarchy_ext.cpython-311-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/19/55f7de8ad1420e0bb44ed4ecd3e319e9151905.debug debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_pdb_hierarchy_ext.cpython-311-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7f objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_f_model_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7f/4f2b8aec0e6a5b888849afbf6545c8ede3634e.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7f/4f2b8aec0e6a5b888849afbf6545c8ede3634e.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_f_model_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7f/4f2b8aec0e6a5b888849afbf6545c8ede3634e.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_f_model_ext.cpython-311-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_dynamics_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/0d/6420f5921c4e1428813eec29082d58175e6d92.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/0d/6420f5921c4e1428813eec29082d58175e6d92.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_dynamics_ext.cpython-311-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/0d/6420f5921c4e1428813eec29082d58175e6d92.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_dynamics_ext.cpython-311-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/mmtbx_den_restraints_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7d/56c4df8eae77abd1fb5b87f63c4df351922edb.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7d/56c4df8eae77abd1fb5b87f63c4df351922edb.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_den_restraints_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7d/56c4df8eae77abd1fb5b87f63c4df351922edb.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_den_restraints_ext.cpython-311-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_dynamics_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/0d/6420f5921c4e1428813eec29082d58175e6d92.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/0d/6420f5921c4e1428813eec29082d58175e6d92.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_dynamics_ext.cpython-311-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/0d/6420f5921c4e1428813eec29082d58175e6d92.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_dynamics_ext.cpython-311-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/mmtbx_bulk_solvent_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/c3/f15919ccdb8424d891bcb30ac1e312eb7d565b.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/c3/f15919ccdb8424d891bcb30ac1e312eb7d565b.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_bulk_solvent_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/c3/f15919ccdb8424d891bcb30ac1e312eb7d565b.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_bulk_solvent_ext.cpython-311-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/22 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_mtz_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/22/f5baf6fa66b2c2353f486c4106f0dc53b28b1b.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/22/f5baf6fa66b2c2353f486c4106f0dc53b28b1b.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_mtz_ext.cpython-311-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/22/f5baf6fa66b2c2353f486c4106f0dc53b28b1b.debug debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_mtz_ext.cpython-311-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/mmtbx_dssp_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/dd/a01c29dd7de815bfe02939b70ebca086b245eb.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/dd/a01c29dd7de815bfe02939b70ebca086b245eb.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_dssp_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/dd/a01c29dd7de815bfe02939b70ebca086b245eb.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_dssp_ext.cpython-311-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/mmtbx_building_loop_closure_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1f/e4a7fc93113b22466ac40d2b643bcf9d7f53e0.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1f/e4a7fc93113b22466ac40d2b643bcf9d7f53e0.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_building_loop_closure_ext.cpython-311-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1f/e4a7fc93113b22466ac40d2b643bcf9d7f53e0.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_building_loop_closure_ext.cpython-311-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/22 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_mtz_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/22/f5baf6fa66b2c2353f486c4106f0dc53b28b1b.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/22/f5baf6fa66b2c2353f486c4106f0dc53b28b1b.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_mtz_ext.cpython-311-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/22/f5baf6fa66b2c2353f486c4106f0dc53b28b1b.debug debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_mtz_ext.cpython-311-aarch64-linux-gnu.so 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/python3/dist-packages/mmtbx_cablam_align_utils_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d5/a293d82edad09970de0dbd93892918a2488dd7.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d5/a293d82edad09970de0dbd93892918a2488dd7.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_cablam_align_utils_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d5/a293d82edad09970de0dbd93892918a2488dd7.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_cablam_align_utils_ext.cpython-311-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/mmtbx_alignment_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/16/9994a6642ac13dee7c8915a7ac890cc8f8f475.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/16/9994a6642ac13dee7c8915a7ac890cc8f8f475.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_alignment_ext.cpython-311-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/16/9994a6642ac13dee7c8915a7ac890cc8f8f475.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_alignment_ext.cpython-311-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/mmtbx_building_loop_closure_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1f/e4a7fc93113b22466ac40d2b643bcf9d7f53e0.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1f/e4a7fc93113b22466ac40d2b643bcf9d7f53e0.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_building_loop_closure_ext.cpython-311-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1f/e4a7fc93113b22466ac40d2b643bcf9d7f53e0.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_building_loop_closure_ext.cpython-311-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/de objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_pdb_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/de/57677a6f1fd6e8e38483e295a486202bac57c9.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/de/57677a6f1fd6e8e38483e295a486202bac57c9.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_pdb_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/de/57677a6f1fd6e8e38483e295a486202bac57c9.debug debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_pdb_ext.cpython-311-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/mmtbx_alignment_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/16/9994a6642ac13dee7c8915a7ac890cc8f8f475.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/16/9994a6642ac13dee7c8915a7ac890cc8f8f475.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_alignment_ext.cpython-311-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/16/9994a6642ac13dee7c8915a7ac890cc8f8f475.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_alignment_ext.cpython-311-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/iotbx_xplor_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d4/4910fa0c3c46b8beded4a25084a171ecc8b647.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d4/4910fa0c3c46b8beded4a25084a171ecc8b647.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_xplor_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d4/4910fa0c3c46b8beded4a25084a171ecc8b647.debug debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_xplor_ext.cpython-311-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/cf - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_shelx_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/cf/dd0f7264379883f306e6ec917fd8593c8f45ee.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/cf/dd0f7264379883f306e6ec917fd8593c8f45ee.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_shelx_ext.cpython-311-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/cf/dd0f7264379883f306e6ec917fd8593c8f45ee.debug debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_shelx_ext.cpython-311-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/eb objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_wildcard_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/eb/d19616d5280aee38efe01dca27121f78a363be.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/eb/d19616d5280aee38efe01dca27121f78a363be.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_wildcard_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/eb/d19616d5280aee38efe01dca27121f78a363be.debug debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_wildcard_ext.cpython-311-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/cf + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_shelx_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/cf/dd0f7264379883f306e6ec917fd8593c8f45ee.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/cf/dd0f7264379883f306e6ec917fd8593c8f45ee.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_shelx_ext.cpython-311-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/cf/dd0f7264379883f306e6ec917fd8593c8f45ee.debug debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_shelx_ext.cpython-311-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/iotbx_scalepack_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a0/7e0e22adfb5b51ca3ea8124fd0658b21e74d06.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a0/7e0e22adfb5b51ca3ea8124fd0658b21e74d06.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_scalepack_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a0/7e0e22adfb5b51ca3ea8124fd0658b21e74d06.debug debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_scalepack_ext.cpython-311-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/2e - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_xray_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/2e/0ea9dea1a16c76315e9287d2f20064cbfdb312.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/2e/0ea9dea1a16c76315e9287d2f20064cbfdb312.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_xray_ext.cpython-311-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/2e/0ea9dea1a16c76315e9287d2f20064cbfdb312.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_xray_ext.cpython-311-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7f - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_detectors_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7f/02664f20f560b4270246ad372a44f4fb1c3830.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7f/02664f20f560b4270246ad372a44f4fb1c3830.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_detectors_ext.cpython-311-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7f/02664f20f560b4270246ad372a44f4fb1c3830.debug debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_detectors_ext.cpython-311-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/fd objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_gl_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/fd/fcb044836d8ce346bf303230d3f3f80cd76715.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/fd/fcb044836d8ce346bf303230d3f3f80cd76715.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_gl_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/fd/fcb044836d8ce346bf303230d3f3f80cd76715.debug debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_gl_ext.cpython-311-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7f + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_detectors_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7f/02664f20f560b4270246ad372a44f4fb1c3830.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7f/02664f20f560b4270246ad372a44f4fb1c3830.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_detectors_ext.cpython-311-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7f/02664f20f560b4270246ad372a44f4fb1c3830.debug debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_detectors_ext.cpython-311-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/4c objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_dtrek_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/4c/f28f78ea03f03e88ecb116cec86754218ea402.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/4c/f28f78ea03f03e88ecb116cec86754218ea402.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_dtrek_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/4c/f28f78ea03f03e88ecb116cec86754218ea402.debug debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_dtrek_ext.cpython-311-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/2e + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_xray_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/2e/0ea9dea1a16c76315e9287d2f20064cbfdb312.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/2e/0ea9dea1a16c76315e9287d2f20064cbfdb312.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_xray_ext.cpython-311-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/2e/0ea9dea1a16c76315e9287d2f20064cbfdb312.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_xray_ext.cpython-311-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d7 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_dsn6_map_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d7/04c24f1b94d5441d0557ecf376ab1d8fd2e030.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d7/04c24f1b94d5441d0557ecf376ab1d8fd2e030.debug @@ -39609,46 +39647,36 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/00/5fdc1d76ae47db17e8da238a489c4c26cb1a0d.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_cif_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/00/5fdc1d76ae47db17e8da238a489c4c26cb1a0d.debug debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_cif_ext.cpython-311-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/iotbx_ccp4_map_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/fb/b6afebae88b17afe6c9aa4b1d976cd2e5cb094.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/fb/b6afebae88b17afe6c9aa4b1d976cd2e5cb094.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_ccp4_map_ext.cpython-311-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/fb/b6afebae88b17afe6c9aa4b1d976cd2e5cb094.debug debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_ccp4_map_ext.cpython-311-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/gltbx_util_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/91/0d6db5848699c3ca831f05c03fdc6acd0e703f.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/91/0d6db5848699c3ca831f05c03fdc6acd0e703f.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_util_ext.cpython-311-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/91/0d6db5848699c3ca831f05c03fdc6acd0e703f.debug debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_util_ext.cpython-311-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/3f objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_viewer_utils_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/3f/5208d97e721eb79d883304ffdf97af45669d10.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/3f/5208d97e721eb79d883304ffdf97af45669d10.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_viewer_utils_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/3f/5208d97e721eb79d883304ffdf97af45669d10.debug debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_viewer_utils_ext.cpython-311-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f3 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_geometry_restraints_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f3/8044bf06ec3777b20327f1125292d754f69b32.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f3/8044bf06ec3777b20327f1125292d754f69b32.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_geometry_restraints_ext.cpython-311-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f3/8044bf06ec3777b20327f1125292d754f69b32.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_geometry_restraints_ext.cpython-311-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/70 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_quadrics_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/70/66aa7c76daaa3bb63ef2b519c56c0b9a0ee118.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/70/66aa7c76daaa3bb63ef2b519c56c0b9a0ee118.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_quadrics_ext.cpython-311-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/70/66aa7c76daaa3bb63ef2b519c56c0b9a0ee118.debug debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_quadrics_ext.cpython-311-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/iotbx_ccp4_map_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/fb/b6afebae88b17afe6c9aa4b1d976cd2e5cb094.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/fb/b6afebae88b17afe6c9aa4b1d976cd2e5cb094.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_ccp4_map_ext.cpython-311-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/fb/b6afebae88b17afe6c9aa4b1d976cd2e5cb094.debug debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_ccp4_map_ext.cpython-311-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/68 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_glu_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/68/f8dc1503482c64429c1622a56876e063648876.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/68/f8dc1503482c64429c1622a56876e063648876.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_glu_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/68/f8dc1503482c64429c1622a56876e063648876.debug debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_glu_ext.cpython-311-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/70 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_quadrics_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/70/66aa7c76daaa3bb63ef2b519c56c0b9a0ee118.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/70/66aa7c76daaa3bb63ef2b519c56c0b9a0ee118.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_quadrics_ext.cpython-311-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/70/66aa7c76daaa3bb63ef2b519c56c0b9a0ee118.debug debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_quadrics_ext.cpython-311-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/gltbx_util_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/91/0d6db5848699c3ca831f05c03fdc6acd0e703f.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/91/0d6db5848699c3ca831f05c03fdc6acd0e703f.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_util_ext.cpython-311-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/91/0d6db5848699c3ca831f05c03fdc6acd0e703f.debug debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_util_ext.cpython-311-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8a objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_fonts_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8a/7ac1404631fd8463502d18f0f298774d673923.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8a/7ac1404631fd8463502d18f0f298774d673923.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_fonts_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8a/7ac1404631fd8463502d18f0f298774d673923.debug debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_fonts_ext.cpython-311-aarch64-linux-gnu.so - 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/python3/dist-packages/cctbx_sgtbx_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/4d/0aabb28e2c246782dc50da7a06f6bf345a32b0.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/4d/0aabb28e2c246782dc50da7a06f6bf345a32b0.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_sgtbx_ext.cpython-311-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/4d/0aabb28e2c246782dc50da7a06f6bf345a32b0.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_sgtbx_ext.cpython-311-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_imageset_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/36/e339109fb9c763805cfe4406745c799c9072da.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/36/e339109fb9c763805cfe4406745c799c9072da.debug @@ -39659,11 +39687,21 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/55/d0e519d2a1acef970427d721b4febff6fcb5cc.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/fable_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/55/d0e519d2a1acef970427d721b4febff6fcb5cc.debug debian/python3-cctbx/usr/lib/python3/dist-packages/fable_ext.cpython-311-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f3 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_geometry_restraints_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f3/8044bf06ec3777b20327f1125292d754f69b32.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f3/8044bf06ec3777b20327f1125292d754f69b32.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_geometry_restraints_ext.cpython-311-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f3/8044bf06ec3777b20327f1125292d754f69b32.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_geometry_restraints_ext.cpython-311-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b1 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_masking_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b1/28dd46167cd53b575f5a0fbcaa1be4d970bd4c.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b1/28dd46167cd53b575f5a0fbcaa1be4d970bd4c.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_masking_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b1/28dd46167cd53b575f5a0fbcaa1be4d970bd4c.debug debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_masking_ext.cpython-311-aarch64-linux-gnu.so + 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/python3/dist-packages/cctbx_sgtbx_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/4d/0aabb28e2c246782dc50da7a06f6bf345a32b0.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/4d/0aabb28e2c246782dc50da7a06f6bf345a32b0.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_sgtbx_ext.cpython-311-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/4d/0aabb28e2c246782dc50da7a06f6bf345a32b0.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_sgtbx_ext.cpython-311-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/dxtbx_format_image_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d2/c59663a76d062e0e5371f8acae537853a65be1.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d2/c59663a76d062e0e5371f8acae537853a65be1.debug @@ -39679,31 +39717,31 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a8/c810bd6e9ab20509914448e8a0773c2a05fec6.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_format_nexus_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a8/c810bd6e9ab20509914448e8a0773c2a05fec6.debug debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_format_nexus_ext.cpython-311-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1d - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_miller_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1d/aff074ec9fa44ce247723d4f6629ef41d0e1aa.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1d/aff074ec9fa44ce247723d4f6629ef41d0e1aa.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_miller_ext.cpython-311-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1d/aff074ec9fa44ce247723d4f6629ef41d0e1aa.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_miller_ext.cpython-311-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/11 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/11/0b07e0de9cf5b95abac0d56289836ca723539a.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/11/0b07e0de9cf5b95abac0d56289836ca723539a.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/11/0b07e0de9cf5b95abac0d56289836ca723539a.debug debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_ext.cpython-311-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1d + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_miller_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1d/aff074ec9fa44ce247723d4f6629ef41d0e1aa.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1d/aff074ec9fa44ce247723d4f6629ef41d0e1aa.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_miller_ext.cpython-311-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1d/aff074ec9fa44ce247723d4f6629ef41d0e1aa.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_miller_ext.cpython-311-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b1 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/determine_unit_cell_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b1/9b449231ea1ac8a74108bf05751f3845a39a20.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b1/9b449231ea1ac8a74108bf05751f3845a39a20.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/determine_unit_cell_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b1/9b449231ea1ac8a74108bf05751f3845a39a20.debug debian/python3-cctbx/usr/lib/python3/dist-packages/determine_unit_cell_ext.cpython-311-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/cma_es_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/3b/7026bdfb5a64e76c0fb7bd6bc6a7e400fd0dbe.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/3b/7026bdfb5a64e76c0fb7bd6bc6a7e400fd0dbe.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cma_es_ext.cpython-311-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/3b/7026bdfb5a64e76c0fb7bd6bc6a7e400fd0dbe.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cma_es_ext.cpython-311-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/cctbx_xray_observations_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/dd/c7acea4f19086884ba115d2eaccee7872c6a02.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/dd/c7acea4f19086884ba115d2eaccee7872c6a02.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_xray_observations_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/dd/c7acea4f19086884ba115d2eaccee7872c6a02.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_xray_observations_ext.cpython-311-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/cma_es_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/3b/7026bdfb5a64e76c0fb7bd6bc6a7e400fd0dbe.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/3b/7026bdfb5a64e76c0fb7bd6bc6a7e400fd0dbe.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cma_es_ext.cpython-311-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/3b/7026bdfb5a64e76c0fb7bd6bc6a7e400fd0dbe.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cma_es_ext.cpython-311-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/2e objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_maptbx_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/2e/ac827c892d7777b7cd17de4b4d57c733a3c3b9.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/2e/ac827c892d7777b7cd17de4b4d57c733a3c3b9.debug @@ -39719,16 +39757,16 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d6/5d67a5f5e87a4744ea8deda50e86b700deba1f.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_translation_search_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d6/5d67a5f5e87a4744ea8deda50e86b700deba1f.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_translation_search_ext.cpython-311-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_crystal_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ba/3fc239b72277c365586b15d1f63d8dbcb22546.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ba/3fc239b72277c365586b15d1f63d8dbcb22546.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_crystal_ext.cpython-311-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ba/3fc239b72277c365586b15d1f63d8dbcb22546.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_crystal_ext.cpython-311-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/49 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_symmetry_search_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/49/0c8be11275724132711969ccf853add2ac01f8.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/49/0c8be11275724132711969ccf853add2ac01f8.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_symmetry_search_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/49/0c8be11275724132711969ccf853add2ac01f8.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_symmetry_search_ext.cpython-311-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_crystal_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ba/3fc239b72277c365586b15d1f63d8dbcb22546.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ba/3fc239b72277c365586b15d1f63d8dbcb22546.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_crystal_ext.cpython-311-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ba/3fc239b72277c365586b15d1f63d8dbcb22546.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_crystal_ext.cpython-311-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7f objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_statistics_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7f/125460407d888f6bba8b6bdf5fc9c727c7d915.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7f/125460407d888f6bba8b6bdf5fc9c727c7d915.debug @@ -39739,11 +39777,6 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/71/b3d8f454efae7864722596dd23afef27d62cc8.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_sgtbx_asu_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/71/b3d8f454efae7864722596dd23afef27d62cc8.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_sgtbx_asu_ext.cpython-311-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/6a - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_adp_restraints_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/6a/872e65b42f30cbd346d3768dc301b2d6c2b4ad.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/6a/872e65b42f30cbd346d3768dc301b2d6c2b4ad.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_adp_restraints_ext.cpython-311-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/6a/872e65b42f30cbd346d3768dc301b2d6c2b4ad.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_adp_restraints_ext.cpython-311-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/75 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_orientation_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/75/f78c3313af0d86a15026d233689afa3194f47f.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/75/f78c3313af0d86a15026d233689afa3194f47f.debug @@ -39764,51 +39797,56 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1d/2878a0099c43754668979e7a96e947d1c5489d.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_merging_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1d/2878a0099c43754668979e7a96e947d1c5489d.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_merging_ext.cpython-311-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/cctbx_math_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/4e/c0b02a531507e5bb861d81ae36c677f67b3890.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/4e/c0b02a531507e5bb861d81ae36c677f67b3890.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_math_ext.cpython-311-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/4e/c0b02a531507e5bb861d81ae36c677f67b3890.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_math_ext.cpython-311-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/10 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_maptbx_bcr_bcr_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/10/59ce49708ac7f2967e3abceaecd0088e12c5de.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/10/59ce49708ac7f2967e3abceaecd0088e12c5de.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_maptbx_bcr_bcr_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/10/59ce49708ac7f2967e3abceaecd0088e12c5de.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_maptbx_bcr_bcr_ext.cpython-311-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/62 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_array_family_flex_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/62/5586e63501c1fd214d60031728adca3e65f948.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/62/5586e63501c1fd214d60031728adca3e65f948.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_array_family_flex_ext.cpython-311-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/62/5586e63501c1fd214d60031728adca3e65f948.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_array_family_flex_ext.cpython-311-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/cctbx_math_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/4e/c0b02a531507e5bb861d81ae36c677f67b3890.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/4e/c0b02a531507e5bb861d81ae36c677f67b3890.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_math_ext.cpython-311-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/4e/c0b02a531507e5bb861d81ae36c677f67b3890.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_math_ext.cpython-311-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/6a + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_adp_restraints_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/6a/872e65b42f30cbd346d3768dc301b2d6c2b4ad.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/6a/872e65b42f30cbd346d3768dc301b2d6c2b4ad.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_adp_restraints_ext.cpython-311-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/6a/872e65b42f30cbd346d3768dc301b2d6c2b4ad.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_adp_restraints_ext.cpython-311-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/cctbx_geometry_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/35/7a38eaa3909f8fd9e8c53c2a0e5de8db4bde7f.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/35/7a38eaa3909f8fd9e8c53c2a0e5de8db4bde7f.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_geometry_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/35/7a38eaa3909f8fd9e8c53c2a0e5de8db4bde7f.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_geometry_ext.cpython-311-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ae - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_xray_scattering_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ae/22a0d62ca27e7bf9c57d754dd2bc4cc7d8d3d1.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ae/22a0d62ca27e7bf9c57d754dd2bc4cc7d8d3d1.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_xray_scattering_ext.cpython-311-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ae/22a0d62ca27e7bf9c57d754dd2bc4cc7d8d3d1.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_xray_scattering_ext.cpython-311-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/14 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_emma_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/14/e54874ae5a2cfce19639abf9e9bd784d61e174.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/14/e54874ae5a2cfce19639abf9e9bd784d61e174.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_emma_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/14/e54874ae5a2cfce19639abf9e9bd784d61e174.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_emma_ext.cpython-311-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ae + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_xray_scattering_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ae/22a0d62ca27e7bf9c57d754dd2bc4cc7d8d3d1.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ae/22a0d62ca27e7bf9c57d754dd2bc4cc7d8d3d1.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_xray_scattering_ext.cpython-311-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ae/22a0d62ca27e7bf9c57d754dd2bc4cc7d8d3d1.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_xray_scattering_ext.cpython-311-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_french_wilson_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/af/4adcbf44ae934f109ea458ae6f21503492a5dd.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/af/4adcbf44ae934f109ea458ae6f21503492a5dd.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_french_wilson_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/af/4adcbf44ae934f109ea458ae6f21503492a5dd.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_french_wilson_ext.cpython-311-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ad - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_wavelengths_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ad/715abdd087e7671da3421a78461325e5d55c2e.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ad/715abdd087e7671da3421a78461325e5d55c2e.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_wavelengths_ext.cpython-311-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ad/715abdd087e7671da3421a78461325e5d55c2e.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_wavelengths_ext.cpython-311-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/62 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_array_family_flex_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/62/5586e63501c1fd214d60031728adca3e65f948.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/62/5586e63501c1fd214d60031728adca3e65f948.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_array_family_flex_ext.cpython-311-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/62/5586e63501c1fd214d60031728adca3e65f948.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_array_family_flex_ext.cpython-311-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/dc objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_tiny_pse_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/dc/cb13bc387e134defdd92bfec5a255353cb2821.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/dc/cb13bc387e134defdd92bfec5a255353cb2821.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_tiny_pse_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/dc/cb13bc387e134defdd92bfec5a255353cb2821.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_tiny_pse_ext.cpython-311-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ad + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_wavelengths_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ad/715abdd087e7671da3421a78461325e5d55c2e.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ad/715abdd087e7671da3421a78461325e5d55c2e.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_wavelengths_ext.cpython-311-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ad/715abdd087e7671da3421a78461325e5d55c2e.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_wavelengths_ext.cpython-311-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1a objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_sasaki_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1a/60782e2a1edbafba6be61aa4a35809674b6144.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1a/60782e2a1edbafba6be61aa4a35809674b6144.debug @@ -39829,11 +39867,6 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/38/4ca2db1f2ec25c81dca44ee66fe248f7132097.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_henke_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/38/4ca2db1f2ec25c81dca44ee66fe248f7132097.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_henke_ext.cpython-311-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/61 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_dmtbx_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/61/6ae3b2a1f2dcc70f1d38ab8a8ed58ae2fa77d9.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/61/6ae3b2a1f2dcc70f1d38ab8a8ed58ae2fa77d9.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_dmtbx_ext.cpython-311-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/61/6ae3b2a1f2dcc70f1d38ab8a8ed58ae2fa77d9.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_dmtbx_ext.cpython-311-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/39 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_covalent_radii_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/39/5d2b238e426218171f4d845a0870ca307e7781.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/39/5d2b238e426218171f4d845a0870ca307e7781.debug @@ -39854,6 +39887,11 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/23/d0ac6abc1431226cd36b0f84f7c0f456477c38.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_attenuation_coefficient_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/23/d0ac6abc1431226cd36b0f84f7c0f456477c38.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_attenuation_coefficient_ext.cpython-311-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/61 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_dmtbx_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/61/6ae3b2a1f2dcc70f1d38ab8a8ed58ae2fa77d9.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/61/6ae3b2a1f2dcc70f1d38ab8a8ed58ae2fa77d9.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_dmtbx_ext.cpython-311-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/61/6ae3b2a1f2dcc70f1d38ab8a8ed58ae2fa77d9.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_dmtbx_ext.cpython-311-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/cctbx_adptbx_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/13/4435375c27ac34beb107c4a81e204104e117b9.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/13/4435375c27ac34beb107c4a81e204104e117b9.debug @@ -39864,76 +39902,76 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1d/d36d49faa4276d40496bd26520b1c26666f231.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_covariance_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1d/d36d49faa4276d40496bd26520b1c26666f231.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_covariance_ext.cpython-311-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e3 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_anharmonic_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e3/43f8d0287d8c276b5dfbbe675562c99a7c9ed4.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e3/43f8d0287d8c276b5dfbbe675562c99a7c9ed4.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_anharmonic_ext.cpython-311-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e3/43f8d0287d8c276b5dfbbe675562c99a7c9ed4.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_anharmonic_ext.cpython-311-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/33 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_asymmetric_map_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/33/d829506e7baa061f26c4f005e7c166b16f25cd.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/33/d829506e7baa061f26c4f005e7c166b16f25cd.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_asymmetric_map_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/33/d829506e7baa061f26c4f005e7c166b16f25cd.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_asymmetric_map_ext.cpython-311-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ab - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ab/880feb25e445fdfced2881ce4dcafaa5e4a1ca.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ab/880feb25e445fdfced2881ce4dcafaa5e4a1ca.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_ext.cpython-311-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ab/880feb25e445fdfced2881ce4dcafaa5e4a1ca.debug debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_ext.cpython-311-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/ccp4io_adaptbx_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1f/2789dbbd7486ec6a0834619a8e12c05b9d39c1.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1f/2789dbbd7486ec6a0834619a8e12c05b9d39c1.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/ccp4io_adaptbx_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1f/2789dbbd7486ec6a0834619a8e12c05b9d39c1.debug debian/python3-cctbx/usr/lib/python3/dist-packages/ccp4io_adaptbx_ext.cpython-311-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e3 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_anharmonic_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e3/43f8d0287d8c276b5dfbbe675562c99a7c9ed4.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e3/43f8d0287d8c276b5dfbbe675562c99a7c9ed4.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_anharmonic_ext.cpython-311-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e3/43f8d0287d8c276b5dfbbe675562c99a7c9ed4.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_anharmonic_ext.cpython-311-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ab + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ab/880feb25e445fdfced2881ce4dcafaa5e4a1ca.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ab/880feb25e445fdfced2881ce4dcafaa5e4a1ca.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_ext.cpython-311-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ab/880feb25e445fdfced2881ce4dcafaa5e4a1ca.debug debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_ext.cpython-311-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f1 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cbflib_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f1/d39a4eeef2bb83b58d0253bf72f558886cca9c.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f1/d39a4eeef2bb83b58d0253bf72f558886cca9c.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cbflib_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f1/d39a4eeef2bb83b58d0253bf72f558886cca9c.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cbflib_ext.cpython-311-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_python_meta_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/27/66b434015e284f909cbc33eff94e39e5fbc47f.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/27/66b434015e284f909cbc33eff94e39e5fbc47f.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/boost_python_meta_ext.cpython-311-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/27/66b434015e284f909cbc33eff94e39e5fbc47f.debug debian/python3-cctbx/usr/lib/python3/dist-packages/boost_python_meta_ext.cpython-311-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f6 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/boost_rational_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f6/0ef8a29f9cb2d495137e24b2b5827e18685fc9.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f6/0ef8a29f9cb2d495137e24b2b5827e18685fc9.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/boost_rational_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f6/0ef8a29f9cb2d495137e24b2b5827e18685fc9.debug debian/python3-cctbx/usr/lib/python3/dist-packages/boost_rational_ext.cpython-311-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/dc - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_maximum_clique_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/dc/5f20f81e3e17385327b178aba77e5271607e5b.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/dc/5f20f81e3e17385327b178aba77e5271607e5b.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_maximum_clique_ext.cpython-311-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/dc/5f20f81e3e17385327b178aba77e5271607e5b.debug debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_maximum_clique_ext.cpython-311-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a2 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_min_cut_max_flow_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a2/0180622630d0505f83758848a81041ea0baed0.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a2/0180622630d0505f83758848a81041ea0baed0.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_min_cut_max_flow_ext.cpython-311-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a2/0180622630d0505f83758848a81041ea0baed0.debug debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_min_cut_max_flow_ext.cpython-311-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_python_meta_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/27/66b434015e284f909cbc33eff94e39e5fbc47f.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/27/66b434015e284f909cbc33eff94e39e5fbc47f.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/boost_python_meta_ext.cpython-311-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/27/66b434015e284f909cbc33eff94e39e5fbc47f.debug debian/python3-cctbx/usr/lib/python3/dist-packages/boost_python_meta_ext.cpython-311-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/84 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/boost_tuple_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/84/464b5872f35e7ac75fe4a3c489dcbe01312bfd.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/84/464b5872f35e7ac75fe4a3c489dcbe01312bfd.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/boost_tuple_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/84/464b5872f35e7ac75fe4a3c489dcbe01312bfd.debug debian/python3-cctbx/usr/lib/python3/dist-packages/boost_tuple_ext.cpython-311-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/dc + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_maximum_clique_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/dc/5f20f81e3e17385327b178aba77e5271607e5b.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/dc/5f20f81e3e17385327b178aba77e5271607e5b.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_maximum_clique_ext.cpython-311-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/dc/5f20f81e3e17385327b178aba77e5271607e5b.debug debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_maximum_clique_ext.cpython-311-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d9 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/boost_python_hybrid_times_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d9/1966c374550bb0acf0459b0b55c97b64593861.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d9/1966c374550bb0acf0459b0b55c97b64593861.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/boost_python_hybrid_times_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d9/1966c374550bb0acf0459b0b55c97b64593861.debug debian/python3-cctbx/usr/lib/python3/dist-packages/boost_python_hybrid_times_ext.cpython-311-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a2 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_min_cut_max_flow_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a2/0180622630d0505f83758848a81041ea0baed0.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a2/0180622630d0505f83758848a81041ea0baed0.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_min_cut_max_flow_ext.cpython-311-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a2/0180622630d0505f83758848a81041ea0baed0.debug debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_min_cut_max_flow_ext.cpython-311-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/19 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_utility_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/19/9a3a299ddc12e5d121d98d5b594a2dd60cd31b.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/19/9a3a299ddc12e5d121d98d5b594a2dd60cd31b.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_utility_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/19/9a3a299ddc12e5d121d98d5b594a2dd60cd31b.debug debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_utility_ext.cpython-311-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/bf - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_metric_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/bf/dcb08549c6ba2e52c2401a7d811847e3414a7c.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/bf/dcb08549c6ba2e52c2401a7d811847e3414a7c.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_metric_ext.cpython-311-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/bf/dcb08549c6ba2e52c2401a7d811847e3414a7c.debug debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_metric_ext.cpython-311-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/boost_optional_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/31/72f39455f4f168af4c064945d245514793bc2f.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/31/72f39455f4f168af4c064945d245514793bc2f.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/boost_optional_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/31/72f39455f4f168af4c064945d245514793bc2f.debug debian/python3-cctbx/usr/lib/python3/dist-packages/boost_optional_ext.cpython-311-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/bf + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_metric_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/bf/dcb08549c6ba2e52c2401a7d811847e3414a7c.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/bf/dcb08549c6ba2e52c2401a7d811847e3414a7c.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_metric_ext.cpython-311-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/bf/dcb08549c6ba2e52c2401a7d811847e3414a7c.debug debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_metric_ext.cpython-311-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/boost_adaptbx_python_streambuf_test_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8f/883269f63a4ace504a132b52238b5dcaf2e617.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8f/883269f63a4ace504a132b52238b5dcaf2e617.debug @@ -39944,16 +39982,16 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d7/703da55526f7ce1bf5f2e4391df426f8425c8a.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-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d7/703da55526f7ce1bf5f2e4391df426f8425c8a.debug debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_clustering_algorithm_ext.cpython-311-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ad - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_graph_structure_comparison_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ad/6a4e3cc8c7f156b8e68f43e4ed0cb871868ac8.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ad/6a4e3cc8c7f156b8e68f43e4ed0cb871868ac8.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-311-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ad/6a4e3cc8c7f156b8e68f43e4ed0cb871868ac8.debug debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_graph_structure_comparison_ext.cpython-311-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/boost_adaptbx_graph_connected_component_algorithm_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/fe/98bfc3702d46937fb0306b8f53a49525322852.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/fe/98bfc3702d46937fb0306b8f53a49525322852.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-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/fe/98bfc3702d46937fb0306b8f53a49525322852.debug debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_connected_component_algorithm_ext.cpython-311-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ad + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_graph_structure_comparison_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ad/6a4e3cc8c7f156b8e68f43e4ed0cb871868ac8.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ad/6a4e3cc8c7f156b8e68f43e4ed0cb871868ac8.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-311-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ad/6a4e3cc8c7f156b8e68f43e4ed0cb871868ac8.debug debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_graph_structure_comparison_ext.cpython-311-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e4 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_breadth_first_search_ext.cpython-311-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e4/d0b5d5271c5ca90d6c555b499c8f4baf96cf61.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e4/d0b5d5271c5ca90d6c555b499c8f4baf96cf61.debug @@ -39969,16 +40007,16 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a0/4e2e8daa843f590ac40b3cb52940ea8a375958.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/annlib_ext.cpython-311-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a0/4e2e8daa843f590ac40b3cb52940ea8a375958.debug debian/python3-cctbx/usr/lib/python3/dist-packages/annlib_ext.cpython-311-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/python3.11/smtbx/refinement/constraints/tests/tst_reparametrisation debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7b/f344a8f71be3cb66b0d82f3577500b428a7987.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7b/f344a8f71be3cb66b0d82f3577500b428a7987.debug - strip --remove-section=.comment --remove-section=.note debian/python3-cctbx/usr/lib/cctbx/python3.11/smtbx/refinement/constraints/tests/tst_reparametrisation - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7b/f344a8f71be3cb66b0d82f3577500b428a7987.debug debian/python3-cctbx/usr/lib/cctbx/python3.11/smtbx/refinement/constraints/tests/tst_reparametrisation 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/cctbx/python3.11/smtbx/refinement/constraints/tests/tst_special_position debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b7/4fb0bc79b3445f0d0a7c3766299b739ca46829.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b7/4fb0bc79b3445f0d0a7c3766299b739ca46829.debug strip --remove-section=.comment --remove-section=.note debian/python3-cctbx/usr/lib/cctbx/python3.11/smtbx/refinement/constraints/tests/tst_special_position objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b7/4fb0bc79b3445f0d0a7c3766299b739ca46829.debug debian/python3-cctbx/usr/lib/cctbx/python3.11/smtbx/refinement/constraints/tests/tst_special_position + 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/python3.11/smtbx/refinement/constraints/tests/tst_reparametrisation debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7b/f344a8f71be3cb66b0d82f3577500b428a7987.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7b/f344a8f71be3cb66b0d82f3577500b428a7987.debug + strip --remove-section=.comment --remove-section=.note debian/python3-cctbx/usr/lib/cctbx/python3.11/smtbx/refinement/constraints/tests/tst_reparametrisation + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7b/f344a8f71be3cb66b0d82f3577500b428a7987.debug debian/python3-cctbx/usr/lib/cctbx/python3.11/smtbx/refinement/constraints/tests/tst_reparametrisation install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f7 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/cctbx/python3.11/smtbx/refinement/constraints/tests/tst_geometrical_hydrogens debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f7/8153aa8573301726756aed1b5371c38de6a581.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f7/8153aa8573301726756aed1b5371c38de6a581.debug @@ -39989,16 +40027,16 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/55/edeecbb9772f512bda2ab855c18b041854f7b6.debug strip --remove-section=.comment --remove-section=.note debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/serialization/tst_base_256 objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/55/edeecbb9772f512bda2ab855c18b041854f7b6.debug debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/serialization/tst_base_256 - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/14 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/matrix/tests/tst_svd debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/14/12469ec54021b03769461f66f28a0d74209e62.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/14/12469ec54021b03769461f66f28a0d74209e62.debug - strip --remove-section=.comment --remove-section=.note debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/matrix/tests/tst_svd - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/14/12469ec54021b03769461f66f28a0d74209e62.debug debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/matrix/tests/tst_svd 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/cctbx/python3.11/scitbx/matrix/tests/tst_householder debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/af/b03223d17d20642fa465d3d197d060376fa8c6.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/af/b03223d17d20642fa465d3d197d060376fa8c6.debug strip --remove-section=.comment --remove-section=.note debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/matrix/tests/tst_householder objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/af/b03223d17d20642fa465d3d197d060376fa8c6.debug debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/matrix/tests/tst_householder + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/14 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/matrix/tests/tst_svd debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/14/12469ec54021b03769461f66f28a0d74209e62.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/14/12469ec54021b03769461f66f28a0d74209e62.debug + strip --remove-section=.comment --remove-section=.note debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/matrix/tests/tst_svd + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/14/12469ec54021b03769461f66f28a0d74209e62.debug debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/matrix/tests/tst_svd 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/cctbx/python3.11/scitbx/matrix/tests/tst_cholesky debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/6f/ebec57363b1781d4107922f7ef5dc712534055.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/6f/ebec57363b1781d4107922f7ef5dc712534055.debug @@ -40029,16 +40067,21 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/10/bcf7ecfe48cbe5467ded3c11d608e2dc5dfa9e.debug strip --remove-section=.comment --remove-section=.note debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_af_4 objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/10/bcf7ecfe48cbe5467ded3c11d608e2dc5dfa9e.debug debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_af_4 + 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/cctbx/python3.11/scitbx/array_family/tst_vec3 debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/dd/3414e962f38bdad2acb502258fc7cd6eab38fc.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/dd/3414e962f38bdad2acb502258fc7cd6eab38fc.debug + strip --remove-section=.comment --remove-section=.note debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_vec3 + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/dd/3414e962f38bdad2acb502258fc7cd6eab38fc.debug debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_vec3 install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/68 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_sym_mat3 debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/68/0eee13f5cd21423f0986991fe6f924f4b8fa65.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/68/0eee13f5cd21423f0986991fe6f924f4b8fa65.debug strip --remove-section=.comment --remove-section=.note debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_sym_mat3 objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/68/0eee13f5cd21423f0986991fe6f924f4b8fa65.debug debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_sym_mat3 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/cctbx/python3.11/scitbx/array_family/tst_vec3 debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/dd/3414e962f38bdad2acb502258fc7cd6eab38fc.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/dd/3414e962f38bdad2acb502258fc7cd6eab38fc.debug - strip --remove-section=.comment --remove-section=.note debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_vec3 - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/dd/3414e962f38bdad2acb502258fc7cd6eab38fc.debug debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_vec3 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_rectangular_full_packed debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/dd/57172d5a90d725971ebe883647e8e094251b88.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/dd/57172d5a90d725971ebe883647e8e094251b88.debug + strip --remove-section=.comment --remove-section=.note debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_rectangular_full_packed + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/dd/57172d5a90d725971ebe883647e8e094251b88.debug debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_rectangular_full_packed 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/cctbx/python3.11/scitbx/array_family/tst_unsigned_float_arithmetic debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/3d/b254c537a8d442d453cbf09a3fca82fe82aeed.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/3d/b254c537a8d442d453cbf09a3fca82fe82aeed.debug @@ -40054,26 +40097,21 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/5e/5dd0a0bf1097957f3fcab3183a539f0fcca25e.debug strip --remove-section=.comment --remove-section=.note debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_optional_copy objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/5e/5dd0a0bf1097957f3fcab3183a539f0fcca25e.debug debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_optional_copy - 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/cctbx/python3.11/scitbx/array_family/tst_rectangular_full_packed debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/dd/57172d5a90d725971ebe883647e8e094251b88.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/dd/57172d5a90d725971ebe883647e8e094251b88.debug - strip --remove-section=.comment --remove-section=.note debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_rectangular_full_packed - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/dd/57172d5a90d725971ebe883647e8e094251b88.debug debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_rectangular_full_packed 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/cctbx/python3.11/scitbx/array_family/tst_af_5 debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/76/de060f7f738c869656014fac03af5f47f762f0.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/76/de060f7f738c869656014fac03af5f47f762f0.debug strip --remove-section=.comment --remove-section=.note debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_af_5 objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/76/de060f7f738c869656014fac03af5f47f762f0.debug debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_af_5 - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/80 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_mat3 debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/80/fa003fdcbfa974725e9e4736fe7f4086043dca.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/80/fa003fdcbfa974725e9e4736fe7f4086043dca.debug - strip --remove-section=.comment --remove-section=.note debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_mat3 - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/80/fa003fdcbfa974725e9e4736fe7f4086043dca.debug debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_mat3 install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e0 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_af_3 debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e0/cebac74103f54e7e37d0872cdf623914ec91d4.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e0/cebac74103f54e7e37d0872cdf623914ec91d4.debug strip --remove-section=.comment --remove-section=.note debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_af_3 objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e0/cebac74103f54e7e37d0872cdf623914ec91d4.debug debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_af_3 + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/80 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_mat3 debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/80/fa003fdcbfa974725e9e4736fe7f4086043dca.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/80/fa003fdcbfa974725e9e4736fe7f4086043dca.debug + strip --remove-section=.comment --remove-section=.note debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_mat3 + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/80/fa003fdcbfa974725e9e4736fe7f4086043dca.debug debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_mat3 install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ff objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_af_1 debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ff/c9b2ad2b6ba926bc30ab1fec7f23df58784d49.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ff/c9b2ad2b6ba926bc30ab1fec7f23df58784d49.debug @@ -40099,16 +40137,16 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8d/c2162d1669e4870573895d93a0cd1d3b306bcc.debug strip --remove-section=.comment --remove-section=.note debian/python3-cctbx/usr/lib/cctbx/python3.11/boost_adaptbx/tests/tst_optional_copy objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8d/c2162d1669e4870573895d93a0cd1d3b306bcc.debug debian/python3-cctbx/usr/lib/cctbx/python3.11/boost_adaptbx/tests/tst_optional_copy - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/49 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/bin/cctbx.find_distances debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/49/46c906edebf413fcc8b0b5aee45cdb1762e3ec.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/49/46c906edebf413fcc8b0b5aee45cdb1762e3ec.debug - strip --remove-section=.comment --remove-section=.note debian/python3-cctbx/usr/bin/cctbx.find_distances - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/49/46c906edebf413fcc8b0b5aee45cdb1762e3ec.debug debian/python3-cctbx/usr/bin/cctbx.find_distances 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/bin/cctbx_blobs debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1e/448a313f18fda986d3a42e85e779e9f0ba2e68.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1e/448a313f18fda986d3a42e85e779e9f0ba2e68.debug strip --remove-section=.comment --remove-section=.note debian/python3-cctbx/usr/bin/cctbx_blobs objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1e/448a313f18fda986d3a42e85e779e9f0ba2e68.debug debian/python3-cctbx/usr/bin/cctbx_blobs + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/49 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/bin/cctbx.find_distances debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/49/46c906edebf413fcc8b0b5aee45cdb1762e3ec.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/49/46c906edebf413fcc8b0b5aee45cdb1762e3ec.debug + strip --remove-section=.comment --remove-section=.note debian/python3-cctbx/usr/bin/cctbx.find_distances + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/49/46c906edebf413fcc8b0b5aee45cdb1762e3ec.debug debian/python3-cctbx/usr/bin/cctbx.find_distances install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8a objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/bin/cctbx.lattice_symmetry debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8a/e20476edd53f411d8a04558da8dced3dbdeb0c.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8a/e20476edd53f411d8a04558da8dced3dbdeb0c.debug @@ -40345,354 +40383,354 @@ mv debian/.debhelper/generated/python3-cctbx/triggers.new debian/.debhelper/generated/python3-cctbx/triggers dh_shlibdeps -a -O--buildsystem=pybuild install -m0755 -d debian/libcctbx0/DEBIAN - dpkg-shlibdeps -Tdebian/libcctbx0.substvars debian/libcctbx0/usr/lib/aarch64-linux-gnu/libiotbx_pdb.so.0.0.1 debian/libcctbx0/usr/lib/aarch64-linux-gnu/libsmtbx_refinement_constraints.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/librstbx.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/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/libmmtbx_tls.so.0.0.1 debian/libcctbx0/usr/lib/aarch64-linux-gnu/libomptbx.so.0.0.1 debian/libcctbx0/usr/lib/aarch64-linux-gnu/libasymmetric_map.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: 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 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 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 -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/libmmtbx_masks.so.0.0.1 debian/libcctbx0/usr/lib/aarch64-linux-gnu/librstbx.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/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/libasymmetric_map.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 + 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-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_refinement_constraints_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_math_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_distltbx_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/std_pair_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_hough_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_array_family_flex_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_dxtbx_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_structure_factors_direct_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_refinement_least_squares_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_refinement_restraints_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_stl_map_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_suffixtree_single_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_array_family_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_sparse_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_wigner_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_ab_initio_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_stl_vector_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_stl_map_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_suffixtree_shared_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_rigid_body_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_stl_set_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_random_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_linalg_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_r3_utils_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_lstbx_normal_equations_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_minpack_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_lbfgs_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_lbfgsb_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_array_family_shared_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_fftpack_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_glmtbx_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_iso_surface_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_graphics_utils_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_cubicle_neighbors_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_symmetry_constraints_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_integration_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_simage_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_indexing_api_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_simulation_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_array_family_flex_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_diffraction_fastbragg_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_bandpass_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_scaling_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_utils_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_bpcx_detector_model_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/regression_test_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_validation_ramachandran_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/omptbx_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_utils_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_optimise_amplitudes_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_probe_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_decompose_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_secondary_structure_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_rotamer_fit_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_ramachandran_restraints_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_rsr_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_reference_coordinate_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_pair_interaction_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_ncs_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_ncs_cartesian_restraints_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_max_lik_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_masks_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_asa_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_mosaic_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_hydrogens_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_clash_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_sphere_surface_sampling_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_indexing_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_primitive_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_model_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_shared_types_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_pdb_hierarchy_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_f_model_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_den_restraints_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_dynamics_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_bulk_solvent_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_dssp_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_mtz_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_cablam_align_utils_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_building_loop_closure_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_pdb_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_alignment_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_xplor_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_wildcard_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_shelx_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_scalepack_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_gl_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_detectors_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_dtrek_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_xray_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_dsn6_map_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_detectors_bruker_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_cif_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_viewer_utils_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_ccp4_map_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_glu_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_quadrics_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_util_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_fonts_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_imageset_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/fable_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_geometry_restraints_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_masking_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_sgtbx_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_format_image_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_flumpy.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_format_nexus_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_miller_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/determine_unit_cell_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_xray_observations_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cma_es_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_maptbx_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_uctbx_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_translation_search_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_symmetry_search_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_crystal_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_statistics_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_sgtbx_asu_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_orientation_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_multipolar_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_masks_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_merging_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_maptbx_bcr_bcr_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_math_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_adp_restraints_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_geometry_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_emma_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_xray_scattering_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_french_wilson_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_array_family_flex_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_tiny_pse_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_wavelengths_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_sasaki_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_neutron_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_icsd_radii_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_henke_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_covalent_radii_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_fp_fdp_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_chemical_elements_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_attenuation_coefficient_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_dmtbx_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_adptbx_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_covariance_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_anharmonic_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_asymmetric_map_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/ccp4io_adaptbx_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cbflib_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_rational_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_python_meta_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_tuple_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_maximum_clique_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_python_hybrid_times_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_min_cut_max_flow_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_utility_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_optional_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_metric_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_python_streambuf_test_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_clustering_algorithm_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_connected_component_algorithm_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_graph_structure_comparison_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_breadth_first_search_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_boost_thread_test_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/annlib_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/cctbx/python3.11/smtbx/refinement/constraints/tests/tst_special_position debian/python3-cctbx/usr/lib/cctbx/python3.11/smtbx/refinement/constraints/tests/tst_reparametrisation debian/python3-cctbx/usr/lib/cctbx/python3.11/smtbx/refinement/constraints/tests/tst_geometrical_hydrogens debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/serialization/tst_base_256 debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/matrix/tests/tst_householder debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/matrix/tests/tst_svd debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/matrix/tests/tst_cholesky debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/matrix/tests/tst_givens debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/math/tests/tst debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/lbfgs/tst_lbfgs debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/error/tst_error debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_af_4 debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_vec3 debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_sym_mat3 debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_rectangular_full_packed debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_unsigned_float_arithmetic debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_ref_matrix_facet debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_optional_copy debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_af_5 debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_af_3 debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_mat3 debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_af_1 debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_af_2 debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_accessors debian/python3-cctbx/usr/lib/cctbx/python3.11/iotbx/pdb/hybrid_36_fem debian/python3-cctbx/usr/lib/cctbx/python3.11/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.lattice_symmetry debian/python3-cctbx/usr/bin/cctbx.sym_equiv_sites debian/python3-cctbx/usr/bin/cctbx.getting_started debian/python3-cctbx/usr/bin/cctbx.sys_abs_equiv_space_groups debian/python3-cctbx/usr/bin/cctbx.convert_ccp4_symop_lib debian/python3-cctbx/usr/bin/cbflib.tst_memory +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_ext.cpython-311-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/cbflib_ext.cpython-311-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: 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 _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 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 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_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 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 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 PyObject_IsTrue used by debian/libcctbx0/usr/lib/aarch64-linux-gnu/libscitbx_boost_python.so.0.0.1 found in none of the libraries - 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-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_refinement_constraints_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_math_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_array_family_flex_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/std_pair_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_distltbx_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_hough_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_dxtbx_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_structure_factors_direct_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_refinement_least_squares_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_refinement_restraints_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_stl_map_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_sparse_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_suffixtree_single_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_array_family_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_wigner_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_ab_initio_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_stl_map_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_stl_vector_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_suffixtree_shared_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_stl_set_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_rigid_body_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_random_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_linalg_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_r3_utils_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_minpack_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_lstbx_normal_equations_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_lbfgs_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_array_family_shared_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_lbfgsb_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_fftpack_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_iso_surface_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_graphics_utils_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_glmtbx_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_cubicle_neighbors_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_symmetry_constraints_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_simulation_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_integration_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_array_family_flex_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_simage_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_indexing_api_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_utils_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_diffraction_fastbragg_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_scaling_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_bandpass_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_bpcx_detector_model_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/regression_test_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_validation_ramachandran_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/omptbx_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_utils_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_probe_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_optimise_amplitudes_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_decompose_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_ramachandran_restraints_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_secondary_structure_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_rsr_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_rotamer_fit_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_reference_coordinate_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_pair_interaction_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_max_lik_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_ncs_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_masks_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_asa_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_ncs_cartesian_restraints_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_mosaic_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_hydrogens_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_sphere_surface_sampling_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_model_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_clash_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_pdb_hierarchy_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_shared_types_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_indexing_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_primitive_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_f_model_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_dynamics_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_den_restraints_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_bulk_solvent_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_mtz_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_dssp_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_building_loop_closure_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_cablam_align_utils_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_alignment_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_pdb_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_xplor_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_shelx_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_wildcard_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_scalepack_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_xray_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_detectors_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_gl_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_dtrek_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_dsn6_map_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_detectors_bruker_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_cif_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_ccp4_map_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_util_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_viewer_utils_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_geometry_restraints_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_quadrics_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_glu_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_fonts_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_sgtbx_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_imageset_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/fable_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_masking_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_format_image_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_flumpy.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_format_nexus_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_miller_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/determine_unit_cell_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cma_es_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_xray_observations_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_maptbx_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_uctbx_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_translation_search_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_crystal_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_symmetry_search_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_statistics_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_sgtbx_asu_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_adp_restraints_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_orientation_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_multipolar_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_masks_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_merging_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_math_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_maptbx_bcr_bcr_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_array_family_flex_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_geometry_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_xray_scattering_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_emma_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_french_wilson_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_wavelengths_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_tiny_pse_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_sasaki_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_neutron_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_icsd_radii_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_henke_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_dmtbx_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_covalent_radii_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_fp_fdp_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_chemical_elements_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_attenuation_coefficient_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_adptbx_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_covariance_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_asymmetric_map_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/ccp4io_adaptbx_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_anharmonic_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cbflib_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_python_meta_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_rational_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_maximum_clique_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_min_cut_max_flow_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_tuple_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_python_hybrid_times_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_utility_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_metric_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_optional_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_python_streambuf_test_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_clustering_algorithm_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_graph_structure_comparison_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_connected_component_algorithm_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_breadth_first_search_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_boost_thread_test_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/annlib_ext.cpython-311-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/cctbx/python3.11/smtbx/refinement/constraints/tests/tst_reparametrisation debian/python3-cctbx/usr/lib/cctbx/python3.11/smtbx/refinement/constraints/tests/tst_special_position debian/python3-cctbx/usr/lib/cctbx/python3.11/smtbx/refinement/constraints/tests/tst_geometrical_hydrogens debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/serialization/tst_base_256 debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/matrix/tests/tst_svd debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/matrix/tests/tst_householder debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/matrix/tests/tst_cholesky debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/matrix/tests/tst_givens debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/math/tests/tst debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/lbfgs/tst_lbfgs debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/error/tst_error debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_af_4 debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_sym_mat3 debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_vec3 debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_unsigned_float_arithmetic debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_ref_matrix_facet debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_optional_copy debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_rectangular_full_packed debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_af_5 debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_mat3 debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_af_3 debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_af_1 debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_af_2 debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_accessors debian/python3-cctbx/usr/lib/cctbx/python3.11/iotbx/pdb/hybrid_36_fem debian/python3-cctbx/usr/lib/cctbx/python3.11/boost_adaptbx/tests/tst_optional_copy debian/python3-cctbx/usr/bin/cctbx.find_distances debian/python3-cctbx/usr/bin/cctbx_blobs debian/python3-cctbx/usr/bin/cctbx.lattice_symmetry debian/python3-cctbx/usr/bin/cctbx.sym_equiv_sites debian/python3-cctbx/usr/bin/cctbx.getting_started debian/python3-cctbx/usr/bin/cctbx.sys_abs_equiv_space_groups debian/python3-cctbx/usr/bin/cctbx.convert_ccp4_symop_lib debian/python3-cctbx/usr/bin/cbflib.tst_memory -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/boost_python_meta_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyList_Type: 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/iotbx_shelx_ext.cpython-311-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/rstbx_bpcx_detector_model_ext.cpython-311-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/cbflib_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_FromDouble: it's probably a plugin +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: debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_dxtbx_ext.cpython-311-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/cctbx_masks_ext.cpython-311-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_symmetry_search_ext.cpython-311-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/gltbx_gl_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyUnicode_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_adptbx_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyErr_SetString: 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/cctbx_multipolar_ext.cpython-311-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/scitbx_stl_map_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_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/iotbx_wildcard_ext.cpython-311-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_wigner_ext.cpython-311-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/regression_test_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyErr_Clear: 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-311-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/scitbx_lbfgs_ext.cpython-311-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_max_lik_ext.cpython-311-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/cctbx_eltbx_covalent_radii_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyExc_StopIteration: 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_simage_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyErr_SetString: 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_wavelengths_ext.cpython-311-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_glmtbx_ext.cpython-311-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_symmetry_constraints_ext.cpython-311-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/mmtbx_building_loop_closure_ext.cpython-311-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/rstbx_bpcx_detector_model_ext.cpython-311-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/boost_python_hybrid_times_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_FromDouble: 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_mosaic_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyErr_Occurred: 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_dssp_ext.cpython-311-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/mmtbx_hydrogens_ext.cpython-311-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/rstbx_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyTuple_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_henke_ext.cpython-311-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/cctbx_eltbx_icsd_radii_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyExc_StopIteration: 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_building_loop_closure_ext.cpython-311-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/mmtbx_ncs_cartesian_restraints_ext.cpython-311-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/mmtbx_probe_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyObject_IsInstance: 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/mmtbx_f_model_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyTuple_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/scitbx_iso_surface_ext.cpython-311-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_clustering_algorithm_ext.cpython-311-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-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyObject_Free: 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/boost_tuple_ext.cpython-311-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/determine_unit_cell_ext.cpython-311-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/mmtbx_tls_utils_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_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/mmtbx_secondary_structure_ext.cpython-311-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/ccp4io_adaptbx_ext.cpython-311-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/mmtbx_rsr_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_FromLong: 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-311-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/scitbx_lstbx_normal_equations_ext.cpython-311-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/dxtbx_ext.cpython-311-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_alignment_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyUnicode_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_xray_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_FromLong: 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/cctbx_eltbx_tiny_pse_ext.cpython-311-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_cif_ext.cpython-311-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/cctbx_adp_restraints_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyObject_GetIter: 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/scitbx_r3_utils_ext.cpython-311-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_emma_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyErr_SetString: 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_python_streambuf_test_ext.cpython-311-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/cma_es_ext.cpython-311-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_adaptbx_graph_connected_component_algorithm_ext.cpython-311-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/iotbx_detectors_bruker_ext.cpython-311-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/regression_test_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_NoneStruct: 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_detectors_bruker_ext.cpython-311-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/mmtbx_rotamer_fit_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyList_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-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyUnicode_AsUTF8: 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/smtbx_array_family_ext.cpython-311-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_connected_component_algorithm_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_FromUnsignedLong: 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_geometry_shared_types_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_FromLong: 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/spotfinder_array_family_flex_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyIter_Next: 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/mmtbx_alignment_ext.cpython-311-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/cctbx_xray_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyErr_SetString: 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/cctbx_statistics_ext.cpython-311-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/cctbx_miller_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyIter_Next: it's probably a plugin -dpkg-shlibdeps: warning: 26 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-311-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_scalepack_ext.cpython-311-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_adaptbx_python_streambuf_test_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyUnicode_FromStringAndSize: 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_geometry_restraints_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: 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/scitbx_suffixtree_single_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyObject_Hash: 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_masks_ext.cpython-311-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/cctbx_adp_restraints_ext.cpython-311-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/cctbx_eltbx_henke_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyUnicode_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/gltbx_quadrics_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyErr_Clear: 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_detectors_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_FromLong: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_stl_map_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyList_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/mmtbx_geometry_sphere_surface_sampling_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_NoneStruct: 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_maptbx_ext.cpython-311-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/boost_adaptbx_graph_utility_ext.cpython-311-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_validation_ramachandran_ext.cpython-311-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/spotfinder_distltbx_ext.cpython-311-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/gltbx_util_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_FromDouble: 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_tls_decompose_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyBool_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_asymmetric_map_ext.cpython-311-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/cctbx_eltbx_fp_fdp_ext.cpython-311-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_eltbx_chemical_elements_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyList_New: 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/cctbx_eltbx_sasaki_ext.cpython-311-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-311-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_rigid_body_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_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_merging_ext.cpython-311-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/scitbx_array_family_flex_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyBool_Type: it's probably a plugin -dpkg-shlibdeps: warning: 50 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-311-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/smtbx_refinement_constraints_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyTuple_GetItem: 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/std_pair_ext.cpython-311-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_graphics_utils_ext.cpython-311-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/boost_adaptbx_graph_metric_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyTuple_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_rsr_ext.cpython-311-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_rational_ext.cpython-311-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_ext.cpython-311-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/rstbx_symmetry_constraints_ext.cpython-311-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/smtbx_array_family_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_NoneStruct: 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/boost_python_meta_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyUnicode_Type: 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_vector_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyTuple_New: 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/mmtbx_ncs_ext.cpython-311-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/gltbx_fonts_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyUnicode_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_math_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_FromLong: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_wildcard_ext.cpython-311-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/rstbx_bandpass_ext.cpython-311-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_geometry_ext.cpython-311-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/determine_unit_cell_ext.cpython-311-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/iotbx_pdb_hierarchy_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyIter_Next: it's probably a plugin -dpkg-shlibdeps: warning: 33 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-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: 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_eltbx_wavelengths_ext.cpython-311-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/gltbx_gl_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyList_Append: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cma_es_ext.cpython-311-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/rstbx_simulation_ext.cpython-311-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_rotamer_fit_ext.cpython-311-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_reference_coordinate_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_FromUnsignedLong: 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/rstbx_simage_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyUnicode_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/dxtbx_format_nexus_ext.cpython-311-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/mmtbx_geometry_asa_ext.cpython-311-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_indexing_api_ext.cpython-311-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/mmtbx_den_restraints_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyObject_IsInstance: 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/mmtbx_geometry_asa_ext.cpython-311-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/scitbx_lstbx_normal_equations_ext.cpython-311-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_scaling_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_FromDouble: 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/smtbx_refinement_restraints_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyTuple_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/annlib_ext.cpython-311-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/cctbx_geometry_restraints_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyTuple_GetItem: 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/scitbx_suffixtree_shared_ext.cpython-311-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/rstbx_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyBool_Type: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_hydrogens_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyErr_Occurred: 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_sasaki_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyExc_StopIteration: 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_sgtbx_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyRange_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/std_pair_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyTuple_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_french_wilson_ext.cpython-311-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/boost_adaptbx_graph_maximum_clique_ext.cpython-311-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/iotbx_xplor_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyErr_SetString: 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/omptbx_ext.cpython-311-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/scitbx_array_family_shared_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyErr_Clear: 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_scaling_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_FromDouble: 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_dtrek_ext.cpython-311-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_shelx_ext.cpython-311-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/cctbx_orientation_ext.cpython-311-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_uctbx_ext.cpython-311-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/scitbx_linalg_ext.cpython-311-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_eltbx_icsd_radii_ext.cpython-311-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_geometry_clash_ext.cpython-311-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/iotbx_pdb_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_FromUnsignedLong: 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_pair_interaction_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyTuple_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/mmtbx_validation_ramachandran_ext.cpython-311-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/omptbx_ext.cpython-311-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/rstbx_integration_ext.cpython-311-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_ab_initio_ext.cpython-311-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_utils_ext.cpython-311-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/dxtbx_flumpy.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_NotImplementedStruct: it's probably a plugin -dpkg-shlibdeps: warning: 120 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-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyComplex_FromDoubles: 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_glmtbx_ext.cpython-311-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/cctbx_translation_search_ext.cpython-311-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_tuple_ext.cpython-311-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/cctbx_eltbx_attenuation_coefficient_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_FromUnsignedLong: 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_dmtbx_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyErr_Clear: 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/smtbx_refinement_restraints_ext.cpython-311-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_lbfgsb_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_NoneStruct: 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-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyComplex_FromDoubles: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_indexing_ext.cpython-311-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/cctbx_eltbx_fp_fdp_ext.cpython-311-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/cctbx_uctbx_ext.cpython-311-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/cctbx_adptbx_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_FromDouble: 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_ramachandran_restraints_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyBool_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/mmtbx_dssp_ext.cpython-311-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/dxtbx_imageset_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyDict_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/spotfinder_hough_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_FromDouble: 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/spotfinder_distltbx_ext.cpython-311-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/scitbx_math_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyExc_StopIteration: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_sgtbx_asu_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyObject_Size: 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/gltbx_fonts_ext.cpython-311-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_math_ext.cpython-311-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/mmtbx_ramachandran_restraints_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyErr_Clear: 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/mmtbx_secondary_structure_ext.cpython-311-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/cctbx_covariance_ext.cpython-311-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/scitbx_r3_utils_ext.cpython-311-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_maptbx_bcr_bcr_ext.cpython-311-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/smtbx_stl_map_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyExc_KeyError: 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/dxtbx_format_image_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyUnicode_Type: 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_eltbx_xray_scattering_ext.cpython-311-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/boost_adaptbx_graph_graph_structure_comparison_ext.cpython-311-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_tls_optimise_amplitudes_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyObject_IsInstance: 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/spotfinder_dxtbx_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_FromLong: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_emma_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyExc_IndexError: 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_suffixtree_shared_ext.cpython-311-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/annlib_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyErr_SetString: 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_dynamics_ext.cpython-311-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/mmtbx_utils_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_FromDouble: 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_ext.cpython-311-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/boost_python_hybrid_times_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_FromDouble: 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_model_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_FromDouble: it's probably a plugin -dpkg-shlibdeps: warning: 31 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-311-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/smtbx_stl_map_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyExc_KeyError: 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_symmetry_search_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_FromDouble: 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/gltbx_util_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyIter_Check: 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/gltbx_quadrics_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyErr_Clear: 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_ccp4_map_ext.cpython-311-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/cctbx_xray_observations_ext.cpython-311-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/dxtbx_imageset_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_FromLong: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_detectors_ext.cpython-311-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/scitbx_suffixtree_single_ext.cpython-311-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/scitbx_array_family_flex_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyBytes_FromStringAndSize: it's probably a plugin +dpkg-shlibdeps: warning: 50 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-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyErr_Occurred: 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/boost_rational_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyTuple_New: 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_diffraction_fastbragg_ext.cpython-311-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/scitbx_lbfgs_ext.cpython-311-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/iotbx_mtz_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyObject_HasAttrString: 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/scitbx_random_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_FromLong: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_ccp4_map_ext.cpython-311-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_bulk_solvent_ext.cpython-311-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/cctbx_miller_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_FromUnsignedLong: it's probably a plugin +dpkg-shlibdeps: warning: 26 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-311-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/scitbx_stl_set_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyTuple_New: 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/boost_adaptbx_graph_metric_ext.cpython-311-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/boost_adaptbx_boost_thread_test_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_FromDouble: 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/spotfinder_hough_ext.cpython-311-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_covalent_radii_ext.cpython-311-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_tls_decompose_ext.cpython-311-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_minpack_ext.cpython-311-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_stl_vector_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_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/spotfinder_array_family_flex_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyBool_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/mmtbx_geometry_sphere_surface_sampling_ext.cpython-311-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/scitbx_sparse_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyBool_FromLong: 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_format_image_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyExc_ValueError: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_structure_factors_direct_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyBool_FromLong: 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_crystal_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyBool_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/scitbx_sparse_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyObject_IsInstance: 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_maptbx_bcr_bcr_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyObject_IsInstance: 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_simulation_ext.cpython-311-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/cctbx_multipolar_ext.cpython-311-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_cablam_align_utils_ext.cpython-311-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_merging_ext.cpython-311-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_tls_utils_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyUnicode_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/rstbx_indexing_api_ext.cpython-311-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/iotbx_pdb_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyUnicode_FromStringAndSize: 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/scitbx_wigner_ext.cpython-311-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_masks_ext.cpython-311-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/cctbx_math_ext.cpython-311-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_sgtbx_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PySlice_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/cctbx_eltbx_tiny_pse_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyExc_StopIteration: 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_covariance_ext.cpython-311-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/dxtbx_masking_ext.cpython-311-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-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyExc_TypeError: it's probably a plugin +dpkg-shlibdeps: warning: 120 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-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyTuple_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_geometry_shared_types_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_NoneStruct: 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/mmtbx_pair_interaction_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyObject_Size: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_maptbx_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyBool_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-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_FromLong: 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_geometry_clash_ext.cpython-311-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/smtbx_structure_factors_direct_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyComplex_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/cctbx_sgtbx_asu_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyIter_Next: 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/scitbx_fftpack_ext.cpython-311-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/boost_optional_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyUnicode_FromWideChar: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_dynamics_ext.cpython-311-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/boost_optional_ext.cpython-311-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_linalg_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyBool_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/boost_adaptbx_graph_graph_structure_comparison_ext.cpython-311-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_utility_ext.cpython-311-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-311-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_geometry_primitive_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_FromDouble: 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_orientation_ext.cpython-311-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/scitbx_cubicle_neighbors_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_FromUnsignedLong: 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_probe_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyObject_IsInstance: 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/mmtbx_bulk_solvent_ext.cpython-311-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_geometry_primitive_ext.cpython-311-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_model_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PySlice_Type: it's probably a plugin +dpkg-shlibdeps: warning: 31 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-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyEval_CallFunction: 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_ncs_ext.cpython-311-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/boost_adaptbx_graph_min_cut_max_flow_ext.cpython-311-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/scitbx_minpack_ext.cpython-311-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_cif_ext.cpython-311-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_french_wilson_ext.cpython-311-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/dxtbx_format_nexus_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyErr_Occurred: 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_reference_coordinate_ext.cpython-311-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/cctbx_translation_search_ext.cpython-311-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/smtbx_refinement_least_squares_ext.cpython-311-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/mmtbx_masks_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_FromUnsignedLong: 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_eltbx_neutron_ext.cpython-311-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/gltbx_viewer_utils_ext.cpython-311-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/rstbx_bandpass_ext.cpython-311-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_tls_optimise_amplitudes_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyTuple_New: 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_maximum_clique_ext.cpython-311-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/iotbx_scalepack_ext.cpython-311-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-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyTuple_New: 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_fftpack_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyErr_SetString: 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_array_family_flex_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyIter_Next: 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_cablam_align_utils_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_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_adaptbx_graph_clustering_algorithm_ext.cpython-311-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/scitbx_lbfgsb_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyUnicode_FromStringAndSize: 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_mosaic_ext.cpython-311-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/cctbx_anharmonic_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyComplex_FromDoubles: 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/iotbx_dsn6_map_ext.cpython-311-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_xray_observations_ext.cpython-311-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_rigid_body_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyBool_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/ccp4io_adaptbx_ext.cpython-311-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/mmtbx_geometry_indexing_ext.cpython-311-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_min_cut_max_flow_ext.cpython-311-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/smtbx_refinement_constraints_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PySlice_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/cctbx_eltbx_xray_scattering_ext.cpython-311-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/rstbx_array_family_flex_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_FromUnsignedLong: 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/scitbx_stl_set_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_FromUnsignedLong: 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_den_restraints_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_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/cctbx_crystal_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyBool_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/smtbx_refinement_least_squares_ext.cpython-311-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/mmtbx_max_lik_ext.cpython-311-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/cctbx_eltbx_chemical_elements_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_NoneStruct: 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/scitbx_cubicle_neighbors_ext.cpython-311-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/smtbx_ab_initio_ext.cpython-311-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_array_family_shared_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyErr_Occurred: 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_random_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyBool_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/iotbx_pdb_hierarchy_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_NoneStruct: it's probably a plugin +dpkg-shlibdeps: warning: 33 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-311-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/mmtbx_f_model_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_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/fable_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyTuple_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/iotbx_dtrek_ext.cpython-311-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_tls_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyBool_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/iotbx_xplor_ext.cpython-311-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/gltbx_glu_ext.cpython-311-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyType_Ready: it's probably a plugin +dpkg-shlibdeps: warning: 11 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 @@ -40728,15 +40766,15 @@ chmod 0644 -- debian/.debhelper/libcctbx0/dbgsym-root/DEBIAN/control dpkg-gencontrol -plibcctbx0 -ldebian/changelog -Tdebian/libcctbx0.substvars -Pdebian/libcctbx0 dpkg-gencontrol: warning: package libcctbx-dev: substitution variable ${python3:Depends} unused, but is defined + chmod 0644 -- debian/libcctbx-dev/DEBIAN/control chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/DEBIAN/control dpkg-gencontrol -ppython3-cctbx -ldebian/changelog -Tdebian/python3-cctbx.substvars -Pdebian/python3-cctbx - chmod 0644 -- debian/libcctbx-dev/DEBIAN/control dpkg-gencontrol: warning: package libcctbx0: substitution variable ${python3:Depends} unused, but is defined - chmod 0644 -- debian/python3-cctbx/DEBIAN/control chmod 0644 -- debian/libcctbx0/DEBIAN/control + chmod 0644 -- debian/python3-cctbx/DEBIAN/control dh_md5sums -O--buildsystem=pybuild - install -m0755 -d debian/libcctbx-dev/DEBIAN install -m0755 -d debian/libcctbx0/DEBIAN + install -m0755 -d debian/libcctbx-dev/DEBIAN install -m0755 -d debian/python3-cctbx/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 @@ -40751,16 +40789,16 @@ 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/python3-cctbx .. dpkg-deb --root-owner-group --build debian/libcctbx0 .. 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/python3-cctbx .. dpkg-deb --root-owner-group --build debian/.debhelper/python3-cctbx/dbgsym-root .. dpkg-deb: building package 'libcctbx0-dbgsym' in '../libcctbx0-dbgsym_2022.9+ds2+~3.11.2+ds1-6_arm64.deb'. dpkg-deb: building package 'libcctbx0' in '../libcctbx0_2022.9+ds2+~3.11.2+ds1-6_arm64.deb'. -dpkg-deb: building package 'python3-cctbx' in '../python3-cctbx_2022.9+ds2+~3.11.2+ds1-6_arm64.deb'. -dpkg-deb: building package 'python3-cctbx-dbgsym' in '../python3-cctbx-dbgsym_2022.9+ds2+~3.11.2+ds1-6_arm64.deb'. dpkg-deb: building package 'libcctbx-dev' in '../libcctbx-dev_2022.9+ds2+~3.11.2+ds1-6_arm64.deb'. +dpkg-deb: building package 'python3-cctbx-dbgsym' in '../python3-cctbx-dbgsym_2022.9+ds2+~3.11.2+ds1-6_arm64.deb'. +dpkg-deb: building package 'python3-cctbx' in '../python3-cctbx_2022.9+ds2+~3.11.2+ds1-6_arm64.deb'. dpkg-genbuildinfo --build=binary -O../cctbx_2022.9+ds2+~3.11.2+ds1-6_arm64.buildinfo dpkg-genchanges --build=binary -O../cctbx_2022.9+ds2+~3.11.2+ds1-6_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -40768,12 +40806,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/1270917/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1270917/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/2841186 and its subdirectories -I: Current time: Wed Mar 5 05:26:13 -12 2025 -I: pbuilder-time-stamp: 1741195573 +I: removing directory /srv/workspace/pbuilder/1270917 and its subdirectories +I: Current time: Thu Mar 6 07:41:31 +14 2025 +I: pbuilder-time-stamp: 1741196491