Diff of the two buildlogs: -- --- b1/build.log 2024-01-06 13:27:33.943147212 +0000 +++ b2/build.log 2024-01-06 13:49:09.380041372 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Jan 6 00:14:09 -12 2024 -I: pbuilder-time-stamp: 1704543249 +I: Current time: Sat Feb 8 09:50:39 +14 2025 +I: pbuilder-time-stamp: 1738957839 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/2033141/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/21364/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-amd64. +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 Feb 7 19:50 /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/21364/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/21364/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='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15 ' - DISTRIBUTION='bookworm' - HOME='/root' - HOST_ARCH='amd64' + 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]="x86_64-pc-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=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16 ' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='575baa39e5d94012b5115c82eff24216' - 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='2033141' - PS1='# ' - PS2='> ' + INVOCATION_ID=d73ebc84ad3a4cedb8473be5d4b7bc44 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-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=21364 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.xpfY7xJE/pbuilderrc_rk6s --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.xpfY7xJE/b1 --logfile b1/build.log cctbx_2022.9+ds2+~3.11.2+ds1-6.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://78.137.99.97:3128' + 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.xpfY7xJE/pbuilderrc_opst --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.xpfY7xJE/b2 --logfile b2/build.log cctbx_2022.9+ds2+~3.11.2+ds1-6.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://85.184.249.68:3128 I: uname -a - Linux ionos11-amd64 6.1.0-17-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.69-1 (2023-12-30) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.5.0-0.deb12.4-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.5.10-1~bpo12+1 (2023-11-23) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Apr 23 2023 bash @@ -157,15 +189,15 @@ -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 27560 Jul 28 23:46 run-parts + -rwxr-xr-x 1 root root 27560 Jul 28 2023 run-parts -rwxr-xr-x 1 root root 126424 Jan 5 2023 sed - lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash + lrwxrwxrwx 1 root root 9 Feb 7 19:50 sh -> /bin/bash -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty -rwsr-xr-x 1 root root 72000 Mar 23 2023 su -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync -rwxr-xr-x 1 root root 531984 Apr 6 2023 tar - -rwxr-xr-x 1 root root 14520 Jul 28 23:46 tempfile + -rwxr-xr-x 1 root root 14520 Jul 28 2023 tempfile -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch -rwxr-xr-x 1 root root 35664 Sep 20 2022 true -rwxr-xr-x 1 root root 14568 Mar 23 2023 ulockmgr_server @@ -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/2033141/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/21364/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -771,7 +803,7 @@ Get: 455 http://deb.debian.org/debian bookworm/main amd64 python3-tqdm all 4.64.1-1 [97.7 kB] Get: 456 http://deb.debian.org/debian bookworm/main amd64 python3-wxgtk4.0 amd64 4.2.0+dfsg-3 [7200 kB] Get: 457 http://deb.debian.org/debian bookworm/main amd64 scons all 4.4.0+dfsg-1 [663 kB] -Fetched 280 MB in 27s (10.3 MB/s) +Fetched 280 MB in 4s (79.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libargon2-1:amd64. (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 ... 18148 files and directories currently installed.) @@ -2231,8 +2263,8 @@ Setting up tzdata (2023c-5+deb12u1) ... Current default time zone: 'Etc/UTC' -Local time is now: Sat Jan 6 12:17:54 UTC 2024. -Universal Time is now: Sat Jan 6 12:17:54 UTC 2024. +Local time is now: Fri Feb 7 19:51:57 UTC 2025. +Universal Time is now: Fri Feb 7 19:51:57 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libdconf1:amd64 (0.40.0-4) ... @@ -2660,7 +2692,11 @@ 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/21364/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for bookworm +I: user script /srv/workspace/pbuilder/21364/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 @@ -2836,8 +2872,8 @@ 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=8b1d0a9b12fbbce77f09d6bcff6ca9d16e6664aa3c3277369d2a60c5737c23ad - Stored in directory: /tmp/pip-ephem-wheel-cache-8fffduzc/wheels/c9/65/9f/2b98990eed63492b01400828d96e4dbc5e74502aed74937ddf + Created wheel for dxtbx: filename=dxtbx-3.11.2-0.editable-py3-none-any.whl size=6141 sha256=19a3cd28f647fba10c1c439089d463940dcbd2c8c6dbf60d988433429d952a5a + Stored in directory: /tmp/pip-ephem-wheel-cache-8nzyxqfc/wheels/c9/65/9f/2b98990eed63492b01400828d96e4dbc5e74502aed74937ddf Successfully built dxtbx Installing collected packages: dxtbx Successfully installed dxtbx-3.11.2 @@ -6769,9 +6805,9 @@ copying src/dxtbx/format/boost_python/cbf_read_buffer.cpp -> /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build/dxtbx/format/boost_python copying src/dxtbx/data/detectors.lib -> /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build/dxtbx/data # build the cctbx extensions and libraries -dh_auto_build -- -s custom --build-args="cd {build_dir}_ && ./bin/libtbx.scons -j 15 " - pybuild --build -i python{version} -p 3.11 -s custom "--build-args=cd {build_dir}_ && ./bin/libtbx.scons -j 15 " -I: pybuild base:240: cd '/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build'_ && ./bin/libtbx.scons -j 15 +dh_auto_build -- -s custom --build-args="cd {build_dir}_ && ./bin/libtbx.scons -j 16 " + pybuild --build -i python{version} -p 3.11 -s custom "--build-args=cd {build_dir}_ && ./bin/libtbx.scons -j 16 " +I: pybuild base:240: cd '/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build'_ && ./bin/libtbx.scons -j 16 scons: Reading SConscript files ... libtbx.scons: using flags from initial environment: CXXFLAGS = -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/hdf5/serial @@ -6819,6 +6855,14 @@ g++ -o cctbx/eltbx/henke_tables_85_92.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/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_85_92.cpp g++ -o cctbx/eltbx/icsd_radii.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/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/icsd_radii.cpp g++ -o cctbx/eltbx/covalent_radii.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/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/covalent_radii.cpp +g++ -o cctbx/eltbx/neutron.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/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/neutron.cpp +g++ -o cctbx/eltbx/sasaki.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/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/sasaki.cpp +g++ -o cctbx/eltbx/sasaki_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/sasaki_tables_01_12.cpp +g++ -o cctbx/eltbx/sasaki_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/sasaki_tables_13_24.cpp +g++ -o cctbx/eltbx/sasaki_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/sasaki_tables_25_36.cpp +g++ -o cctbx/eltbx/sasaki_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/sasaki_tables_37_48.cpp +g++ -o cctbx/eltbx/sasaki_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/sasaki_tables_49_60.cpp +g++ -o cctbx/eltbx/sasaki_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/sasaki_tables_61_72.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, @@ -6834,23 +6878,15 @@ /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/neutron.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/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/neutron.cpp -g++ -o cctbx/eltbx/sasaki.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/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/sasaki.cpp -g++ -o cctbx/eltbx/sasaki_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/sasaki_tables_01_12.cpp -g++ -o cctbx/eltbx/sasaki_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/sasaki_tables_13_24.cpp -g++ -o cctbx/eltbx/sasaki_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/sasaki_tables_25_36.cpp -g++ -o cctbx/eltbx/sasaki_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/sasaki_tables_37_48.cpp -g++ -o cctbx/eltbx/sasaki_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/sasaki_tables_49_60.cpp -g++ -o cctbx/eltbx/sasaki_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/sasaki_tables_61_72.cpp g++ -o cctbx/eltbx/sasaki_tables_73_82.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/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/sasaki_tables_73_82.cpp g++ -o cctbx/eltbx/tiny_pse.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/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/tiny_pse.cpp -g++ -o lib/libiotbx_xplor.so.0.0.1 -shared -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-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/x86_64-linux-gnu -Llib -L/build/reproducible-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/wavelengths.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/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/wavelengths.cpp +g++ -o lib/libiotbx_xplor.so.0.0.1 -shared -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-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/x86_64-linux-gnu -Llib -L/build/reproducible-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/electron_scattering/peng1996.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/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/electron_scattering/peng1996.cpp +g++ -o cctbx/eltbx/attenuation_coefficient.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/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/attenuation_coefficient.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/electron_scattering/peng1996.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/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/electron_scattering/peng1996.cpp -g++ -o cctbx/eltbx/attenuation_coefficient.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/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/attenuation_coefficient.cpp g++ -o cctbx/miller/asu.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/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/miller/asu.cpp g++ -o cctbx/miller/bins.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/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/miller/bins.cpp g++ -o cctbx/miller/index_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 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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/miller/index_generator.cpp @@ -6909,12 +6945,15 @@ g++ -o boost_adaptbx/meta_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/meta_ext.cpp g++ -o boost_adaptbx/optional_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/optional_ext.cpp g++ -o boost_adaptbx/rational_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/boost_adaptbx/rational_ext.cpp -g++ -o lib/libcctbx.so.0.0.1 -shared -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -Wl,-soname=libcctbx.so.0 cctbx/eltbx/basic.o cctbx/eltbx/xray_scattering/it1992.o cctbx/eltbx/xray_scattering/wk1995.o cctbx/eltbx/xray_scattering/n_gaussian_raw.o cctbx/eltbx/xray_scattering/n_gaussian.o cctbx/eltbx/fp_fdp.o cctbx/eltbx/henke.o cctbx/eltbx/henke_tables_01_12.o cctbx/eltbx/henke_tables_13_24.o cctbx/eltbx/henke_tables_25_36.o cctbx/eltbx/henke_tables_37_48.o cctbx/eltbx/henke_tables_49_60.o cctbx/eltbx/henke_tables_61_72.o cctbx/eltbx/henke_tables_73_84.o cctbx/eltbx/henke_tables_85_92.o cctbx/eltbx/icsd_radii.o cctbx/eltbx/covalent_radii.o cctbx/eltbx/neutron.o cctbx/eltbx/sasaki.o cctbx/eltbx/sasaki_tables_01_12.o cctbx/eltbx/sasaki_tables_13_24.o cctbx/eltbx/sasaki_tables_25_36.o cctbx/eltbx/sasaki_tables_37_48.o cctbx/eltbx/sasaki_tables_49_60.o cctbx/eltbx/sasaki_tables_61_72.o cctbx/eltbx/sasaki_tables_73_82.o cctbx/eltbx/tiny_pse.o cctbx/eltbx/wavelengths.o cctbx/eltbx/electron_scattering/peng1996.o cctbx/eltbx/attenuation_coefficient.o cctbx/miller/asu.o cctbx/miller/bins.o cctbx/miller/index_generator.o cctbx/miller/index_span.o cctbx/miller/match_bijvoet_mates.o cctbx/miller/match_indices.o cctbx/miller/match_multi_indices.o cctbx/miller/sym_equiv.o cctbx/sgtbx/bricks.o cctbx/sgtbx/change_of_basis_op.o cctbx/sgtbx/find_affine.o cctbx/sgtbx/group_codes.o cctbx/sgtbx/hall_in.o cctbx/sgtbx/lattice_tr.o cctbx/sgtbx/lattice_symmetry.o cctbx/sgtbx/miller.o cctbx/sgtbx/reciprocal_space_asu.o cctbx/sgtbx/reciprocal_space_ref_asu.o cctbx/sgtbx/rot_mx.o cctbx/sgtbx/rot_mx_info.o cctbx/sgtbx/row_echelon_solve.o cctbx/sgtbx/rt_mx.o cctbx/sgtbx/select_generators.o cctbx/sgtbx/seminvariant.o cctbx/sgtbx/site_symmetry.o cctbx/sgtbx/space_group.o cctbx/sgtbx/space_group_type.o cctbx/sgtbx/symbols.o cctbx/sgtbx/tensor_rank_2.o cctbx/sgtbx/tr_group.o cctbx/sgtbx/tr_vec.o cctbx/sgtbx/utils.o cctbx/sgtbx/wyckoff.o cctbx/sgtbx/reference_settings/hall_symbol_table.o cctbx/sgtbx/reference_settings/matrix_group_code_table.o cctbx/sgtbx/reference_settings/normalizer.o cctbx/sgtbx/reference_settings/wyckoff.o cctbx/uctbx/uctbx.o cctbx/uctbx/spoil_optimization.o cctbx/uctbx/crystal_orientation.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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 boost_adaptbx/std_pair_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/std_pair_ext.cpp +g++ -o lib/libcctbx.so.0.0.1 -shared -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -Wl,-soname=libcctbx.so.0 cctbx/eltbx/basic.o cctbx/eltbx/xray_scattering/it1992.o cctbx/eltbx/xray_scattering/wk1995.o cctbx/eltbx/xray_scattering/n_gaussian_raw.o cctbx/eltbx/xray_scattering/n_gaussian.o cctbx/eltbx/fp_fdp.o cctbx/eltbx/henke.o cctbx/eltbx/henke_tables_01_12.o cctbx/eltbx/henke_tables_13_24.o cctbx/eltbx/henke_tables_25_36.o cctbx/eltbx/henke_tables_37_48.o cctbx/eltbx/henke_tables_49_60.o cctbx/eltbx/henke_tables_61_72.o cctbx/eltbx/henke_tables_73_84.o cctbx/eltbx/henke_tables_85_92.o cctbx/eltbx/icsd_radii.o cctbx/eltbx/covalent_radii.o cctbx/eltbx/neutron.o cctbx/eltbx/sasaki.o cctbx/eltbx/sasaki_tables_01_12.o cctbx/eltbx/sasaki_tables_13_24.o cctbx/eltbx/sasaki_tables_25_36.o cctbx/eltbx/sasaki_tables_37_48.o cctbx/eltbx/sasaki_tables_49_60.o cctbx/eltbx/sasaki_tables_61_72.o cctbx/eltbx/sasaki_tables_73_82.o cctbx/eltbx/tiny_pse.o cctbx/eltbx/wavelengths.o cctbx/eltbx/electron_scattering/peng1996.o cctbx/eltbx/attenuation_coefficient.o cctbx/miller/asu.o cctbx/miller/bins.o cctbx/miller/index_generator.o cctbx/miller/index_span.o cctbx/miller/match_bijvoet_mates.o cctbx/miller/match_indices.o cctbx/miller/match_multi_indices.o cctbx/miller/sym_equiv.o cctbx/sgtbx/bricks.o cctbx/sgtbx/change_of_basis_op.o cctbx/sgtbx/find_affine.o cctbx/sgtbx/group_codes.o cctbx/sgtbx/hall_in.o cctbx/sgtbx/lattice_tr.o cctbx/sgtbx/lattice_symmetry.o cctbx/sgtbx/miller.o cctbx/sgtbx/reciprocal_space_asu.o cctbx/sgtbx/reciprocal_space_ref_asu.o cctbx/sgtbx/rot_mx.o cctbx/sgtbx/rot_mx_info.o cctbx/sgtbx/row_echelon_solve.o cctbx/sgtbx/rt_mx.o cctbx/sgtbx/select_generators.o cctbx/sgtbx/seminvariant.o cctbx/sgtbx/site_symmetry.o cctbx/sgtbx/space_group.o cctbx/sgtbx/space_group_type.o cctbx/sgtbx/symbols.o cctbx/sgtbx/tensor_rank_2.o cctbx/sgtbx/tr_group.o cctbx/sgtbx/tr_vec.o cctbx/sgtbx/utils.o cctbx/sgtbx/wyckoff.o cctbx/sgtbx/reference_settings/hall_symbol_table.o cctbx/sgtbx/reference_settings/matrix_group_code_table.o cctbx/sgtbx/reference_settings/normalizer.o cctbx/sgtbx/reference_settings/wyckoff.o cctbx/uctbx/uctbx.o cctbx/uctbx/spoil_optimization.o cctbx/uctbx/crystal_orientation.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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: 'lib/libcctbx.so.0.0.1' 'lib/libcctbx.so.0'->'lib/libcctbx.so.0.0.1' 'lib/libcctbx.so'->'lib/libcctbx.so.0.0.1' 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/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, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -6928,7 +6967,7 @@ 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/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( | ^~~~~~~~~~~~~~~~~~~~ @@ -6945,12 +6984,13 @@ 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/min_cut_max_flow_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( | ^~~~~~~~~~~~~~~~~~~~ -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 +/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, @@ -6959,15 +6999,14 @@ 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/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: -/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 /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/boost_adaptbx/tests/python_streambuf_test_ext.cpp:2: +/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 " ) + | ^~~~~~~~~~~~~~~~~~~~~~~ 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, @@ -6986,7 +7025,6 @@ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ g++ -o boost_adaptbx/tests/tst_optional_copy -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-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/x86_64-linux-gnu -Llib -L/build/reproducible-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, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -7000,7 +7038,7 @@ 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/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( | ^~~~~~~~~~~~~~~~~~~~ @@ -7017,7 +7055,7 @@ 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/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( | ^~~~~~~~~~~~~~~~~~~~ @@ -7034,11 +7072,10 @@ 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_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( | ^~~~~~~~~~~~~~~~~~~~ -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 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, @@ -7047,14 +7084,17 @@ 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/boost_adaptbx/tests/python_streambuf_test_ext.cpp:2: -/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 " ) - | ^~~~~~~~~~~~~~~~~~~~~~~ + 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 /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: +/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 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 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, @@ -7068,15 +7108,10 @@ 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/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( | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -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 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, @@ -7090,13 +7125,22 @@ 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/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( | ^~~~~~~~~~~~~~~~~~~~ +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 g++ -o cbflib_adaptbx/detectors/cbf_byte_offset_optimized.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/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_byte_offset_optimized.cpp g++ -o cbflib_adaptbx/detectors/mar_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/mar_adaptor.cpp g++ -o cbflib_adaptbx/detectors/tst_memory.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/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 -DCBF_NO_REGEX -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/hdf5/serial /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cbflib_adaptbx/detectors/tst_memory.cpp +g++ -o ccp4io_adaptbx/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/ccp4io -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/ccp4io_adaptbx/ext.cpp +gcc -o ccp4io_adaptbx/fortran_call_stubs.o -c -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DMSETS=32 -DMXTALS=32 -DMCOLUMNS=128 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/ccp4 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/ccp4io -I. -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/ccp4io_adaptbx/fortran_call_stubs.c +gcc -o ccp4io_adaptbx/printf_wrappers.o -c -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DMSETS=32 -DMXTALS=32 -DMCOLUMNS=128 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/ccp4 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/ccp4io -I. -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/ccp4io_adaptbx/printf_wrappers.c +g++ -o cctbx/adp_restraints/adp_restraints_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/adp_restraints_bpl.cpp +g++ -o cctbx/adp_restraints/adp_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/cctbx/adp_restraints/adp_restraints_ext.cpp +g++ -o cctbx/adp_restraints/adp_similarity_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/adp_similarity_bpl.cpp +g++ -o cctbx/adp_restraints/aniso_restraints_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/aniso_restraints_bpl.cpp +g++ -o cctbx/adp_restraints/fixed_u_eq_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/fixed_u_eq_adp_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, @@ -7117,14 +7161,8 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -g++ -o ccp4io_adaptbx/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/ccp4io -I/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/ccp4io_adaptbx/ext.cpp -gcc -o ccp4io_adaptbx/fortran_call_stubs.o -c -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DMSETS=32 -DMXTALS=32 -DMCOLUMNS=128 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/ccp4 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/ccp4io -I. -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/ccp4io_adaptbx/fortran_call_stubs.c -gcc -o ccp4io_adaptbx/printf_wrappers.o -c -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DMSETS=32 -DMXTALS=32 -DMCOLUMNS=128 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -I/usr/include/ccp4 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/ccp4io -I. -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/ccp4io_adaptbx/printf_wrappers.c -g++ -o cctbx/adp_restraints/adp_restraints_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/adp_restraints_bpl.cpp -g++ -o cctbx/adp_restraints/adp_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/cctbx/adp_restraints/adp_restraints_ext.cpp -g++ -o cctbx/adp_restraints/adp_similarity_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/adp_similarity_bpl.cpp -g++ -o cctbx/adp_restraints/aniso_restraints_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/aniso_restraints_bpl.cpp -g++ -o cctbx/adp_restraints/fixed_u_eq_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/fixed_u_eq_adp_bpl.cpp +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 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, @@ -7145,8 +7183,6 @@ /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 @@ -7169,7 +7205,20 @@ 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 lib/libcctbx_sgtbx_asu.so.0.0.1 -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -pthread -shared -Wl,-z,relro -L/usr/lib/x86_64-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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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 +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 +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' +g++ -o lib/libasymmetric_map.so.0.0.1 -shared -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -Wl,-soname=libasymmetric_map.so.0 cctbx/maptbx/asymmetric_map.o cctbx/maptbx/skeletons.o cctbx/maptbx/dijkstra.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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_sgtbx_asu -lcctbx -lomptbx -lm +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 +Create symlinks for: 'lib/libasymmetric_map.so.0.0.1' + 'lib/libasymmetric_map.so.0'->'lib/libasymmetric_map.so.0.0.1' + 'lib/libasymmetric_map.so'->'lib/libasymmetric_map.so.0.0.1' +g++ -o bin/cctbx_blobs -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -pthread cctbx/maptbx/blobs_cmd.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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/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/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 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, @@ -7190,8 +7239,6 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -g++ -o cctbx/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 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, @@ -7212,7 +7259,6 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -g++ -o cctbx/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, @@ -7233,11 +7279,9 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -g++ -o cctbx/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, @@ -7258,6 +7302,7 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +g++ -o cctbx/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 @@ -7267,28 +7312,21 @@ g++ -o cctbx/examples/convert_ccp4_symop_lib.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/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 -Icctbx/examples -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/examples /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/examples/convert_ccp4_symop_lib.cpp g++ -o cctbx/examples/find_distances.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/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 -Icctbx/examples -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/examples /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/examples/find_distances.cpp g++ -o cctbx/examples/getting_started.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/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 -Icctbx/examples -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/examples /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/examples/getting_started.cpp -g++ -o lib/libcctbx_sgtbx_asu.so.0.0.1 -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -pthread -shared -Wl,-z,relro -L/usr/lib/x86_64-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/x86_64-linux-gnu -Llib -L/build/reproducible-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/examples/lattice_symmetry.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/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 -Icctbx/examples -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/examples /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/examples/lattice_symmetry.cpp g++ -o cctbx/examples/sym_equiv_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 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/usr/include -Icctbx/examples -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/examples /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/examples/sym_equiv_sites.cpp g++ -o cctbx/examples/sys_abs_equiv_space_groups.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/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 -Icctbx/examples -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/examples /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/examples/sys_abs_equiv_space_groups.cpp g++ -o cctbx/geometry/boost_python/geometry_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/geometry/boost_python/geometry_ext.cpp g++ -o cctbx/geometry_restraints/angle_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/angle_bpl.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' g++ -o cctbx/geometry_restraints/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 -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/bond_bpl.cpp -g++ -o lib/libasymmetric_map.so.0.0.1 -shared -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -Wl,-soname=libasymmetric_map.so.0 cctbx/maptbx/asymmetric_map.o cctbx/maptbx/skeletons.o cctbx/maptbx/dijkstra.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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_sgtbx_asu -lcctbx -lomptbx -lm g++ -o cctbx/geometry_restraints/bond_similarity_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/bond_similarity_bpl.cpp g++ -o cctbx/geometry_restraints/bond_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/bond_sorted_bpl.cpp g++ -o cctbx/geometry_restraints/chirality_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/chirality_bpl.cpp g++ -o cctbx/geometry_restraints/dihedral_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/dihedral_bpl.cpp -Create symlinks for: 'lib/libasymmetric_map.so.0.0.1' - 'lib/libasymmetric_map.so.0'->'lib/libasymmetric_map.so.0.0.1' - 'lib/libasymmetric_map.so'->'lib/libasymmetric_map.so.0.0.1' -g++ -o bin/cctbx_blobs -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -pthread cctbx/maptbx/blobs_cmd.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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/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 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 /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, @@ -7297,6 +7335,14 @@ /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, 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] 108 | 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("") + | ^~~~~~~~~~~~~~~~~~~~~~~ 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]’ @@ -7316,39 +7383,6 @@ /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 /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); - | ~~^~~~~~~~~~~ -/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 /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/angle.h:6, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/angle_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::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]’ @@ -7360,33 +7394,6 @@ /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 /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/angle_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::angle_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/angle_bpl.cpp:75:65: 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); - | ~~^~~~~~~~~~~ -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 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/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("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -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, @@ -7450,11 +7425,35 @@ 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_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); + | ~~^~~~~~~~~~~ +/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, + 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/angle_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::angle_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/angle_bpl.cpp:75:65: 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); | ~~^~~~~~~~~~~ @@ -7469,12 +7468,18 @@ /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::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]’ +/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/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 instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -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, @@ -7540,19 +7547,14 @@ 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/nonbonded_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 = cctbx::geometry_restraints::nonbonded_simple_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/nonbonded_bpl.cpp:92:25: 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); | ~~^~~~~~~~~~~ -/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::nonbonded_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/nonbonded_bpl.cpp:125:25: 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/geometry_restraints/dihedral_bpl.cpp:13: /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 = dihedral_proxy]’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/dihedral_bpl.cpp:110:17: required from here @@ -7566,11 +7568,21 @@ /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/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/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/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/assert.hpp:58, from /usr/include/boost/move/detail/type_traits.hpp:33, from /usr/include/boost/move/traits.hpp:31, @@ -7613,17 +7625,6 @@ /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] -/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 > 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]’ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/bond_bpl.cpp:232:25: 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] +/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::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_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] -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 +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/crystal/direct_space_asu.h:869:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] + 869 | for(int i_sym=0; i_sym::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::nonbonded_simple_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/nonbonded_bpl.cpp:92:25: 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] + 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::nonbonded_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/nonbonded_bpl.cpp:125:25: 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 /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, @@ -7685,6 +7719,26 @@ /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/crystal/neighbors_fast.h:5, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/crystal/pair_tables.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/nonbonded_sorted.h:5: +/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 = cctbx::cartesian; CubicleContentType = std::vector; FloatType = double]’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/crystal/neighbors_fast.h:77:34: required from ‘cctbx::crystal::neighbors::fast_pair_generator::fast_pair_generator(const boost::shared_ptr >&, const FloatType&, bool, const FloatType&, const FloatType&) [with FloatType = double; IntShiftType = int]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/nonbonded_sorted.h:80:27: required from here +/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 /usr/include/boost/assert.hpp:58, from /usr/include/boost/move/detail/type_traits.hpp:33, from /usr/include/boost/move/traits.hpp:31, @@ -7704,6 +7758,10 @@ /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 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, @@ -7745,28 +7803,6 @@ /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()); | ^~~~~~~~~~~~~ -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 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/crystal/neighbors_fast.h:5, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/crystal/pair_tables.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/nonbonded_sorted.h:5: -/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 = cctbx::cartesian; CubicleContentType = std::vector; FloatType = double]’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/crystal/neighbors_fast.h:77:34: required from ‘cctbx::crystal::neighbors::fast_pair_generator::fast_pair_generator(const boost::shared_ptr >&, const FloatType&, bool, const FloatType&, const FloatType&) [with FloatType = double; IntShiftType = int]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/geometry_restraints/nonbonded_sorted.h:80:27: required from here -/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/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 g++ -o cctbx/maptbx/boost_python/gridding.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-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/gridding.cpp g++ -o cctbx/maptbx/boost_python/maptbx_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/maptbx/boost_python/maptbx_ext.cpp @@ -7792,8 +7828,8 @@ /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 cctbx/math/time_trigonometry -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -pthread cctbx/math/time_trigonometry.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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 -lm g++ -o cctbx/miller/boost_python/amplitude_normalisation.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-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/miller/boost_python/amplitude_normalisation.cpp +g++ -o cctbx/math/time_trigonometry -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -pthread cctbx/math/time_trigonometry.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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 -lm g++ -o cctbx/miller/boost_python/asu.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-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/miller/boost_python/asu.cpp g++ -o cctbx/miller/boost_python/bins.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-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/miller/boost_python/bins.cpp g++ -o cctbx/miller/boost_python/change_basis.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-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/miller/boost_python/change_basis.cpp @@ -7821,6 +7857,22 @@ g++ -o cctbx/sgtbx/boost_python/reciprocal_space_asu.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-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/sgtbx/boost_python/reciprocal_space_asu.cpp g++ -o cctbx/sgtbx/boost_python/rot_mx.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-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/sgtbx/boost_python/rot_mx.cpp g++ -o cctbx/sgtbx/boost_python/rt_mx.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-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/sgtbx/boost_python/rt_mx.cpp +In file included from /usr/include/boost/math/tools/cxx03_warn.hpp:9, + from /usr/include/boost/math/constants/constants.hpp:11, + from /usr/include/boost/math/special_functions/gamma.hpp:24, + from /usr/include/boost/math/special_functions/detail/bessel_jy.hpp:14, + from /usr/include/boost/math/special_functions/bessel.hpp:20, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/math/bessel.h:9, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/hendrickson_lattman.h:6, + 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/boost_python/miller_ext.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("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +g++ -o cctbx/sgtbx/boost_python/search_symmetry.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-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/sgtbx/boost_python/search_symmetry.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, @@ -7842,23 +7894,7 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -g++ -o cctbx/sgtbx/boost_python/search_symmetry.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-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/sgtbx/boost_python/search_symmetry.cpp g++ -o cctbx/sgtbx/boost_python/select_generators.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-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/sgtbx/boost_python/select_generators.cpp -In file included from /usr/include/boost/math/tools/cxx03_warn.hpp:9, - from /usr/include/boost/math/constants/constants.hpp:11, - from /usr/include/boost/math/special_functions/gamma.hpp:24, - from /usr/include/boost/math/special_functions/detail/bessel_jy.hpp:14, - from /usr/include/boost/math/special_functions/bessel.hpp:20, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/math/bessel.h:9, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/hendrickson_lattman.h:6, - 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/boost_python/miller_ext.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("") - | ^~~~~~~~~~~~~~~~~~~~~~~ g++ -o cctbx/sgtbx/boost_python/seminvariant.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-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/sgtbx/boost_python/seminvariant.cpp g++ -o cctbx/sgtbx/boost_python/sgtbx_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/sgtbx/boost_python/sgtbx_ext.cpp g++ -o cctbx/sgtbx/boost_python/site_symmetry.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-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/sgtbx/boost_python/site_symmetry.cpp @@ -7875,8 +7911,8 @@ g++ -o cctbx/symmetry_search/boost_python/symmetry_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/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/symmetry_search/boost_python/symmetry_search_ext.cpp g++ -o cctbx/translation_search/boost_python/fast_nv1995.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-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/translation_search/boost_python/fast_nv1995.cpp g++ -o cctbx/translation_search/boost_python/fast_terms.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-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/translation_search/boost_python/fast_terms.cpp -g++ -o cctbx/sgtbx/direct_space_asu/proto/tst_asu -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -pthread cctbx/sgtbx/direct_space_asu/proto/tst_asu.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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 -lm g++ -o cctbx/translation_search/boost_python/symmetry_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 -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_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/translation_search/boost_python/symmetry_flags.cpp +g++ -o cctbx/sgtbx/direct_space_asu/proto/tst_asu -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -pthread cctbx/sgtbx/direct_space_asu/proto/tst_asu.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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 -lm g++ -o cctbx/translation_search/boost_python/translation_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/usr/include -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/translation_search/boost_python/translation_search_ext.cpp g++ -o cctbx/uctbx/boost_python/fast_minimum_reduction.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-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/uctbx/boost_python/fast_minimum_reduction.cpp g++ -o cctbx/uctbx/boost_python/uctbx_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/uctbx/boost_python/uctbx_ext.cpp @@ -7886,6 +7922,9 @@ g++ -o cctbx/xray/boost_python/each_hkl_gradients_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/each_hkl_gradients_direct.cpp g++ -o cctbx/xray/boost_python/extinction.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-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/extinction.cpp g++ -o cctbx/xray/boost_python/f_model_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 -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/f_model_bpl.cpp +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 +g++ -o cctbx/xray/boost_python/gradient_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/gradient_flags.cpp +g++ -o cctbx/xray/boost_python/gradients_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/gradients_direct.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/curvatures_simple.h:4, @@ -7894,7 +7933,27 @@ /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]’ +/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]’ @@ -7920,29 +7979,6 @@ /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/gradient_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/gradient_flags.cpp -g++ -o cctbx/xray/boost_python/gradients_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/gradients_direct.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::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/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, @@ -7970,25 +8006,49 @@ /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]’ -/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/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 +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, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/boost_python/f_model_bpl.cpp:3: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/miller/match.h:16:34: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] + 16 | struct additive_sigma : std::binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/string:48, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/istream:38, + from /usr/include/c++/12/sstream:38, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/error_utils.h:4, + 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, + 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/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/cctbx/xray/f_model.h:4: +/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/miller/match.h:18:20: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] + 18 | typedef std::binary_function base_type; + | ^~~~~~~~~~~~~~~ +/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/miller/match.h:31:27: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] + 31 | struct average : std::binary_function + | ^~~~~~~~~~~~~~~ +/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/miller/match.h:33:20: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] + 33 | typedef std::binary_function base_type; + | ^~~~~~~~~~~~~~~ +/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/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]’ @@ -8014,6 +8074,35 @@ /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/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/boost_python/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 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]::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/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, @@ -8028,14 +8117,6 @@ /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/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 -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 + 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/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]’ @@ -8069,16 +8158,6 @@ /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/sampled_model_density.h:6, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/boost_python/sampled_model_density.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] @@ -8096,69 +8175,15 @@ /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/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, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/boost_python/f_model_bpl.cpp:3: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/miller/match.h:16:34: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] - 16 | struct additive_sigma : std::binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/string:48, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/istream:38, - from /usr/include/c++/12/sstream:38, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/error_utils.h:4, - 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, - 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/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/cctbx/xray/f_model.h:4: -/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/miller/match.h:18:20: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] - 18 | typedef std::binary_function base_type; - | ^~~~~~~~~~~~~~~ -/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/miller/match.h:31:27: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] - 31 | struct average : std::binary_function - | ^~~~~~~~~~~~~~~ -/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/miller/match.h:33:20: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] - 33 | typedef std::binary_function base_type; - | ^~~~~~~~~~~~~~~ -/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/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/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::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/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<>]’ +/usr/include/boost/python/object/value_holder.hpp:131:11: required from ‘boost::python::objects::value_holder::value_holder(PyObject*, A0) [with A0 = boost::python::objects::reference_to_value, scitbx::af::trivial_accessor>&>; Value = cctbx::xray::parameter_map >; PyObject = _object]’ +/usr/include/boost/python/object/make_holder.hpp:94:18: required from ‘static void boost::python::objects::make_holder<1>::apply::execute(PyObject*, t0) [with Holder = boost::python::objects::value_holder > >; ArgList = boost::mpl::vector1, scitbx::af::trivial_accessor>&>; PyObject = _object; t0 = const scitbx::af::const_ref, scitbx::af::trivial_accessor>&]’ +/usr/include/boost/python/detail/make_keyword_range_fn.hpp:63:47: required from ‘boost::python::api::object boost::python::detail::make_keyword_range_constructor(const CallPolicies&, const keyword_range&, Holder*, ArgList*, Arity*) [with ArgList = boost::mpl::vector1, scitbx::af::trivial_accessor>&>; Arity = boost::mpl::size, scitbx::af::trivial_accessor>&> >; Holder = boost::python::objects::value_holder > >; CallPolicies = boost::python::default_call_policies; keyword_range = std::pair]’ +/usr/include/boost/python/init.hpp:311:66: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/usr/include/boost/python/init.hpp:150:67: required from ‘void boost::python::init_base::visit(classT&) const [with classT = boost::python::class_ >, boost::python::detail::not_specified, boost::python::detail::not_specified, boost::python::detail::not_specified>; DerivedT = boost::python::init, scitbx::af::trivial_accessor>&, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_>]’ +/usr/include/boost/python/def_visitor.hpp:31:34: required from ‘static void boost::python::def_visitor_access::visit(const V&, classT&) [with V = boost::python::def_visitor, scitbx::af::trivial_accessor>&, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_> >; classT = boost::python::class_ >, boost::python::detail::not_specified, boost::python::detail::not_specified, boost::python::detail::not_specified>]’ +/usr/include/boost/python/def_visitor.hpp:67:34: required from ‘void boost::python::def_visitor::visit(classT&) const [with classT = boost::python::class_ >, boost::python::detail::not_specified, boost::python::detail::not_specified, boost::python::detail::not_specified>; DerivedVisitor = boost::python::init, scitbx::af::trivial_accessor>&, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_>]’ +/usr/include/boost/python/class.hpp:221:22: required from ‘boost::python::class_::self& boost::python::class_::def(const boost::python::def_visitor&) [with Derived = boost::python::init, scitbx::af::trivial_accessor>&, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_>; W = cctbx::xray::parameter_map >; 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/cctbx/xray/boost_python/parameter_map.cpp:46:11: required from ‘static void cctbx::xray::boost_python::parameter_map_wrapper::wrap(const char*) [with XRayScattererType = cctbx::xray::scatterer<>]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/boost_python/parameter_map.cpp:60:50: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/parameter_map.h:61:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::const_ref, scitbx::af::trivial_accessor>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] + 61 | for(int i_sc=0; i_sc < scatterers.size(); ++i_sc) { + | ~~~~~^~~~~~~~~~~~~~~~~~~ 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, @@ -8223,53 +8250,23 @@ /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/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<>]’ -/usr/include/boost/python/object/value_holder.hpp:131:11: required from ‘boost::python::objects::value_holder::value_holder(PyObject*, A0) [with A0 = boost::python::objects::reference_to_value, scitbx::af::trivial_accessor>&>; Value = cctbx::xray::parameter_map >; PyObject = _object]’ -/usr/include/boost/python/object/make_holder.hpp:94:18: required from ‘static void boost::python::objects::make_holder<1>::apply::execute(PyObject*, t0) [with Holder = boost::python::objects::value_holder > >; ArgList = boost::mpl::vector1, scitbx::af::trivial_accessor>&>; PyObject = _object; t0 = const scitbx::af::const_ref, scitbx::af::trivial_accessor>&]’ -/usr/include/boost/python/detail/make_keyword_range_fn.hpp:63:47: required from ‘boost::python::api::object boost::python::detail::make_keyword_range_constructor(const CallPolicies&, const keyword_range&, Holder*, ArgList*, Arity*) [with ArgList = boost::mpl::vector1, scitbx::af::trivial_accessor>&>; Arity = boost::mpl::size, scitbx::af::trivial_accessor>&> >; Holder = boost::python::objects::value_holder > >; CallPolicies = boost::python::default_call_policies; keyword_range = std::pair]’ -/usr/include/boost/python/init.hpp:311:66: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/usr/include/boost/python/init.hpp:150:67: required from ‘void boost::python::init_base::visit(classT&) const [with classT = boost::python::class_ >, boost::python::detail::not_specified, boost::python::detail::not_specified, boost::python::detail::not_specified>; DerivedT = boost::python::init, scitbx::af::trivial_accessor>&, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_>]’ -/usr/include/boost/python/def_visitor.hpp:31:34: required from ‘static void boost::python::def_visitor_access::visit(const V&, classT&) [with V = boost::python::def_visitor, scitbx::af::trivial_accessor>&, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_> >; classT = boost::python::class_ >, boost::python::detail::not_specified, boost::python::detail::not_specified, boost::python::detail::not_specified>]’ -/usr/include/boost/python/def_visitor.hpp:67:34: required from ‘void boost::python::def_visitor::visit(classT&) const [with classT = boost::python::class_ >, boost::python::detail::not_specified, boost::python::detail::not_specified, boost::python::detail::not_specified>; DerivedVisitor = boost::python::init, scitbx::af::trivial_accessor>&, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_>]’ -/usr/include/boost/python/class.hpp:221:22: required from ‘boost::python::class_::self& boost::python::class_::def(const boost::python::def_visitor&) [with Derived = boost::python::init, scitbx::af::trivial_accessor>&, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_>; W = cctbx::xray::parameter_map >; 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/cctbx/xray/boost_python/parameter_map.cpp:46:11: required from ‘static void cctbx::xray::boost_python::parameter_map_wrapper::wrap(const char*) [with XRayScattererType = cctbx::xray::scatterer<>]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/boost_python/parameter_map.cpp:60:50: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/parameter_map.h:61:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::const_ref, scitbx::af::trivial_accessor>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] - 61 | for(int i_sc=0; i_sc < scatterers.size(); ++i_sc) { - | ~~~~~^~~~~~~~~~~~~~~~~~~ -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 /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(); - | ~~^~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/grouped_data.h: In instantiation of ‘FloatType cctbx::xray::grouped_data::merger::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] + 257 | for (long int ii=0;ii::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 100 | for (int i=0; i::r_abs() [with FloatType = double]’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/boost_python/grouped_data.cpp:69:31: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/grouped_data.h:271:30: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘scitbx::af::shared_plain >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] + 271 | for (long int ii=0;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]’ @@ -8281,35 +8278,6 @@ /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 /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/xray/scatterer.h:5, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/scatterer_utils.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/boost_python/scatterer.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::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] - 257 | for (long int ii=0;ii::r_abs() [with FloatType = double]’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/boost_python/grouped_data.cpp:69:31: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/grouped_data.h:271:30: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘scitbx::af::shared_plain >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] - 271 | for (long int ii=0;ii cctbx::xray::grouped_data::merger::combine_obs(long int) [with FloatType = double]’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/grouped_data.h:258:24: required from ‘FloatType cctbx::xray::grouped_data::merger::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 @@ -8319,13 +8287,6 @@ /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] - 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]’ @@ -8337,7 +8298,20 @@ /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] -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, + 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(); + | ~~^~~~~~~~~~~~~~ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/grouped_data.h: In instantiation of ‘cctbx::xray::grouped_data::unmerged_data::unmerged_data(scitbx::af::const_ref >, scitbx::af::const_ref >, const cctbx::sgtbx::space_group&, const bool&) [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) [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; Value = cctbx::xray::grouped_data::unmerged_data; PyObject = _object]’ /usr/include/boost/python/object/make_holder.hpp:94:18: required from ‘static void boost::python::objects::make_holder<4>::apply::execute(PyObject*, t0, t1, t2, t3) [with Holder = boost::python::objects::value_holder >; ArgList = boost::mpl::vector4 >&, const scitbx::af::const_ref >&, const cctbx::sgtbx::space_group&, const bool&>; PyObject = _object; t0 = const scitbx::af::const_ref >&; t1 = const scitbx::af::const_ref >&; t2 = const cctbx::sgtbx::space_group&; t3 = const bool&]’ @@ -8380,6 +8354,21 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/grouped_data.h:167:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 167 | for (int ii=0; ii::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 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 /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] @@ -8400,8 +8389,6 @@ /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_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 -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 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: @@ -8409,7 +8396,13 @@ /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 class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 49 | std::auto_ptr @@ -8433,7 +8426,18 @@ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ -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/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 +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 /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]’ @@ -8445,6 +8449,18 @@ /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/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/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, @@ -8459,7 +8475,39 @@ /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/sigmaa.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/boost_python/sigmaa.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/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 +g++ -o cctbx/xray/observations/boost_python/observations_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/xray/observations/boost_python/observations_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/xray/scattering_type_registry.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/structure_factors_direct.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/boost_python/structure_factors_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]’ @@ -8494,15 +8541,10 @@ /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/targets/shelxl_wght_ls_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 -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/targets/shelxl_wght_ls_bpl.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/structure_factors_direct.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/boost_python/structure_factors_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::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]’ @@ -8514,7 +8556,6 @@ /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 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 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, @@ -8529,15 +8570,10 @@ /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 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 -g++ -o chiltbx/handle_test -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -pthread chiltbx/handle_test.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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_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 -g++ -o dxtbx/src/dxtbx/boost_python/compression.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-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/boost_python/compression.cc /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/boost_python/compression.cc: In function ‘unsigned int dxtbx::boost_python::cbf_decompress(const char*, std::size_t, int*, std::size_t)’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/boost_python/compression.cc:122:50: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 122 | while ((j < packed_sz) && ((values - original) < values_sz)) { | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ -g++ -o dxtbx/src/dxtbx/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 -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/boost_python/ext.cpp g++ -o dxtbx/src/dxtbx/boost_python/flumpy.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-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 -fvisibility=hidden -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/boost_python/flumpy.cc In file included from /usr/include/boost/assert.hpp:58, from /usr/include/boost/smart_ptr/shared_ptr.hpp:24, @@ -8564,6 +8600,8 @@ /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] +g++ -o dxtbx/src/dxtbx/boost_python/imageset_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 -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/boost_python/imageset_ext.cc +g++ -o dxtbx/src/dxtbx/format/boost_python/cbf_read_buffer.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-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/format/boost_python/cbf_read_buffer.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/twin_targets.h:14, @@ -8626,6 +8664,7 @@ /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/format/boost_python/image_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 -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/format/boost_python/image_ext.cc 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, @@ -8638,16 +8677,6 @@ /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/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] - 128 | CCTBX_ASSERT( index < flags.size() ); -/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/cctbx/xray/twin_targets.h:128:11: note: in expansion of macro ‘CCTBX_ASSERT’ - 128 | CCTBX_ASSERT( index < flags.size() ); - | ^~~~~~~~~~~~ /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()) { @@ -8658,6 +8687,20 @@ /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()) { + | ~~~~~^~~~~~~~~~~~ +/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] + 128 | CCTBX_ASSERT( index < flags.size() ); +/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/cctbx/xray/twin_targets.h:128:11: note: in expansion of macro ‘CCTBX_ASSERT’ + 128 | CCTBX_ASSERT( index < flags.size() ); + | ^~~~~~~~~~~~ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/twin_targets.h: In instantiation of ‘FloatType cctbx::xray::twin_targets::hemihedral_r_values::r_intensity_abs(const scitbx::af::const_ref&, const scitbx::af::const_ref >&, const scitbx::af::const_ref&, const FloatType&) [with FloatType = double]’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/boost_python/twin_targets.cpp:182:39: required from here /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/twin_targets.h:559:31: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘scitbx::af::const_ref::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] @@ -8676,6 +8719,12 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/twin_targets.h:560:6: note: in expansion of macro ‘CCTBX_ASSERT’ 560 | CCTBX_ASSERT( calc_size_ == f_model.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) { + | ~~~~~~~^~~~~ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/twin_targets.h:561:31: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘scitbx::af::const_ref::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 561 | CCTBX_ASSERT( (obs_size_ == selection.size()) || (selection.size()==0) ); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ @@ -8685,10 +8734,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/twin_targets.h:561:6: note: in expansion of macro ‘CCTBX_ASSERT’ 561 | CCTBX_ASSERT( (obs_size_ == selection.size()) || (selection.size()==0) ); | ^~~~~~~~~~~~ -/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()) { - | ~~~~~^~~~~~~~~~~~ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/twin_targets.h: In instantiation of ‘FloatType cctbx::xray::twin_targets::hemihedral_r_values::r_intensity_sq(const scitbx::af::const_ref&, const scitbx::af::const_ref >&, const scitbx::af::const_ref&, const FloatType&) [with FloatType = double]’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/boost_python/twin_targets.cpp:189:38: required from here /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/twin_targets.h:604:30: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘scitbx::af::const_ref::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] @@ -8838,47 +8883,12 @@ /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 /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 ‘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&]’ -/usr/include/boost/python/detail/make_keyword_range_fn.hpp:63:47: required from ‘boost::python::api::object boost::python::detail::make_keyword_range_constructor(const CallPolicies&, const keyword_range&, Holder*, ArgList*, Arity*) [with ArgList = boost::mpl::vector5 >&, const scitbx::af::const_ref >&, const cctbx::sgtbx::space_group&, const bool&, const scitbx::mat3&>; Arity = boost::mpl::size >&, const scitbx::af::const_ref >&, const cctbx::sgtbx::space_group&, const bool&, const scitbx::mat3&> >; Holder = boost::python::objects::value_holder >; CallPolicies = boost::python::default_call_policies; keyword_range = std::pair]’ -/usr/include/boost/python/init.hpp:311:66: required from ‘void boost::python::detail::def_init_aux(ClassT&, const Signature&, NArgs, const CallPoliciesT&, const char*, const keyword_range&) [with ClassT = boost::python::class_ >; CallPoliciesT = boost::python::default_call_policies; Signature = boost::mpl::vector5 >&, const scitbx::af::const_ref >&, const cctbx::sgtbx::space_group&, const bool&, const scitbx::mat3&>; NArgs = boost::mpl::size >&, const scitbx::af::const_ref >&, const cctbx::sgtbx::space_group&, const bool&, const scitbx::mat3&> >; keyword_range = std::pair]’ -/usr/include/boost/python/init.hpp:378:31: required from ‘static void boost::python::detail::define_class_init_helper<0>::apply(ClassT&, const CallPoliciesT&, const Signature&, NArgs, const char*, const boost::python::detail::keyword_range&) [with ClassT = boost::python::class_ >; CallPoliciesT = boost::python::default_call_policies; Signature = boost::mpl::vector5 >&, const scitbx::af::const_ref >&, const cctbx::sgtbx::space_group&, const bool&, const scitbx::mat3&>; NArgs = boost::mpl::size >&, const scitbx::af::const_ref >&, const cctbx::sgtbx::space_group&, const bool&, const scitbx::mat3&> >; boost::python::detail::keyword_range = std::pair]’ -/usr/include/boost/python/init.hpp:150:67: required from ‘void boost::python::init_base::visit(classT&) const [with classT = boost::python::class_ >; DerivedT = boost::python::init >&, const scitbx::af::const_ref >&, const cctbx::sgtbx::space_group&, const bool&, const scitbx::mat3&>]’ -/usr/include/boost/python/def_visitor.hpp:31:34: required from ‘static void boost::python::def_visitor_access::visit(const V&, classT&) [with V = boost::python::def_visitor >&, const scitbx::af::const_ref >&, const cctbx::sgtbx::space_group&, const bool&, const scitbx::mat3&> >; classT = boost::python::class_ >]’ -/usr/include/boost/python/def_visitor.hpp:67:34: required from ‘void boost::python::def_visitor::visit(classT&) const [with classT = boost::python::class_ >; DerivedVisitor = boost::python::init >&, const scitbx::af::const_ref >&, const cctbx::sgtbx::space_group&, const bool&, const scitbx::mat3&>]’ -/usr/include/boost/python/class.hpp:221:22: required from ‘boost::python::class_::self& boost::python::class_::def(const boost::python::def_visitor&) [with Derived = boost::python::init >&, const scitbx::af::const_ref >&, const cctbx::sgtbx::space_group&, const bool&, const scitbx::mat3&>; W = cctbx::xray::twin_targets::hemihedral_r_values; X1 = boost::python::detail::not_specified; X2 = boost::python::detail::not_specified; X3 = boost::python::detail::not_specified; self = boost::python::class_ >]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/boost_python/twin_targets.cpp:169:13: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/twin_targets.h:544:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘scitbx::af::const_ref >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] - 544 | for (long ii=0;ii::refine(const FloatType&) [with FloatType = double]’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/math/quadrature.h:523:14: required from ‘scitbx::math::quadrature::gauss_legendre_engine::gauss_legendre_engine(const int&) [with FloatType = double]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/twin_targets.h:1070:68: required from ‘cctbx::xray::twin_targets::single_twin_likelihood::single_twin_likelihood(const FloatType&, const FloatType&, const FloatType&, const FloatType&, const FloatType&, const FloatType&, const FloatType&, const FloatType&, const bool&, const bool&, const FloatType&, 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, A9, A10, A11, A12, A13) [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 = boost::python::objects::reference_to_value; A6 = boost::python::objects::reference_to_value; A7 = boost::python::objects::reference_to_value; A8 = boost::python::objects::reference_to_value; A9 = boost::python::objects::reference_to_value; A10 = boost::python::objects::reference_to_value; A11 = boost::python::objects::reference_to_value; A12 = boost::python::objects::reference_to_value; A13 = boost::python::objects::reference_to_value; Value = cctbx::xray::twin_targets::single_twin_likelihood; PyObject = _object]’ -/usr/include/boost/python/object/make_holder.hpp:94:18: required from ‘static void boost::python::objects::make_holder<14>::apply::execute(PyObject*, t0, t1, t2, t3, t4, t5, t6, t7, t8, t9, t10, t11, t12, t13) [with Holder = boost::python::objects::value_holder >; ArgList = boost::mpl::vector14; PyObject = _object; t0 = const double&; t1 = const double&; t2 = const double&; t3 = const double&; t4 = const double&; t5 = const double&; t6 = const double&; t7 = const double&; t8 = const bool&; t9 = const bool&; t10 = const double&; t11 = const double&; t12 = const double&; t13 = const int&]’ -/usr/include/boost/python/detail/make_keyword_range_fn.hpp:63:47: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/usr/include/boost/python/init.hpp:378:31: required from ‘static void boost::python::detail::define_class_init_helper<0>::apply(ClassT&, const CallPoliciesT&, const Signature&, NArgs, const char*, const boost::python::detail::keyword_range&) [with ClassT = boost::python::class_ >; CallPoliciesT = boost::python::default_call_policies; Signature = boost::mpl::vector14; NArgs = boost::mpl::size >; boost::python::detail::keyword_range = std::pair]’ -/usr/include/boost/python/init.hpp:150:67: required from ‘void boost::python::init_base::visit(classT&) const [with classT = boost::python::class_ >; DerivedT = boost::python::init]’ -/usr/include/boost/python/def_visitor.hpp:31:34: required from ‘static void boost::python::def_visitor_access::visit(const V&, classT&) [with V = boost::python::def_visitor >; classT = boost::python::class_ >]’ -/usr/include/boost/python/def_visitor.hpp:67:34: required from ‘void boost::python::def_visitor::visit(classT&) const [with classT = boost::python::class_ >; DerivedVisitor = boost::python::init]’ -/usr/include/boost/python/class.hpp:221:22: required from ‘boost::python::class_::self& boost::python::class_::def(const boost::python::def_visitor&) [with Derived = boost::python::init; W = cctbx::xray::twin_targets::single_twin_likelihood; X1 = boost::python::detail::not_specified; X2 = boost::python::detail::not_specified; X3 = boost::python::detail::not_specified; self = boost::python::class_ >]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/boost_python/twin_targets.cpp:343:14: required from here -/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 instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +g++ -o dxtbx/src/dxtbx/masking/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 -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/masking/boost_python/ext.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, @@ -8916,6 +8927,36 @@ /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/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&]’ +/usr/include/boost/python/detail/make_keyword_range_fn.hpp:63:47: required from ‘boost::python::api::object boost::python::detail::make_keyword_range_constructor(const CallPolicies&, const keyword_range&, Holder*, ArgList*, Arity*) [with ArgList = boost::mpl::vector5 >&, const scitbx::af::const_ref >&, const cctbx::sgtbx::space_group&, const bool&, const scitbx::mat3&>; Arity = boost::mpl::size >&, const scitbx::af::const_ref >&, const cctbx::sgtbx::space_group&, const bool&, const scitbx::mat3&> >; Holder = boost::python::objects::value_holder >; CallPolicies = boost::python::default_call_policies; keyword_range = std::pair]’ +/usr/include/boost/python/init.hpp:311:66: required from ‘void boost::python::detail::def_init_aux(ClassT&, const Signature&, NArgs, const CallPoliciesT&, const char*, const keyword_range&) [with ClassT = boost::python::class_ >; CallPoliciesT = boost::python::default_call_policies; Signature = boost::mpl::vector5 >&, const scitbx::af::const_ref >&, const cctbx::sgtbx::space_group&, const bool&, const scitbx::mat3&>; NArgs = boost::mpl::size >&, const scitbx::af::const_ref >&, const cctbx::sgtbx::space_group&, const bool&, const scitbx::mat3&> >; keyword_range = std::pair]’ +/usr/include/boost/python/init.hpp:378:31: required from ‘static void boost::python::detail::define_class_init_helper<0>::apply(ClassT&, const CallPoliciesT&, const Signature&, NArgs, const char*, const boost::python::detail::keyword_range&) [with ClassT = boost::python::class_ >; CallPoliciesT = boost::python::default_call_policies; Signature = boost::mpl::vector5 >&, const scitbx::af::const_ref >&, const cctbx::sgtbx::space_group&, const bool&, const scitbx::mat3&>; NArgs = boost::mpl::size >&, const scitbx::af::const_ref >&, const cctbx::sgtbx::space_group&, const bool&, const scitbx::mat3&> >; boost::python::detail::keyword_range = std::pair]’ +/usr/include/boost/python/init.hpp:150:67: required from ‘void boost::python::init_base::visit(classT&) const [with classT = boost::python::class_ >; DerivedT = boost::python::init >&, const scitbx::af::const_ref >&, const cctbx::sgtbx::space_group&, const bool&, const scitbx::mat3&>]’ +/usr/include/boost/python/def_visitor.hpp:31:34: required from ‘static void boost::python::def_visitor_access::visit(const V&, classT&) [with V = boost::python::def_visitor >&, const scitbx::af::const_ref >&, const cctbx::sgtbx::space_group&, const bool&, const scitbx::mat3&> >; classT = boost::python::class_ >]’ +/usr/include/boost/python/def_visitor.hpp:67:34: required from ‘void boost::python::def_visitor::visit(classT&) const [with classT = boost::python::class_ >; DerivedVisitor = boost::python::init >&, const scitbx::af::const_ref >&, const cctbx::sgtbx::space_group&, const bool&, const scitbx::mat3&>]’ +/usr/include/boost/python/class.hpp:221:22: required from ‘boost::python::class_::self& boost::python::class_::def(const boost::python::def_visitor&) [with Derived = boost::python::init >&, const scitbx::af::const_ref >&, const cctbx::sgtbx::space_group&, const bool&, const scitbx::mat3&>; W = cctbx::xray::twin_targets::hemihedral_r_values; X1 = boost::python::detail::not_specified; X2 = boost::python::detail::not_specified; X3 = boost::python::detail::not_specified; self = boost::python::class_ >]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/boost_python/twin_targets.cpp:169:13: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/twin_targets.h:544:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘scitbx::af::const_ref >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] + 544 | for (long ii=0;ii::refine(const FloatType&) [with FloatType = double]’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/math/quadrature.h:523:14: required from ‘scitbx::math::quadrature::gauss_legendre_engine::gauss_legendre_engine(const int&) [with FloatType = double]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/twin_targets.h:1070:68: required from ‘cctbx::xray::twin_targets::single_twin_likelihood::single_twin_likelihood(const FloatType&, const FloatType&, const FloatType&, const FloatType&, const FloatType&, const FloatType&, const FloatType&, const FloatType&, const bool&, const bool&, const FloatType&, 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, A9, A10, A11, A12, A13) [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 = boost::python::objects::reference_to_value; A6 = boost::python::objects::reference_to_value; A7 = boost::python::objects::reference_to_value; A8 = boost::python::objects::reference_to_value; A9 = boost::python::objects::reference_to_value; A10 = boost::python::objects::reference_to_value; A11 = boost::python::objects::reference_to_value; A12 = boost::python::objects::reference_to_value; A13 = boost::python::objects::reference_to_value; Value = cctbx::xray::twin_targets::single_twin_likelihood; PyObject = _object]’ +/usr/include/boost/python/object/make_holder.hpp:94:18: required from ‘static void boost::python::objects::make_holder<14>::apply::execute(PyObject*, t0, t1, t2, t3, t4, t5, t6, t7, t8, t9, t10, t11, t12, t13) [with Holder = boost::python::objects::value_holder >; ArgList = boost::mpl::vector14; PyObject = _object; t0 = const double&; t1 = const double&; t2 = const double&; t3 = const double&; t4 = const double&; t5 = const double&; t6 = const double&; t7 = const double&; t8 = const bool&; t9 = const bool&; t10 = const double&; t11 = const double&; t12 = const double&; t13 = const int&]’ +/usr/include/boost/python/detail/make_keyword_range_fn.hpp:63:47: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/usr/include/boost/python/init.hpp:378:31: required from ‘static void boost::python::detail::define_class_init_helper<0>::apply(ClassT&, const CallPoliciesT&, const Signature&, NArgs, const char*, const boost::python::detail::keyword_range&) [with ClassT = boost::python::class_ >; CallPoliciesT = boost::python::default_call_policies; Signature = boost::mpl::vector14; NArgs = boost::mpl::size >; boost::python::detail::keyword_range = std::pair]’ +/usr/include/boost/python/init.hpp:150:67: required from ‘void boost::python::init_base::visit(classT&) const [with classT = boost::python::class_ >; DerivedT = boost::python::init]’ +/usr/include/boost/python/def_visitor.hpp:31:34: required from ‘static void boost::python::def_visitor_access::visit(const V&, classT&) [with V = boost::python::def_visitor >; classT = boost::python::class_ >]’ +/usr/include/boost/python/def_visitor.hpp:67:34: required from ‘void boost::python::def_visitor::visit(classT&) const [with classT = boost::python::class_ >; DerivedVisitor = boost::python::init]’ +/usr/include/boost/python/class.hpp:221:22: required from ‘boost::python::class_::self& boost::python::class_::def(const boost::python::def_visitor&) [with Derived = boost::python::init; W = cctbx::xray::twin_targets::single_twin_likelihood; X1 = boost::python::detail::not_specified; X2 = boost::python::detail::not_specified; X3 = boost::python::detail::not_specified; self = boost::python::class_ >]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/cctbx/xray/boost_python/twin_targets.cpp:343:14: required from here +/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( + | ^~~~~~~~~~~~~~~~~~~~ +/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/boost_python/imageset_ext.cc: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("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +/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; + | ^~~~~~~ +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/imageset.h:24, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/boost_python/imageset_ext.cc:9: +/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) { + | ~~^~~~ +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/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 @@ -8956,6 +9077,75 @@ /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/scan.h:22, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/imageset.h:26: +/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_; + | ^~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/scan.h:502:9: warning: ‘int dxtbx::model::Scan::batch_offset_’ [-Wreorder] + 502 | int batch_offset_; + | ^~~~~~~~~~~~~ +/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 /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, + 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/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/dxtbx/src/dxtbx/boost_python/imageset_ext.cc:6: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/scan.h: In constructor ‘dxtbx::model::Scan::Scan(scitbx::vec2, scitbx::vec2, const scitbx::af::shared&, const scitbx::af::shared&, int)’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/scan.h:99:43: warning: comparison of integer expressions of different signedness: ‘scitbx::af::shared_plain::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 99 | DXTBX_ASSERT(exposure_times_.size() == num_images_); + | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +/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/scan.h:99:7: note: in expansion of macro ‘DXTBX_ASSERT’ + 99 | DXTBX_ASSERT(exposure_times_.size() == num_images_); + | ^~~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/scan.h:100:35: warning: comparison of integer expressions of different signedness: ‘scitbx::af::shared_plain::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 100 | DXTBX_ASSERT(epochs_.size() == num_images_); + | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +/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/scan.h:100:7: note: in expansion of macro ‘DXTBX_ASSERT’ + 100 | DXTBX_ASSERT(epochs_.size() == num_images_); + | ^~~~~~~~~~~~ +/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_); + | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +/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/scan.h:231:7: note: in expansion of macro ‘DXTBX_ASSERT’ + 231 | DXTBX_ASSERT(exposure_times.size() == num_images_); + | ^~~~~~~~~~~~ +/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_); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +/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/scan.h:237:7: note: in expansion of macro ‘DXTBX_ASSERT’ + 237 | DXTBX_ASSERT(epochs.size() == num_images_); + | ^~~~~~~~~~~~ +/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.") + | ^~~~~~~~~~~~~~~~~~~~ /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]’ @@ -8976,6 +9166,26 @@ /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 /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/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( + | ^~~~~~~~~~~~~~~~~~~~ +/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/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]’ @@ -8996,6 +9206,23 @@ /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 /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/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( + | ^~~~~~~~~~~~~~~~~~~~ /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]’ @@ -9006,6 +9233,9 @@ /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/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/boost_python/flumpy.cc: In instantiation of ‘pybind11::buffer_info get_buffer_specific(grid) [with T = long 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]’ @@ -9116,18 +9346,57 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:190:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 190 | for (int j = i + 1; j < dim_sizes.size(); ++j) { | ~~^~~~~~~~~~~~~~~~~~ -g++ -o dxtbx/src/dxtbx/boost_python/imageset_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 -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/boost_python/imageset_ext.cc -g++ -o dxtbx/src/dxtbx/format/boost_python/cbf_read_buffer.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-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/format/boost_python/cbf_read_buffer.cpp -g++ -o dxtbx/src/dxtbx/format/boost_python/image_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 -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/format/boost_python/image_ext.cc -g++ -o dxtbx/src/dxtbx/format/boost_python/nexus_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 -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/format/boost_python/nexus_ext.cc -g++ -o dxtbx/src/dxtbx/masking/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 -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/masking/boost_python/ext.cc -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 -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 -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 -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 -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 +/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/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/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] +In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/masking/goniometer_shadow_masking.h:13, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/imageset.h:29: +/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/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]’ +/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: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] + 100 | for (std::size_t i = 0; i < boost::python::len(tile_list); ++i) { + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/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 = int]’: +/usr/include/boost/python/class.hpp:345:9: required from ‘boost::python::class_::self& boost::python::class_::def_pickle(const PickleSuiteType&) [with PickleSuiteType = dxtbx::format::boost_python::ImagePickleSuite; W = dxtbx::format::Image; X1 = boost::python::detail::not_specified; X2 = boost::python::detail::not_specified; X3 = boost::python::detail::not_specified; self = boost::python::class_, boost::python::detail::not_specified, boost::python::detail::not_specified, boost::python::detail::not_specified>]’ +/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 = 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: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/format/boost_python/image_ext.cc: In instantiation of ‘static void dxtbx::format::boost_python::ImagePickleSuite::setstate(dxtbx::format::Image&, boost::python::tuple) [with T = double]’: +/usr/include/boost/python/class.hpp:345:9: required from ‘boost::python::class_::self& boost::python::class_::def_pickle(const PickleSuiteType&) [with PickleSuiteType = dxtbx::format::boost_python::ImagePickleSuite; W = dxtbx::format::Image; X1 = boost::python::detail::not_specified; X2 = boost::python::detail::not_specified; X3 = boost::python::detail::not_specified; self = boost::python::class_, boost::python::detail::not_specified, boost::python::detail::not_specified, boost::python::detail::not_specified>]’ +/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] 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, @@ -9141,7 +9410,7 @@ 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/dxtbx/src/dxtbx/format/boost_python/image_ext.cc: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( | ^~~~~~~~~~~~~~~~~~~~ @@ -9161,14 +9430,173 @@ 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: + 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("") | ^~~~~~~~~~~~~~~~~~~~~~~ -g++ -o dxtbx/src/dxtbx/model/boost_python/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 -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/model_ext.cc +/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) { + | ~~~~~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/imageset.h: In member function ‘dxtbx::format::Image dxtbx::ImageSet::get_raw_data_as_double(std::size_t)’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/imageset.h:1114:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 1114 | if (double_raw_data_cache_.index == index) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/imageset.h: In constructor ‘dxtbx::ImageGrid::ImageGrid(const dxtbx::ImageSetData&, scitbx::af::int2)’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/imageset.h:1137:46: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 1137 | DXTBX_ASSERT(grid_size[0] * grid_size[1] == size()); +/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/imageset.h:1137:5: note: in expansion of macro ‘DXTBX_ASSERT’ + 1137 | DXTBX_ASSERT(grid_size[0] * grid_size[1] == size()); + | ^~~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/imageset.h: In constructor ‘dxtbx::ImageGrid::ImageGrid(const dxtbx::ImageSetData&, const scitbx::af::const_ref&, scitbx::af::int2)’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/imageset.h:1151:46: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 1151 | DXTBX_ASSERT(grid_size[0] * grid_size[1] == size()); +/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/imageset.h:1151:5: note: in expansion of macro ‘DXTBX_ASSERT’ + 1151 | DXTBX_ASSERT(grid_size[0] * grid_size[1] == size()); + | ^~~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/imageset.h: In constructor ‘dxtbx::ImageSequence::ImageSequence(const dxtbx::ImageSetData&, const dxtbx::ImageSet::beam_ptr&, const dxtbx::ImageSet::detector_ptr&, const dxtbx::ImageSet::goniometer_ptr&, const dxtbx::ImageSet::scan_ptr&)’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/imageset.h:1236:23: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 1236 | if (data.size() != scan->get_num_images()) { + | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/imageset.h: In constructor ‘dxtbx::ImageSequence::ImageSequence(const dxtbx::ImageSetData&, const scitbx::af::const_ref&, const dxtbx::ImageSet::beam_ptr&, const dxtbx::ImageSet::detector_ptr&, const dxtbx::ImageSet::goniometer_ptr&, const dxtbx::ImageSet::scan_ptr&)’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/imageset.h:1275:26: warning: comparison of integer expressions of different signedness: ‘scitbx::af::const_ref::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 1275 | if (indices.size() != scan->get_num_images()) { + | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/imageset.h: In member function ‘void dxtbx::ImageSequence::set_scan(const dxtbx::ImageSet::scan_ptr&)’: +/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()) { + | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ +/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()); + | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ +/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/imageset.h:1413:5: note: in expansion of macro ‘DXTBX_ASSERT’ + 1413 | DXTBX_ASSERT(scan->get_num_images() == size()); + | ^~~~~~~~~~~~ +/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] + 500 | for (std::size_t i = 0; i < boost::python::len(obj); ++i) { + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ +/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 = float]’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/imageset.h:469:55: 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] +/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 = int]’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/imageset.h:471:53: 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] +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/boost_python/imageset_ext.cc: In instantiation of ‘static void dxtbx::boost_python::ImageSetDataPickleSuite::set_model_list(dxtbx::ImageSetData&, boost::python::tuple, Func) [with Model = dxtbx::model::BeamBase; Func = void (dxtbx::ImageSetData::*)(const boost::shared_ptr&, long unsigned int)]’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/boost_python/imageset_ext.cc:250:56: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/boost_python/imageset_ext.cc:232:33: 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] + 232 | for (std::size_t i = 0; i < boost::python::len(models); ++i) { + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/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) { + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/boost_python/imageset_ext.cc: In instantiation of ‘static void dxtbx::boost_python::ImageSetDataPickleSuite::set_model_list(dxtbx::ImageSetData&, boost::python::tuple, Func) [with Model = dxtbx::model::Detector; Func = void (dxtbx::ImageSetData::*)(const boost::shared_ptr&, long unsigned int)]’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/boost_python/imageset_ext.cc:254:56: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/boost_python/imageset_ext.cc:232:33: 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] + 232 | for (std::size_t i = 0; i < boost::python::len(models); ++i) { + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/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) { + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/boost_python/imageset_ext.cc: In instantiation of ‘static void dxtbx::boost_python::ImageSetDataPickleSuite::set_model_list(dxtbx::ImageSetData&, boost::python::tuple, Func) [with Model = dxtbx::model::Goniometer; Func = void (dxtbx::ImageSetData::*)(const boost::shared_ptr&, long unsigned int)]’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/boost_python/imageset_ext.cc:258:58: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/boost_python/imageset_ext.cc:232:33: 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] + 232 | for (std::size_t i = 0; i < boost::python::len(models); ++i) { + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/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) { + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/boost_python/imageset_ext.cc: In instantiation of ‘static void dxtbx::boost_python::ImageSetDataPickleSuite::set_model_list(dxtbx::ImageSetData&, boost::python::tuple, Func) [with Model = dxtbx::model::Scan; Func = void (dxtbx::ImageSetData::*)(const boost::shared_ptr&, long unsigned int)]’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/boost_python/imageset_ext.cc:262:52: required from here +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/boost_python/imageset_ext.cc:232:33: 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] + 232 | for (std::size_t i = 0; i < boost::python::len(models); ++i) { + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/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/model/boost_python/detector.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 /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/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/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/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, @@ -9183,16 +9611,57 @@ 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; +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/experiment.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/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/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/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_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.") + | ^~~~~~~~~~~~~~~~~~~~ +/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/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) { @@ -9262,144 +9731,9 @@ /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/format/boost_python/cbf_read_buffer.cpp: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( - | ^~~~~~~~~~~~~~~~~~~~ -/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 = 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] -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/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("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -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/detector.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 ‘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]’ -/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: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] - 100 | for (std::size_t i = 0; i < boost::python::len(tile_list); ++i) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/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/boost_python/imageset_ext.cc: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( - | ^~~~~~~~~~~~~~~~~~~~ -/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 = int]’: -/usr/include/boost/python/class.hpp:345:9: required from ‘boost::python::class_::self& boost::python::class_::def_pickle(const PickleSuiteType&) [with PickleSuiteType = dxtbx::format::boost_python::ImagePickleSuite; W = dxtbx::format::Image; X1 = boost::python::detail::not_specified; X2 = boost::python::detail::not_specified; X3 = boost::python::detail::not_specified; self = boost::python::class_, boost::python::detail::not_specified, boost::python::detail::not_specified, boost::python::detail::not_specified>]’ -/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 = 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: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/format/boost_python/cbf_read_buffer.cpp:11:1: warning: ‘typedef’ was ignored in this declaration - 11 | typedef struct cbf_handle_struct; - | ^~~~~~~ -/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 ‘static void dxtbx::format::boost_python::ImagePickleSuite::setstate(dxtbx::format::Image&, boost::python::tuple) [with T = double]’: -/usr/include/boost/python/class.hpp:345:9: required from ‘boost::python::class_::self& boost::python::class_::def_pickle(const PickleSuiteType&) [with PickleSuiteType = dxtbx::format::boost_python::ImagePickleSuite; W = dxtbx::format::Image; X1 = boost::python::detail::not_specified; X2 = boost::python::detail::not_specified; X3 = boost::python::detail::not_specified; self = boost::python::class_, boost::python::detail::not_specified, boost::python::detail::not_specified, boost::python::detail::not_specified>]’ -/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] -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/experiment.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/model/detector.h:27, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/experiment.h:23, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/experiment.cc:16: + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/detector.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; @@ -9427,8 +9761,30 @@ /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 dxtbx/src/dxtbx/model/boost_python/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 -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/model_ext.cc +/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) { + | ~~^~~~~~~~~~~~~~~~~~~~~~~ +/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_list(dxtbx::model::Beam&, boost::python::list)’: +/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) { + | ~~^~~~~~~~~~~~~~~~~~~~~~~ +/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/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: + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/to_from_dict.h:20, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/detector.cc:22: /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) { @@ -9443,20 +9799,11 @@ /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() | ^~~~ -/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) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~ -/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_list(dxtbx::model::Beam&, boost::python::list)’: -/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) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~ 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, - 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/dxtbx/src/dxtbx/model/experiment.h:19: + 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/dxtbx/src/dxtbx/model/boost_python/detector.cc:17: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/scan.h: In constructor ‘dxtbx::model::Scan::Scan(scitbx::vec2, scitbx::vec2, const scitbx::af::shared&, const scitbx::af::shared&, int)’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/scan.h:99:43: warning: comparison of integer expressions of different signedness: ‘scitbx::af::shared_plain::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 99 | DXTBX_ASSERT(exposure_times_.size() == num_images_); @@ -9498,8 +9845,8 @@ | ^~~~~~~~~~~~ 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, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/boost_python/imageset_ext.cc:9: + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/experiment.h:23, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/experiment.cc:16: /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; @@ -9527,8 +9874,9 @@ /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 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 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/imageset.h:26: + 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) { @@ -9547,9 +9895,8 @@ 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, 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/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/dxtbx/src/dxtbx/boost_python/imageset_ext.cc:6: + 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/dxtbx/src/dxtbx/model/experiment.h:19: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/scan.h: In constructor ‘dxtbx::model::Scan::Scan(scitbx::vec2, scitbx::vec2, const scitbx::af::shared&, const scitbx::af::shared&, int)’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/scan.h:99:43: warning: comparison of integer expressions of different signedness: ‘scitbx::af::shared_plain::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 99 | DXTBX_ASSERT(exposure_times_.size() == num_images_); @@ -9589,13 +9936,6 @@ /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_); | ^~~~~~~~~~~~ -/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, @@ -9609,13 +9949,92 @@ 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: + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/experiment_list.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("") | ^~~~~~~~~~~~~~~~~~~~~~~ +/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/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 /usr/include/boost/assert.hpp:58, + from /usr/include/boost/variant/detail/forced_return.hpp:17, + from /usr/include/boost/variant/variant.hpp:29, + from /usr/include/boost/variant.hpp:17, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/format/image.h:16, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/to_from_dict.h:22: +/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 = 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] + 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 = 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] +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]’: +/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 = dxtbx::model::Beam; 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 = dxtbx::model::Beam; 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 = 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/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 = dxtbx::model::Beam]’: +/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::Beam; 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 = dxtbx::model::Beam; 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 = 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/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 ‘void scitbx::af::detail::copy_to_slice_detail(scitbx::af::versa >&, scitbx::af::small, const scitbx::af::const_ref >&) [with T = dxtbx::model::Beam]’: +/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::Beam]’ +/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::Beam; 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 = dxtbx::model::Beam; 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 = 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/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/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/detector.cc:21: + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/experiment.h:23, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/experiment_list.h:23, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/experiment_list.cc:19: /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; @@ -9649,9 +10081,6 @@ /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; -/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/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’: @@ -9659,19 +10088,6 @@ 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 /usr/include/boost/assert.hpp:58, - from /usr/include/boost/variant/detail/forced_return.hpp:17, - from /usr/include/boost/variant/variant.hpp:29, - from /usr/include/boost/variant.hpp:17, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/format/image.h:16, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/to_from_dict.h:22: -/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 = 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] - 197 | if (!is_range) assert(i == obj_size); - | ~~^~~~~~~~~~~ /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) { @@ -9679,32 +10095,8 @@ /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/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 = 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] -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]’: -/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 = dxtbx::model::Beam; 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 = dxtbx::model::Beam; 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 = 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/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 = dxtbx::model::Beam]’: -/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::Beam; 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 = dxtbx::model::Beam; 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 = 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/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 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) { @@ -9720,10 +10112,11 @@ 39 | Scan() | ^~~~ 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/dxtbx/src/dxtbx/model/boost_python/detector.cc:17: + 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, + 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/dxtbx/src/dxtbx/model/experiment_list.h:20: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/scan.h: In constructor ‘dxtbx::model::Scan::Scan(scitbx::vec2, scitbx::vec2, const scitbx::af::shared&, const scitbx::af::shared&, int)’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/scan.h:99:43: warning: comparison of integer expressions of different signedness: ‘scitbx::af::shared_plain::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 99 | DXTBX_ASSERT(exposure_times_.size() == num_images_); @@ -9763,32 +10156,10 @@ /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/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 = dxtbx::model::Beam]’: -/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::Beam]’ -/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::Beam; 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 = dxtbx::model::Beam; 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 = 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/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/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 -/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/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, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/experiment_list.h:23, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/experiment_list.cc:19: + 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; @@ -9809,28 +10180,6 @@ 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/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/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) { @@ -9838,29 +10187,28 @@ /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 ‘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) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/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/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/scan.h:22, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/experiment.h:25: + 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) { @@ -9880,7 +10228,8 @@ 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/dxtbx/src/dxtbx/model/experiment_list.h:20: + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/goniometer.h:15, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/goniometer.cc:18: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/scan.h: In constructor ‘dxtbx::model::Scan::Scan(scitbx::vec2, scitbx::vec2, const scitbx::af::shared&, const scitbx::af::shared&, int)’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/scan.h:99:43: warning: comparison of integer expressions of different signedness: ‘scitbx::af::shared_plain::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 99 | DXTBX_ASSERT(exposure_times_.size() == num_images_); @@ -9933,14 +10282,23 @@ 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: + 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/goniometer.cc: In function ‘void dxtbx::model::boost_python::Goniometer_set_S_at_scan_points_from_tuple(dxtbx::model::Goniometer&, boost::python::tuple)’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/goniometer.cc:78:31: 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] + 78 | 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/goniometer.cc: In function ‘void dxtbx::model::boost_python::Goniometer_set_S_at_scan_points_from_list(dxtbx::model::Goniometer&, boost::python::list)’: +/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) { + | ~~^~~~~~~~~~~~~~~~~~~~~~~ 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 +g++ -o dxtbx/src/dxtbx/model/boost_python/parallax_correction.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-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/parallax_correction.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, @@ -9954,13 +10312,14 @@ 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/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/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 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, @@ -9974,50 +10333,19 @@ 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: + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/multi_axis_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) { - | ~~^~~~~~~~~~~~~~ -g++ -o dxtbx/src/dxtbx/model/boost_python/parallax_correction.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-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/parallax_correction.cc -In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/masking/goniometer_shadow_masking.h:13, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/imageset.h:29: -/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/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) { + | ~~^~~~~~~~~~~~~~~~~~~~~~~ +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, @@ -10031,7 +10359,47 @@ 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: + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/panel.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 /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/parallax_correction.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 /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/pixel_to_millimeter.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( | ^~~~~~~~~~~~~~~~~~~~ @@ -10039,9 +10407,7 @@ 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, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/goniometer.cc:21: + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/panel.cc:19: /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; @@ -10070,8 +10436,7 @@ 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/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: + 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’: /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; @@ -10100,7 +10465,8 @@ 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: + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/to_from_dict.h:20, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/panel.cc: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) { @@ -10116,12 +10482,10 @@ 39 | Scan() | ^~~~ 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, - 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/dxtbx/src/dxtbx/model/goniometer.h:15, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/goniometer.cc:18: + 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/dxtbx/src/dxtbx/model/boost_python/panel.cc:17: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/scan.h: In constructor ‘dxtbx::model::Scan::Scan(scitbx::vec2, scitbx::vec2, const scitbx::af::shared&, const scitbx::af::shared&, int)’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/scan.h:99:43: warning: comparison of integer expressions of different signedness: ‘scitbx::af::shared_plain::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 99 | DXTBX_ASSERT(exposure_times_.size() == num_images_); @@ -10161,128 +10525,7 @@ /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/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.") - | ^~~~~~~~~~~~~~~~~~~~ -/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) { - | ~~~~~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/imageset.h: In member function ‘dxtbx::format::Image dxtbx::ImageSet::get_raw_data_as_double(std::size_t)’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/imageset.h:1114:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 1114 | if (double_raw_data_cache_.index == index) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/imageset.h: In constructor ‘dxtbx::ImageGrid::ImageGrid(const dxtbx::ImageSetData&, scitbx::af::int2)’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/imageset.h:1137:46: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 1137 | DXTBX_ASSERT(grid_size[0] * grid_size[1] == size()); -/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/imageset.h:1137:5: note: in expansion of macro ‘DXTBX_ASSERT’ - 1137 | DXTBX_ASSERT(grid_size[0] * grid_size[1] == size()); - | ^~~~~~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/imageset.h: In constructor ‘dxtbx::ImageGrid::ImageGrid(const dxtbx::ImageSetData&, const scitbx::af::const_ref&, scitbx::af::int2)’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/imageset.h:1151:46: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 1151 | DXTBX_ASSERT(grid_size[0] * grid_size[1] == size()); -/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/imageset.h:1151:5: note: in expansion of macro ‘DXTBX_ASSERT’ - 1151 | DXTBX_ASSERT(grid_size[0] * grid_size[1] == size()); - | ^~~~~~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/imageset.h: In constructor ‘dxtbx::ImageSequence::ImageSequence(const dxtbx::ImageSetData&, const dxtbx::ImageSet::beam_ptr&, const dxtbx::ImageSet::detector_ptr&, const dxtbx::ImageSet::goniometer_ptr&, const dxtbx::ImageSet::scan_ptr&)’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/imageset.h:1236:23: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 1236 | if (data.size() != scan->get_num_images()) { - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/imageset.h: In constructor ‘dxtbx::ImageSequence::ImageSequence(const dxtbx::ImageSetData&, const scitbx::af::const_ref&, const dxtbx::ImageSet::beam_ptr&, const dxtbx::ImageSet::detector_ptr&, const dxtbx::ImageSet::goniometer_ptr&, const dxtbx::ImageSet::scan_ptr&)’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/imageset.h:1275:26: warning: comparison of integer expressions of different signedness: ‘scitbx::af::const_ref::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 1275 | if (indices.size() != scan->get_num_images()) { - | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/imageset.h: In member function ‘void dxtbx::ImageSequence::set_scan(const dxtbx::ImageSet::scan_ptr&)’: -/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()) { - | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ -/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()); - | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ -/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/imageset.h:1413:5: note: in expansion of macro ‘DXTBX_ASSERT’ - 1413 | DXTBX_ASSERT(scan->get_num_images() == size()); - | ^~~~~~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/goniometer.cc: In function ‘void dxtbx::model::boost_python::Goniometer_set_S_at_scan_points_from_tuple(dxtbx::model::Goniometer&, boost::python::tuple)’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/goniometer.cc:78:31: 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] - 78 | 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/goniometer.cc: In function ‘void dxtbx::model::boost_python::Goniometer_set_S_at_scan_points_from_list(dxtbx::model::Goniometer&, boost::python::list)’: -/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/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] - 500 | for (std::size_t i = 0; i < boost::python::len(obj); ++i) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ -/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 = float]’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/imageset.h:469:55: 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] -/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 = int]’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/imageset.h:471:53: 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] -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/boost_python/imageset_ext.cc: In instantiation of ‘static void dxtbx::boost_python::ImageSetDataPickleSuite::set_model_list(dxtbx::ImageSetData&, boost::python::tuple, Func) [with Model = dxtbx::model::BeamBase; Func = void (dxtbx::ImageSetData::*)(const boost::shared_ptr&, long unsigned int)]’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/boost_python/imageset_ext.cc:250:56: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/boost_python/imageset_ext.cc:232:33: 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] - 232 | for (std::size_t i = 0; i < boost::python::len(models); ++i) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/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) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/boost_python/imageset_ext.cc: In instantiation of ‘static void dxtbx::boost_python::ImageSetDataPickleSuite::set_model_list(dxtbx::ImageSetData&, boost::python::tuple, Func) [with Model = dxtbx::model::Detector; Func = void (dxtbx::ImageSetData::*)(const boost::shared_ptr&, long unsigned int)]’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/boost_python/imageset_ext.cc:254:56: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/boost_python/imageset_ext.cc:232:33: 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] - 232 | for (std::size_t i = 0; i < boost::python::len(models); ++i) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/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) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/boost_python/imageset_ext.cc: In instantiation of ‘static void dxtbx::boost_python::ImageSetDataPickleSuite::set_model_list(dxtbx::ImageSetData&, boost::python::tuple, Func) [with Model = dxtbx::model::Goniometer; Func = void (dxtbx::ImageSetData::*)(const boost::shared_ptr&, long unsigned int)]’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/boost_python/imageset_ext.cc:258:58: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/boost_python/imageset_ext.cc:232:33: 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] - 232 | for (std::size_t i = 0; i < boost::python::len(models); ++i) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/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) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/boost_python/imageset_ext.cc: In instantiation of ‘static void dxtbx::boost_python::ImageSetDataPickleSuite::set_model_list(dxtbx::ImageSetData&, boost::python::tuple, Func) [with Model = dxtbx::model::Scan; Func = void (dxtbx::ImageSetData::*)(const boost::shared_ptr&, long unsigned int)]’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/boost_python/imageset_ext.cc:262:52: required from here -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/boost_python/imageset_ext.cc:232:33: 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] - 232 | for (std::size_t i = 0; i < boost::python::len(models); ++i) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/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) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/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/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, @@ -10296,13 +10539,10 @@ 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/panel.cc:11: + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/scan.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 /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, @@ -10316,70 +10556,19 @@ 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/multi_axis_goniometer.cc:11: + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/scan_helpers.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 /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/parallax_correction.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/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 -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/panel.cc:19: -/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) { - | ~~^~~~ -/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) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~ +g++ -o lib/libcbf-private.so.0.0.1 -shared -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-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/x86_64-linux-gnu -Llib -L/build/reproducible-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/x86_64-linux-gnu/hdf5/serial -lboost_thread -lboost_system -lhdf5 -lcbf 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, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/panel.cc:20: + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/scan.cc:18: /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) { @@ -10395,10 +10584,11 @@ 39 | Scan() | ^~~~ 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/dxtbx/src/dxtbx/model/boost_python/panel.cc:17: + 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, + 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/vec2.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/scan.h:17: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/scan.h: In constructor ‘dxtbx::model::Scan::Scan(scitbx::vec2, scitbx::vec2, const scitbx::af::shared&, const scitbx::af::shared&, int)’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/scan.h:99:43: warning: comparison of integer expressions of different signedness: ‘scitbx::af::shared_plain::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 99 | DXTBX_ASSERT(exposure_times_.size() == num_images_); @@ -10438,31 +10628,19 @@ /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/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, - 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/pixel_to_millimeter.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("") - | ^~~~~~~~~~~~~~~~~~~~~~~ +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' +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 exe_dev/cbflib.tst_memory -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -pthread cbflib_adaptbx/detectors/tst_memory.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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/x86_64-linux-gnu/hdf5/serial -lcbf -lcbf-private -lm -lhdf5 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: + 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/scan.cc:20: /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; @@ -10490,6 +10668,29 @@ /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/x86_64-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/x86_64-linux-gnu -Llib -L/build/reproducible-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/x86_64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -pthread cctbx/examples/find_distances.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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 +/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) { + | ~~^~~~~~~~~~~~ +g++ -o exe_dev/cctbx.getting_started -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -pthread cctbx/examples/getting_started.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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 +/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 exe_dev/cctbx.lattice_symmetry -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -pthread cctbx/examples/lattice_symmetry.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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/x86_64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -pthread cctbx/examples/sym_equiv_sites.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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/x86_64-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/x86_64-linux-gnu -Llib -L/build/reproducible-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 +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 +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 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, @@ -10510,26 +10711,7 @@ /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 /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/scan_helpers.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 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 /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, @@ -10561,11 +10743,8 @@ /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/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 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)’: @@ -10642,108 +10821,45 @@ 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/scan.cc: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/scan.h:22, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/boost_python/scan.cc:18: -/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_; - | ^~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/scan.h:502:9: warning: ‘int dxtbx::model::Scan::batch_offset_’ [-Wreorder] - 502 | int batch_offset_; - | ^~~~~~~~~~~~~ -/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 /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, - 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/vec2.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/scan.h:17: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/scan.h: In constructor ‘dxtbx::model::Scan::Scan(scitbx::vec2, scitbx::vec2, const scitbx::af::shared&, const scitbx::af::shared&, int)’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/scan.h:99:43: warning: comparison of integer expressions of different signedness: ‘scitbx::af::shared_plain::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 99 | DXTBX_ASSERT(exposure_times_.size() == num_images_); - | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -/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/scan.h:99:7: note: in expansion of macro ‘DXTBX_ASSERT’ - 99 | DXTBX_ASSERT(exposure_times_.size() == num_images_); - | ^~~~~~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx/model/scan.h:100:35: warning: comparison of integer expressions of different signedness: ‘scitbx::af::shared_plain::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 100 | DXTBX_ASSERT(epochs_.size() == num_images_); - | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -/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/scan.h:100:7: note: in expansion of macro ‘DXTBX_ASSERT’ - 100 | DXTBX_ASSERT(epochs_.size() == num_images_); - | ^~~~~~~~~~~~ -/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_); - | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -/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/scan.h:231:7: note: in expansion of macro ‘DXTBX_ASSERT’ - 231 | DXTBX_ASSERT(exposure_times.size() == num_images_); - | ^~~~~~~~~~~~ -/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_); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -/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__, \ +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/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 /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/scan.cc:20: -/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) { - | ~~^~~~ -g++ -o lib/libcbf-private.so.0.0.1 -shared -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-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/x86_64-linux-gnu -Llib -L/build/reproducible-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/x86_64-linux-gnu/hdf5/serial -lboost_thread -lboost_system -lhdf5 -lcbf -g++ -o exe_dev/cctbx.convert_ccp4_symop_lib -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-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/x86_64-linux-gnu -Llib -L/build/reproducible-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/x86_64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -pthread cctbx/examples/find_distances.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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 +/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) { + | ~~^~~~~~~~~~~ +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 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, @@ -10762,18 +10878,7 @@ /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] -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/x86_64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -pthread cbflib_adaptbx/detectors/tst_memory.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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/x86_64-linux-gnu/hdf5/serial -lcbf -lcbf-private -lm -lhdf5 -/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_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 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]’: @@ -10792,8 +10897,7 @@ /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 >]’ @@ -10802,73 +10906,8 @@ /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 exe_dev/cctbx.sym_equiv_sites -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -pthread cctbx/examples/sym_equiv_sites.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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/x86_64-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/x86_64-linux-gnu -Llib -L/build/reproducible-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 -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 -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/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("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -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 /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) { - | ~~^~~~~~~~~~~ -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_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_functions_01_bpl.cpp +g++ -o gltbx/gl_functions_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_functions_02_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]’: @@ -10891,9 +10930,6 @@ /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_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 -g++ -o gltbx/gl_functions_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_functions_01_bpl.cpp -g++ -o gltbx/gl_functions_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_functions_02_bpl.cpp 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 @@ -10926,6 +10962,7 @@ 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 /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++) { @@ -10950,46 +10987,10 @@ /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/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 -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/iotbx/detectors/bruker_ext.cpp:18: -/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 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 -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 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/detectors/scanbox.h:5, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/detectors/image_divider.h:2, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/detectors/detectors_ext.cpp: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 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, @@ -11032,7 +11033,6 @@ /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/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 /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]; \ @@ -11085,8 +11085,6 @@ /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 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 -g++ -o iotbx/mtz/dataset_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/dataset_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, @@ -11128,6 +11126,126 @@ /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, + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/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/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/iotbx/detectors/bruker_ext.cpp:18: +/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 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 /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 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/detectors/scanbox.h:5, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/detectors/image_divider.h:2, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/detectors/detectors_ext.cpp: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 iotbx/mtz/dataset_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/dataset_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&)’: +/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/column.cpp: In member function ‘void iotbx::mtz::column::set_reals(const scitbx::af::const_ref&, const scitbx::af::const_ref&)’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/mtz/column.cpp:253:48: warning: comparison of integer expressions of different signedness: ‘scitbx::af::const_ref::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 253 | IOTBX_ASSERT(mtz_reflection_indices.size() <= nref_at_entry); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-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/column.cpp:253:5: note: in expansion of macro ‘IOTBX_ASSERT’ + 253 | IOTBX_ASSERT(mtz_reflection_indices.size() <= nref_at_entry); + | ^~~~~~~~~~~~ +g++ -o iotbx/mtz/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 /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&)’: @@ -11147,6 +11265,7 @@ /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/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, @@ -11189,68 +11308,7 @@ /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) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/mtz/column.cpp: In member function ‘void iotbx::mtz::column::set_reals(const scitbx::af::const_ref&, const scitbx::af::const_ref&)’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/mtz/column.cpp:253:48: warning: comparison of integer expressions of different signedness: ‘scitbx::af::const_ref::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 253 | IOTBX_ASSERT(mtz_reflection_indices.size() <= nref_at_entry); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-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/column.cpp:253:5: note: in expansion of macro ‘IOTBX_ASSERT’ - 253 | IOTBX_ASSERT(mtz_reflection_indices.size() <= nref_at_entry); - | ^~~~~~~~~~~~ -/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, - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/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, - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 /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]; \ @@ -11303,6 +11361,8 @@ /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/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, @@ -11333,9 +11393,9 @@ /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 -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 +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 +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 +g++ -o iotbx/pdb/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/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, @@ -11348,31 +11408,14 @@ /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); - | ^~~~~~~~~~~~ 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: + 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/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/iotbx/pdb/namespace.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/hierarchy.h:8, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/atom_selection.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]; \ @@ -11426,25 +11469,6 @@ 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: -/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 /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, @@ -11474,31 +11498,100 @@ /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/small_plain.h: In member function ‘ElementType& scitbx::af::small_plain::at(size_type)’: +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/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/iotbx/pdb/namespace.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/hierarchy.h:8, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/input.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/construct_hierarchy.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/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/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/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/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 ‘const ElementType& scitbx::af::small_plain::at(size_type) const’: +/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/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/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/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/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 /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/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/iotbx/pdb/namespace.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/hierarchy.h:8, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/hierarchy.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) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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, @@ -11529,6 +11622,33 @@ /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/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, + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o iotbx/pdb/hierarchy_atom_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_atom_bpl.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, @@ -11541,6 +11661,121 @@ /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/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) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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); + | ~~^~~~~~~~~~~ +/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 /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); + | ^~~~~~~~~~~~ +/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 /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&)’: @@ -11581,18 +11816,9 @@ /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::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); - | ~~^~~~~~~~~~~ +g++ -o iotbx/pdb/hierarchy_atoms.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/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_atoms.cpp +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 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, @@ -11635,165 +11861,6 @@ /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); | ~~^~~~~~~~~~~ -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/batch.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/mtz/object_bpl.cpp:9: -/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/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 -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 -g++ -o iotbx/pdb/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/hierarchy.cpp -g++ -o iotbx/pdb/hierarchy_atom_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_atom_bpl.cpp -g++ -o iotbx/pdb/hierarchy_atoms.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/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_atoms.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/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/iotbx/pdb/namespace.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/hierarchy.h:8, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/atom_selection.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/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, - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 -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/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/iotbx/pdb/namespace.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/hierarchy.h:8, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/input.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/construct_hierarchy.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/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 /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, @@ -11898,68 +11965,37 @@ /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/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/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/iotbx/pdb/namespace.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/hierarchy.h:8, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/hierarchy.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/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, - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 +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/batch.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/mtz/object_bpl.cpp:9: +/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/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 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, @@ -12057,6 +12093,7 @@ /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) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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]; \ @@ -12083,7 +12120,6 @@ /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, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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/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 @@ -12102,7 +12138,6 @@ | ^~~~~~~~ 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 g++ -o iotbx/pdb/hybrid_36_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/usr/include/ccp4 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/fable iotbx/pdb/hybrid_36_fem.cpp -g++ -o iotbx/pdb/input.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/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.cpp In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/hierarchy_ext.cpp:11: /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 @@ -12127,6 +12162,7 @@ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ +g++ -o iotbx/pdb/input.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/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.cpp 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/cctbx/xray/scatterer.h:5, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/hierarchy_atoms_bpl.cpp:2: @@ -12134,8 +12170,6 @@ /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 >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 40 | if (pos < 0 || pos >= command_line_args.buffer.size()) { @@ -12172,6 +12207,29 @@ /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) { | ~~~~^~~~~~~~~~~~~~~~~~~ +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; + | ^~~~~~~~ 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, @@ -12207,6 +12265,14 @@ /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 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 +/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]; \ @@ -12233,6 +12299,17 @@ /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 /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)’: @@ -12251,37 +12328,36 @@ /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; - | ^~~~~~~~ +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); + | ~~^~~~~~~~~~~ +/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/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 +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, 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, @@ -12289,8 +12365,7 @@ 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/iotbx/pdb/namespace.h:4, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/hierarchy.h:8, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/input.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/input_write.cpp:1: + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/overall_counts.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]; \ @@ -12317,32 +12392,6 @@ /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) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/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 /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, @@ -12350,7 +12399,8 @@ 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/iotbx/pdb/namespace.h:4, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/hierarchy.h:8, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/overall_counts.cpp:1: + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/input.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/input_write.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]; \ @@ -12377,17 +12427,6 @@ /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) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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/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]; \ @@ -12414,35 +12453,33 @@ /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/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); - | ~~^~~~~~~~~~~ -/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 +/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, + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o iotbx/pdb/xray_structure_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/xray_structure_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, @@ -12503,7 +12540,6 @@ /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_fem -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -pthread iotbx/pdb/hybrid_36_fem.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/write_utils.cpp: In destructor ‘iotbx::pdb::write_utils::fstream_open_close::~fstream_open_close()’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/write_utils.cpp:42:7: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] 42 | throw std::runtime_error( @@ -12511,37 +12547,44 @@ 43 | "Failure writing to file: \"" + file_name + "\""); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/iotbx/pdb/write_utils.cpp:42:7: note: in C++11 destructors default to ‘noexcept’ -g++ -o iotbx/pdb/xray_structure_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/xray_structure_bpl.cpp 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/pdb/hybrid_36_fem -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -pthread iotbx/pdb/hybrid_36_fem.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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 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 g++ -o lib/libann_adaptor.so.0.0.1 -shared -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -Wl,-soname=libann_adaptor.so.0 annlib_adaptbx/ann/ann_adaptor.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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 -lann-cctbx 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' g++ -o lib/annlib_ext.so.0.0.1 -shared -rdynamic -std=c++11 -Wl,-soname=annlib_ext.so.0 annlib_adaptbx/ann/boost_python/annlib_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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 -lboost_thread -lboost_system -lboost_python311 -lm -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/x86_64-linux-gnu -Llib -L/build/reproducible-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/annlib_ext.so.0.0.1' '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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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_clustering_algorithm_ext.so.0.0.1 -shared -rdynamic -std=c++11 -Wl,-soname=boost_adaptbx_graph_clustering_algorithm_ext.so.0 boost_adaptbx/graph/clustering_algorithm_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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/x86_64-linux-gnu -Llib -L/build/reproducible-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_breadth_first_search_ext.so.0.0.1' 'lib/boost_adaptbx_graph_breadth_first_search_ext.so.0'->'lib/boost_adaptbx_graph_breadth_first_search_ext.so.0.0.1' 'lib/boost_adaptbx_graph_breadth_first_search_ext.so'->'lib/boost_adaptbx_graph_breadth_first_search_ext.so.0.0.1' +g++ -o lib/boost_adaptbx_graph_clustering_algorithm_ext.so.0.0.1 -shared -rdynamic -std=c++11 -Wl,-soname=boost_adaptbx_graph_clustering_algorithm_ext.so.0 boost_adaptbx/graph/clustering_algorithm_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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_connected_component_algorithm_ext.so.0.0.1 -shared -rdynamic -std=c++11 -Wl,-soname=boost_adaptbx_graph_connected_component_algorithm_ext.so.0 boost_adaptbx/graph/connected_component_algorithm_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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_clustering_algorithm_ext.so.0.0.1' 'lib/boost_adaptbx_graph_clustering_algorithm_ext.so.0'->'lib/boost_adaptbx_graph_clustering_algorithm_ext.so.0.0.1' 'lib/boost_adaptbx_graph_clustering_algorithm_ext.so'->'lib/boost_adaptbx_graph_clustering_algorithm_ext.so.0.0.1' +g++ -o lib/boost_adaptbx_graph_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/x86_64-linux-gnu -Llib -L/build/reproducible-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_connected_component_algorithm_ext.so.0.0.1' 'lib/boost_adaptbx_graph_connected_component_algorithm_ext.so.0'->'lib/boost_adaptbx_graph_connected_component_algorithm_ext.so.0.0.1' 'lib/boost_adaptbx_graph_connected_component_algorithm_ext.so'->'lib/boost_adaptbx_graph_connected_component_algorithm_ext.so.0.0.1' g++ -o lib/boost_adaptbx_graph_graph_structure_comparison_ext.so.0.0.1 -shared -rdynamic -std=c++11 -Wl,-soname=boost_adaptbx_graph_graph_structure_comparison_ext.so.0 boost_adaptbx/graph/graph_structure_comparison_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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_graph_structure_comparison_ext.so.0.0.1' + 'lib/boost_adaptbx_graph_graph_structure_comparison_ext.so.0'->'lib/boost_adaptbx_graph_graph_structure_comparison_ext.so.0.0.1' + 'lib/boost_adaptbx_graph_graph_structure_comparison_ext.so'->'lib/boost_adaptbx_graph_graph_structure_comparison_ext.so.0.0.1' g++ -o lib/boost_adaptbx_graph_maximum_clique_ext.so.0.0.1 -shared -rdynamic -std=c++11 -Wl,-soname=boost_adaptbx_graph_maximum_clique_ext.so.0 boost_adaptbx/graph/maximum_clique_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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_ext.so.0.0.1' + 'lib/boost_adaptbx_graph_ext.so.0'->'lib/boost_adaptbx_graph_ext.so.0.0.1' + 'lib/boost_adaptbx_graph_ext.so'->'lib/boost_adaptbx_graph_ext.so.0.0.1' +g++ -o lib/boost_adaptbx_graph_metric_ext.so.0.0.1 -shared -rdynamic -std=c++11 -Wl,-soname=boost_adaptbx_graph_metric_ext.so.0 boost_adaptbx/graph/metric_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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: @@ -12549,6 +12592,15 @@ /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_maximum_clique_ext.so.0.0.1' + 'lib/boost_adaptbx_graph_maximum_clique_ext.so'->'lib/boost_adaptbx_graph_maximum_clique_ext.so.0.0.1' +g++ -o lib/boost_adaptbx_graph_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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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]’ @@ -12560,96 +12612,60 @@ /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/boost_adaptbx_graph_metric_ext.so.0.0.1 -shared -rdynamic -std=c++11 -Wl,-soname=boost_adaptbx_graph_metric_ext.so.0 boost_adaptbx/graph/metric_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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_graph_structure_comparison_ext.so.0.0.1' - 'lib/boost_adaptbx_graph_graph_structure_comparison_ext.so.0'->'lib/boost_adaptbx_graph_graph_structure_comparison_ext.so.0.0.1' - 'lib/boost_adaptbx_graph_graph_structure_comparison_ext.so'->'lib/boost_adaptbx_graph_graph_structure_comparison_ext.so.0.0.1' -g++ -o lib/boost_adaptbx_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/x86_64-linux-gnu -Llib -L/build/reproducible-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' 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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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_python_hybrid_times_ext.so.0.0.1' 'lib/boost_python_hybrid_times_ext.so.0'->'lib/boost_python_hybrid_times_ext.so.0.0.1' 'lib/boost_python_hybrid_times_ext.so'->'lib/boost_python_hybrid_times_ext.so.0.0.1' -g++ -o lib/boost_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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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' -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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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/x86_64-linux-gnu -Llib -L/build/reproducible-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/x86_64-linux-gnu/hdf5/serial -lcbf-private -lcbf -lboost_thread -lboost_system -lboost_python311 -lm -lhdf5 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/x86_64-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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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 +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' 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' +Create symlinks for: 'lib/libccp4io.so.0.0.1' + 'lib/libccp4io.so.0'->'lib/libccp4io.so.0.0.1' + 'lib/libccp4io.so'->'lib/libccp4io.so.0.0.1' +g++ -o scitbx/boost_python/utils.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-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 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/x86_64-linux-gnu -Llib -L/build/reproducible-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 -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 -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' -Create symlinks for: 'lib/boost_adaptbx_graph_ext.so.0.0.1' - 'lib/boost_adaptbx_graph_ext.so.0'->'lib/boost_adaptbx_graph_ext.so.0.0.1' - 'lib/boost_adaptbx_graph_ext.so'->'lib/boost_adaptbx_graph_ext.so.0.0.1' -g++ -o lib/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/x86_64-linux-gnu -Llib -L/build/reproducible-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 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/cbflib_ext.so.0.0.1' 'lib/cbflib_ext.so.0'->'lib/cbflib_ext.so.0.0.1' 'lib/cbflib_ext.so'->'lib/cbflib_ext.so.0.0.1' -Create symlinks for: 'lib/cma_es_ext.so.0.0.1' - 'lib/cma_es_ext.so.0'->'lib/cma_es_ext.so.0.0.1' - 'lib/cma_es_ext.so'->'lib/cma_es_ext.so.0.0.1' +g++ -o 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 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/x86_64-linux-gnu -Llib -L/build/reproducible-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/cma_es_ext.so.0.0.1' + 'lib/cma_es_ext.so.0'->'lib/cma_es_ext.so.0.0.1' + 'lib/cma_es_ext.so'->'lib/cma_es_ext.so.0.0.1' g++ -o lib/dxtbx_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/x86_64-linux-gnu -Llib -L/build/reproducible-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/x86_64-linux-gnu/hdf5/serial -lm -ltiff -lboost_python311 -lcbf g++ -o lib/dxtbx_format_image_ext.so.0.0.1 -shared -rdynamic -std=c++11 -Wl,-soname=dxtbx_format_image_ext.so.0 dxtbx/src/dxtbx/format/boost_python/image_ext.o dxtbx/src/dxtbx/format/boost_python/cbf_read_buffer.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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/x86_64-linux-gnu/hdf5/serial -lm -ltiff -lboost_python311 -lcbf -lhdf5 -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/x86_64-linux-gnu -Llib -L/build/reproducible-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/x86_64-linux-gnu/hdf5/serial -lm -ltiff -lboost_python311 -lcbf -lhdf5 -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/x86_64-linux-gnu -Llib -L/build/reproducible-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/x86_64-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/x86_64-linux-gnu -Llib -L/build/reproducible-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' Create symlinks for: 'lib/dxtbx_ext.so.0.0.1' 'lib/dxtbx_ext.so.0'->'lib/dxtbx_ext.so.0.0.1' 'lib/dxtbx_ext.so'->'lib/dxtbx_ext.so.0.0.1' -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/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/x86_64-linux-gnu -Llib -L/build/reproducible-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 -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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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/x86_64-linux-gnu -Llib -L/build/reproducible-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/x86_64-linux-gnu/hdf5/serial -lm -ltiff -lboost_python311 -lcbf -lhdf5 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, @@ -12684,14 +12700,6 @@ /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 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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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/libiotbx_mtz.so.0.0.1 -shared -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-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/x86_64-linux-gnu -Llib -L/build/reproducible-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' /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]; \ @@ -12718,7 +12726,6 @@ /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 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/x86_64-linux-gnu -Llib -L/build/reproducible-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]; \ @@ -12771,325 +12778,349 @@ /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, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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' +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/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/x86_64-linux-gnu -Llib -L/build/reproducible-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/x86_64-linux-gnu -Llib -L/build/reproducible-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 +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 +Create symlinks for: 'lib/fable_ext.so.0.0.1' + 'lib/fable_ext.so.0'->'lib/fable_ext.so.0.0.1' + 'lib/fable_ext.so'->'lib/fable_ext.so.0.0.1' +g++ -o ucif/cifLexer.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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/libiotbx_mtz.so.0.0.1 -shared -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-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/x86_64-linux-gnu -Llib -L/build/reproducible-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' +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/x86_64-linux-gnu -Llib -L/build/reproducible-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/libiotbx_mtz.so.0.0.1' + 'lib/libiotbx_mtz.so.0'->'lib/libiotbx_mtz.so.0.0.1' + 'lib/libiotbx_mtz.so'->'lib/libiotbx_mtz.so.0.0.1' g++ -o lib/iotbx_wildcard_ext.so.0.0.1 -shared -rdynamic -std=c++11 -Wl,-soname=iotbx_wildcard_ext.so.0 iotbx/wildcard_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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_scalepack_ext.so.0.0.1' 'lib/iotbx_scalepack_ext.so.0'->'lib/iotbx_scalepack_ext.so.0.0.1' 'lib/iotbx_scalepack_ext.so'->'lib/iotbx_scalepack_ext.so.0.0.1' -Create symlinks for: 'lib/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_shelx_ext.so.0.0.1' - 'lib/iotbx_shelx_ext.so.0'->'lib/iotbx_shelx_ext.so.0.0.1' - 'lib/iotbx_shelx_ext.so'->'lib/iotbx_shelx_ext.so.0.0.1' Create symlinks for: 'lib/iotbx_wildcard_ext.so.0.0.1' 'lib/iotbx_wildcard_ext.so.0'->'lib/iotbx_wildcard_ext.so.0.0.1' 'lib/iotbx_wildcard_ext.so'->'lib/iotbx_wildcard_ext.so.0.0.1' 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/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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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 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 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 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 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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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 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 -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 -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 -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 -g++ -o lib/libscitbx_boost_python.so.0.0.1 -shared -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-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/x86_64-linux-gnu -Llib -L/build/reproducible-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 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 -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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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_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/libscitbx_boost_python.so.0.0.1 -shared -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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/x86_64-linux-gnu -Llib -L/build/reproducible-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/x86_64-linux-gnu/hdf5/serial -lm -ltiff -lboost_python311 -lcbf -lhdf5 +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 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 +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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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/cctbx_covariance_ext.so.0.0.1' + 'lib/cctbx_covariance_ext.so.0'->'lib/cctbx_covariance_ext.so.0.0.1' + 'lib/cctbx_covariance_ext.so'->'lib/cctbx_covariance_ext.so.0.0.1' +g++ -o lib/cctbx_eltbx_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/x86_64-linux-gnu -Llib -L/build/reproducible-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/x86_64-linux-gnu -Llib -L/build/reproducible-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/dxtbx_imageset_ext.so.0.0.1' + 'lib/dxtbx_imageset_ext.so.0'->'lib/dxtbx_imageset_ext.so.0.0.1' + 'lib/dxtbx_imageset_ext.so'->'lib/dxtbx_imageset_ext.so.0.0.1' +Create symlinks for: 'lib/cctbx_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_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/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/libiotbx_pdb.so.0.0.1 -shared -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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/x86_64-linux-gnu -Llib -L/build/reproducible-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/x86_64-linux-gnu/hdf5/serial -lboost_thread -lboost_system -lm -lcctbx -lscitbx_boost_python -ltiff -lboost_python311 -lcbf -lhdf5 +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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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_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/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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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 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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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/x86_64-linux-gnu -Llib -L/build/reproducible-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' +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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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/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/x86_64-linux-gnu -Llib -L/build/reproducible-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/x86_64-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/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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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' +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/x86_64-linux-gnu -Llib -L/build/reproducible-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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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/x86_64-linux-gnu -Llib -L/build/reproducible-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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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_math_ext.so.0.0.1' - 'lib/cctbx_math_ext.so.0'->'lib/cctbx_math_ext.so.0.0.1' - 'lib/cctbx_math_ext.so'->'lib/cctbx_math_ext.so.0.0.1' -g++ -o lib/cctbx_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/x86_64-linux-gnu -Llib -L/build/reproducible-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/x86_64-linux-gnu -Llib -L/build/reproducible-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' +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/x86_64-linux-gnu -Llib -L/build/reproducible-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_xray_ext.so.0.0.1' + 'lib/cctbx_xray_ext.so.0'->'lib/cctbx_xray_ext.so.0.0.1' + 'lib/cctbx_xray_ext.so'->'lib/cctbx_xray_ext.so.0.0.1' +Create symlinks for: 'lib/cctbx_eltbx_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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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_xray_observations_ext.so.0.0.1' 'lib/cctbx_xray_observations_ext.so.0'->'lib/cctbx_xray_observations_ext.so.0.0.1' 'lib/cctbx_xray_observations_ext.so'->'lib/cctbx_xray_observations_ext.so.0.0.1' -g++ -o lib/cctbx_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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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_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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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_math_ext.so.0.0.1' + 'lib/cctbx_math_ext.so.0'->'lib/cctbx_math_ext.so.0.0.1' + 'lib/cctbx_math_ext.so'->'lib/cctbx_math_ext.so.0.0.1' +g++ -o lib/cctbx_eltbx_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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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' +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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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/x86_64-linux-gnu -Llib -L/build/reproducible-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' -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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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/x86_64-linux-gnu -Llib -L/build/reproducible-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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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/x86_64-linux-gnu -Llib -L/build/reproducible-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_viewer_utils_ext.so.0.0.1' - 'lib/gltbx_viewer_utils_ext.so.0'->'lib/gltbx_viewer_utils_ext.so.0.0.1' - 'lib/gltbx_viewer_utils_ext.so'->'lib/gltbx_viewer_utils_ext.so.0.0.1' -g++ -o lib/gltbx_gl_ext.so.0.0.1 -shared -rdynamic -std=c++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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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_eltbx_xray_scattering_ext.so.0.0.1' 'lib/cctbx_eltbx_xray_scattering_ext.so.0'->'lib/cctbx_eltbx_xray_scattering_ext.so.0.0.1' 'lib/cctbx_eltbx_xray_scattering_ext.so'->'lib/cctbx_eltbx_xray_scattering_ext.so.0.0.1' -g++ -o lib/cctbx_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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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/libmmtbx_tls.so.0.0.1 -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -pthread -shared -Wl,-z,relro -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5 -Wl,-soname=libmmtbx_tls.so.0 mmtbx/tls/decompose.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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 -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 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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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/x86_64-linux-gnu -Llib -L/build/reproducible-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/x86_64-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/iotbx_mtz_ext.so.0.0.1' - 'lib/iotbx_mtz_ext.so.0'->'lib/iotbx_mtz_ext.so.0.0.1' - 'lib/iotbx_mtz_ext.so'->'lib/iotbx_mtz_ext.so.0.0.1' -g++ -o 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/x86_64-linux-gnu -Llib -L/build/reproducible-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_gl_ext.so.0.0.1' 'lib/gltbx_gl_ext.so.0'->'lib/gltbx_gl_ext.so.0.0.1' 'lib/gltbx_gl_ext.so'->'lib/gltbx_gl_ext.so.0.0.1' -g++ -o lib/cctbx_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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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_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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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/x86_64-linux-gnu -Llib -L/build/reproducible-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 -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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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/x86_64-linux-gnu -Llib -L/build/reproducible-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_sasaki_ext.so.0.0.1' - 'lib/cctbx_eltbx_sasaki_ext.so.0'->'lib/cctbx_eltbx_sasaki_ext.so.0.0.1' - 'lib/cctbx_eltbx_sasaki_ext.so'->'lib/cctbx_eltbx_sasaki_ext.so.0.0.1' -g++ -o lib/gltbx_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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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 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_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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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_multipolar_ext.so.0.0.1' - 'lib/cctbx_multipolar_ext.so.0'->'lib/cctbx_multipolar_ext.so.0.0.1' - 'lib/cctbx_multipolar_ext.so'->'lib/cctbx_multipolar_ext.so.0.0.1' -g++ -o lib/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/x86_64-linux-gnu -Llib -L/build/reproducible-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/x86_64-linux-gnu/hdf5/serial -lboost_thread -lboost_system -lm -lcctbx -lscitbx_boost_python -ltiff -lboost_python311 -lcbf -lhdf5 -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_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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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 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/x86_64-linux-gnu -Llib -L/build/reproducible-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/x86_64-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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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' Create symlinks for: 'lib/cctbx_maptbx_bcr_bcr_ext.so.0.0.1' 'lib/cctbx_maptbx_bcr_bcr_ext.so.0'->'lib/cctbx_maptbx_bcr_bcr_ext.so.0.0.1' 'lib/cctbx_maptbx_bcr_bcr_ext.so'->'lib/cctbx_maptbx_bcr_bcr_ext.so.0.0.1' -g++ -o lib/cctbx_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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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/x86_64-linux-gnu -Llib -L/build/reproducible-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/libspotfinder.so.0.0.1 -shared -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-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/x86_64-linux-gnu -Llib -L/build/reproducible-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 -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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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' -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/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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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/x86_64-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/x86_64-linux-gnu -Llib -L/build/reproducible-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' +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 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 -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 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/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_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 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/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 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 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/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' -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 -g++ -o lib/libscitbx_minpack.so.0.0.1 -shared -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-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/x86_64-linux-gnu -Llib -L/build/reproducible-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 -g++ -o lib/libscitbx_slatec.so.0.0.1 -shared -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-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/x86_64-linux-gnu -Llib -L/build/reproducible-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' 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/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/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 -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 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/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' +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_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 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/libscitbx_slatec.so.0.0.1 -shared -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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/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 lib/libspotfinder.so.0.0.1 -shared -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-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/x86_64-linux-gnu -Llib -L/build/reproducible-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 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 +Create symlinks for: 'lib/cctbx_geometry_restraints_ext.so.0.0.1' + 'lib/cctbx_geometry_restraints_ext.so.0'->'lib/cctbx_geometry_restraints_ext.so.0.0.1' + 'lib/cctbx_geometry_restraints_ext.so'->'lib/cctbx_geometry_restraints_ext.so.0.0.1' +Create symlinks for: 'lib/libspotfinder.so.0.0.1' + 'lib/libspotfinder.so.0'->'lib/libspotfinder.so.0.0.1' + 'lib/libspotfinder.so'->'lib/libspotfinder.so.0.0.1' +g++ -o lib/libdxtbxspotfinder.so.0.0.1 -shared -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-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/x86_64-linux-gnu -Llib -L/build/reproducible-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 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/x86_64-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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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/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 +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/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 -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 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 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 +g++ -o lib/libmmtbx_tls.so.0.0.1 -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -pthread -shared -Wl,-z,relro -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5 -Wl,-soname=libmmtbx_tls.so.0 mmtbx/tls/decompose.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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/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 +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/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 +g++ -o mmtbx/alignment/alignment_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 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/alignment/alignment_ext.cpp g++ -o lib/librstbx.so.0.0.1 -shared -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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/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 -g++ -o mmtbx/alignment/alignment_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 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/.pybuild/cpython3_3.11/build_/include -I/usr/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/alignment/alignment_ext.cpp g++ -o mmtbx/building/loop_closure/ccd_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/building/loop_closure/ccd_bpl.cpp g++ -o mmtbx/bulk_solvent/bulk_solvent_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/bulk_solvent/bulk_solvent_ext.cpp g++ -o mmtbx/bulk_solvent/bulk_solvent.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-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/bulk_solvent/bulk_solvent.cpp g++ -o mmtbx/cablam/boost_python/cablam_align_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/ccp4 -I/usr/include/python3.11 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/cablam/boost_python/cablam_align_utils_ext.cpp g++ -o mmtbx/den/boost_python/den_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/den/boost_python/den_ext.cpp -Create symlinks for: 'lib/cctbx_crystal_ext.so.0.0.1' - 'lib/cctbx_crystal_ext.so.0'->'lib/cctbx_crystal_ext.so.0.0.1' - 'lib/cctbx_crystal_ext.so'->'lib/cctbx_crystal_ext.so.0.0.1' g++ -o mmtbx/secondary_structure/dssp_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/dssp_ext.cpp g++ -o mmtbx/dynamics/dynamics_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/dynamics/dynamics_ext.cpp -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/x86_64-linux-gnu -Llib -L/build/reproducible-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 mmtbx/dynamics/dynamics.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-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/dynamics/dynamics.cpp 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 -Create symlinks for: 'lib/iotbx_pdb_hierarchy_ext.so.0.0.1' - 'lib/iotbx_pdb_hierarchy_ext.so.0'->'lib/iotbx_pdb_hierarchy_ext.so.0.0.1' - 'lib/iotbx_pdb_hierarchy_ext.so'->'lib/iotbx_pdb_hierarchy_ext.so.0.0.1' g++ -o mmtbx/geometry/boost_python/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 g++ -o mmtbx/geometry/boost_python/clash_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/clash_ext.cpp 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 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/libsmtbx_refinement_constraints.so.0.0.1 -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -pthread -shared -Wl,-z,relro -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5 -Wl,-soname=libsmtbx_refinement_constraints.so.0 smtbx/refinement/constraints/affine.o smtbx/refinement/constraints/geometrical_hydrogens.o smtbx/refinement/constraints/occupancy.o smtbx/refinement/constraints/reparametrisation.o smtbx/refinement/constraints/rigid.o smtbx/refinement/constraints/same_group.o smtbx/refinement/constraints/scaled_adp.o smtbx/refinement/constraints/shared.o smtbx/refinement/constraints/special_position.o smtbx/refinement/constraints/symmetry_equivalent.o smtbx/refinement/constraints/u_eq_dependent_u_iso.o smtbx/refinement/constraints/u_iso_dependent_u_iso.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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/libsmtbx_refinement_constraints.so.0.0.1' 'lib/libsmtbx_refinement_constraints.so.0'->'lib/libsmtbx_refinement_constraints.so.0.0.1' 'lib/libsmtbx_refinement_constraints.so'->'lib/libsmtbx_refinement_constraints.so.0.0.1' -g++ -o lib/libmmtbx_masks.so.0.0.1 -shared -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-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/x86_64-linux-gnu -Llib -L/build/reproducible-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 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/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/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 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, @@ -13102,6 +13133,18 @@ /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 /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, @@ -13121,21 +13164,9 @@ /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/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 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 -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/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' 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, @@ -13148,27 +13179,33 @@ /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); | ~~^~~~~~~~~~~ +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 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 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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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/x86_64-linux-gnu -Llib -L/build/reproducible-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 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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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/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 -g++ -o mmtbx/max_lik/max_lik.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-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.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/x86_64-linux-gnu -Llib -L/build/reproducible-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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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_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/max_lik/max_lik.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-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.cpp g++ -o mmtbx/bulk_solvent/mosaic_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/bulk_solvent/mosaic_ext.cpp +Create symlinks for: 'lib/iotbx_pdb_hierarchy_ext.so.0.0.1' + 'lib/iotbx_pdb_hierarchy_ext.so.0'->'lib/iotbx_pdb_hierarchy_ext.so.0.0.1' + 'lib/iotbx_pdb_hierarchy_ext.so'->'lib/iotbx_pdb_hierarchy_ext.so.0.0.1' +g++ -o mmtbx/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 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, @@ -13182,7 +13219,7 @@ 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: + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/geometry/boost_python/asa_ext.cpp:2: /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ @@ -13200,13 +13237,15 @@ 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( | ^~~~~~~~~~~~~~~~~~~~ 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/x86_64-linux-gnu -Llib -L/build/reproducible-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 +/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, @@ -13220,17 +13259,10 @@ 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/asa_ext.cpp:2: -/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/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' + 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( | ^~~~~~~~~~~~~~~~~~~~ -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 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, @@ -13242,19 +13274,20 @@ 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: -/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 /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("") | ^~~~~~~~~~~~~~~~~~~~~~~ -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/x86_64-linux-gnu -Llib -L/build/reproducible-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' - 'lib/mmtbx_geometry_primitive_ext.so.0'->'lib/mmtbx_geometry_primitive_ext.so.0.0.1' - 'lib/mmtbx_geometry_primitive_ext.so'->'lib/mmtbx_geometry_primitive_ext.so.0.0.1' +Create symlinks for: 'lib/mmtbx_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/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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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 /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, @@ -13272,9 +13305,13 @@ /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( | ^~~~~~~~~~~~~~~~~~~~ +Create symlinks for: 'lib/mmtbx_geometry_primitive_ext.so.0.0.1' + 'lib/mmtbx_geometry_primitive_ext.so.0'->'lib/mmtbx_geometry_primitive_ext.so.0.0.1' + 'lib/mmtbx_geometry_primitive_ext.so'->'lib/mmtbx_geometry_primitive_ext.so.0.0.1' /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +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 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, @@ -13295,22 +13332,17 @@ /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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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 Create symlinks for: 'lib/mmtbx_geometry_shared_types_ext.so.0.0.1' 'lib/mmtbx_geometry_shared_types_ext.so.0'->'lib/mmtbx_geometry_shared_types_ext.so.0.0.1' 'lib/mmtbx_geometry_shared_types_ext.so'->'lib/mmtbx_geometry_shared_types_ext.so.0.0.1' g++ -o mmtbx/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 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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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_den_restraints_ext.so.0.0.1 -shared -rdynamic -std=c++11 -Wl,-soname=mmtbx_den_restraints_ext.so.0 mmtbx/den/boost_python/den_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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_den_restraints_ext.so.0.0.1' - '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/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 +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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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, @@ -13331,17 +13363,22 @@ /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/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/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 +g++ -o lib/mmtbx_den_restraints_ext.so.0.0.1 -shared -rdynamic -std=c++11 -Wl,-soname=mmtbx_den_restraints_ext.so.0 mmtbx/den/boost_python/den_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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_den_restraints_ext.so.0.0.1' + '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/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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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 -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/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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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, @@ -13362,6 +13399,9 @@ /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/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' 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, @@ -13382,17 +13422,17 @@ /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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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/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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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 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 +ar rc probe/lib/libprobelib.a mmtbx/probe/Scoring.o mmtbx/probe/DotSpheres.o mmtbx/probe/SpatialQuery.o +ranlib probe/lib/libprobelib.a +g++ -o mmtbx/scaling/twinning_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/twinning_bpl.cpp +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 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, @@ -13404,9 +13444,16 @@ /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 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 @@ -13424,32 +13471,6 @@ /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 /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 = mmtbx::geometry_restraints::reference_coordinate_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/reference_coordinate_ext.cpp:61:25: 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] - 197 | if (!is_range) assert(i == obj_size); - | ~~^~~~~~~~~~~ -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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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/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 -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, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/geometry_restraints/ramachandran.h:10, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/mmtbx/geometry_restraints/boost_python/ramachandran_ext.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 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] @@ -13458,6 +13479,7 @@ /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]’ @@ -13469,6 +13491,22 @@ /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/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' +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 = mmtbx::geometry_restraints::reference_coordinate_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/reference_coordinate_ext.cpp:61:25: 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] + 197 | if (!is_range) assert(i == obj_size); + | ~~^~~~~~~~~~~ +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 /usr/include/boost/assert.hpp:58, from /usr/include/boost/format/parsing.hpp:21, from /usr/include/boost/format.hpp:50, @@ -13480,16 +13518,15 @@ /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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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/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 -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/x86_64-linux-gnu -Llib -L/build/reproducible-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' +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/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 +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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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 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, @@ -13510,17 +13547,27 @@ /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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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/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 -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 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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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/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 +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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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/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 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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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 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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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, @@ -13538,37 +13585,24 @@ /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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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 /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/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/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 -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/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 -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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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/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 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/x86_64-linux-gnu -Llib -L/build/reproducible-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_rsr_ext.so.0.0.1 -shared -rdynamic -std=c++11 -Wl,-soname=mmtbx_rsr_ext.so.0 mmtbx/rsr/rsr_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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_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_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_rsr_ext.so.0.0.1 -shared -rdynamic -std=c++11 -Wl,-soname=mmtbx_rsr_ext.so.0 mmtbx/rsr/rsr_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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_rsr_ext.so.0.0.1' '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/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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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 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, @@ -13589,12 +13623,11 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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 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 +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/x86_64-linux-gnu -Llib -L/build/reproducible-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 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 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, @@ -13615,17 +13648,10 @@ /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/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 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 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 -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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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 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/x86_64-linux-gnu -Llib -L/build/reproducible-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' 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, @@ -13646,8 +13672,14 @@ /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 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 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 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/x86_64-linux-gnu -Llib -L/build/reproducible-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 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 +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 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 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, @@ -13681,16 +13713,118 @@ /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 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/x86_64-linux-gnu -Llib -L/build/reproducible-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 -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 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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-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/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/x86_64-linux-gnu -Llib -L/build/reproducible-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 +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] + 100 | for (int i=0; i < tiles.size()/4; ++i){ + | ~~^~~~~~~~~~~~~~~~ +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, + 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/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/rstbx/bandpass/parameters.h:3: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/parameters.h: In member function ‘bool rstbx::bandpass::active_area_filter::operator()(rstbx::bandpass::vec3, const int&)’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/parameters.h:126:39: warning: comparison of integer expressions of different signedness: ‘scitbx::af::versa_plain >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 126 | SCITBX_ASSERT( adapt.nn.size()== NEAR); + | ~~~~~~~~~~~~~~~^~~~~~~ +/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/rstbx/bandpass/parameters.h:126:9: note: in expansion of macro ‘SCITBX_ASSERT’ + 126 | SCITBX_ASSERT( adapt.nn.size()== NEAR); + | ^~~~~~~~~~~~~ +In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp:11: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/subpixel_joint_model.h: In member function ‘void rstbx::bandpass::subpixel_joint_model::set_subpixel(scitbx::af::shared, scitbx::af::shared)’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/subpixel_joint_model.h:26:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] + 26 | for (int ixx=0; ixx< rotations_deg.size(); ++ixx){ + | ~~~^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/subpixel_joint_model.h:31:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] + 31 | for (int ixx=0; ixx< rotations_deg.size(); ++ixx){ + | ~~~^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp: In member function ‘void rstbx::bandpass::use_case_bp3::prescreen_indices(const double&)’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp:46:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] + 46 | for (int idx = 0; idx < P.indices.size(); ++idx){ + | ~~~~^~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp: In member function ‘scitbx::af::shared rstbx::bandpass::use_case_bp3::selected_partialities() const’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp:93:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] + 93 | for (int idx = 0; idx < lo_E_limit.size(); ++idx){ + | ~~~~^~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp: In member function ‘void rstbx::bandpass::use_case_bp3::picture_fast_slow()’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp:152:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] + 152 | for (int idx = 0; idx < P.indices.size(); ++idx){ + | ~~~~^~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp: In member function ‘void rstbx::bandpass::use_case_bp3::picture_fast_slow_force()’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp:296:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] + 296 | for (int idx = 0; idx < P.indices.size(); ++idx){ + | ~~~~^~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp:462:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] + 462 | for ( int idx = 0; idx < P.indices.size(); ++idx){ + | ~~~~^~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp: In member function ‘scitbx::af::shared > rstbx::bandpass::use_case_bp3::spot_rectangles(rstbx::bandpass::vec3ref)’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp:477:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] + 477 | for (int idx = 0; idx < lo_E_limit.size(); ++idx){ + | ~~~~^~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp: In member function ‘scitbx::af::shared > rstbx::bandpass::use_case_bp3::spot_rectregions(rstbx::bandpass::vec3ref, const double&)’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp:511:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] + 511 | for (int idx = 0; idx < lo_E_limit.size(); ++idx){ + | ~~~~^~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp: In member function ‘scitbx::af::shared > rstbx::bandpass::use_case_bp3::enclosed_pixels() const’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp:543:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] + 543 | for (int idx = 0; idx < spot_rectangle_vertices.size(); idx+=5){ + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp: In member function ‘scitbx::af::shared > rstbx::bandpass::use_case_bp3::selected_hi_predictions() const’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp:752:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] + 752 | for (int idx = 0; idx < lo_E_limit.size(); ++idx){ + | ~~~~^~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp: In member function ‘scitbx::af::shared > rstbx::bandpass::use_case_bp3::selected_lo_predictions() const’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp:763:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] + 763 | for (int idx = 0; idx < lo_E_limit.size(); ++idx){ + | ~~~~^~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp: In member function ‘scitbx::af::shared > rstbx::bandpass::use_case_bp3::selected_predictions() const’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp:774:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] + 774 | for (int idx = 0; idx < lo_E_limit.size(); ++idx){ + | ~~~~^~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp: In member function ‘scitbx::af::shared > rstbx::bandpass::use_case_bp3::selected_predictions_labelit_format() const’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp:787:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] + 787 | for (int idx = 0; idx < lo_E_limit.size(); ++idx){ + | ~~~~^~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp: In member function ‘scitbx::af::shared > rstbx::bandpass::use_case_bp3::selected_hkls() const’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp:802:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] + 802 | for (int idx = 0; idx < lo_E_limit.size(); ++idx){ + | ~~~~^~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp: In member function ‘scitbx::af::shared > rstbx::bandpass::use_case_bp3::restricted_to_active_areas(scitbx::af::shared, scitbx::af::shared >) const’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp:815:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] + 815 | for (int idx = 0; idx < active_areas.size(); idx+=4){ + | ~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp: In member function ‘void rstbx::bandpass::use_case_bp3::set_subpixel(scitbx::af::shared, scitbx::af::shared)’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp:828:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] + 828 | for (int ixx=0; ixx< rotations_deg.size(); ++ixx){ //DEPRECATED + | ~~~^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp: In function ‘scitbx::af::shared > rstbx::bandpass::ext::use_case_bp2_picture_fast_slow(scitbx::af::shared >, const cctbx::crystal_orientation&, const scitbx::vec3&, const double&, const scitbx::vec3&, const scitbx::vec3&, const scitbx::vec3&, const scitbx::vec3&, const scitbx::vec3&, const double&, const scitbx::vec3&, const double&)’: +/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){ + | ~~~~^~~~~~~~~~~~~~~~ +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' +/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] + 631 | for (int idx = 0; idx < spot_rectangle_vertices.size(); idx+=5){ + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/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 = unlimited_pixel_accept_policy]’: +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp:620:78: 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] +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 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, @@ -13825,109 +13959,35 @@ /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){ | ~~~~~~~~~^~~~~~~~~~~~~~~~ -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] - 100 | for (int i=0; i < tiles.size()/4; ++i){ - | ~~^~~~~~~~~~~~~~~~ -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, - 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/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/rstbx/bandpass/parameters.h:3: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/parameters.h: In member function ‘bool rstbx::bandpass::active_area_filter::operator()(rstbx::bandpass::vec3, const int&)’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/parameters.h:126:39: warning: comparison of integer expressions of different signedness: ‘scitbx::af::versa_plain >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 126 | SCITBX_ASSERT( adapt.nn.size()== NEAR); - | ~~~~~~~~~~~~~~~^~~~~~~ -/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/rstbx/bandpass/parameters.h:126:9: note: in expansion of macro ‘SCITBX_ASSERT’ - 126 | SCITBX_ASSERT( adapt.nn.size()== NEAR); - | ^~~~~~~~~~~~~ -In file included from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp:11: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/subpixel_joint_model.h: In member function ‘void rstbx::bandpass::subpixel_joint_model::set_subpixel(scitbx::af::shared, scitbx::af::shared)’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/subpixel_joint_model.h:26:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] - 26 | for (int ixx=0; ixx< rotations_deg.size(); ++ixx){ - | ~~~^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/subpixel_joint_model.h:31:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] - 31 | for (int ixx=0; ixx< rotations_deg.size(); ++ixx){ - | ~~~^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp: In member function ‘void rstbx::bandpass::use_case_bp3::prescreen_indices(const double&)’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp:46:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] - 46 | for (int idx = 0; idx < P.indices.size(); ++idx){ - | ~~~~^~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp: In member function ‘scitbx::af::shared rstbx::bandpass::use_case_bp3::selected_partialities() const’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp:93:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] - 93 | for (int idx = 0; idx < lo_E_limit.size(); ++idx){ - | ~~~~^~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp: In member function ‘void rstbx::bandpass::use_case_bp3::picture_fast_slow()’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp:152:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] - 152 | for (int idx = 0; idx < P.indices.size(); ++idx){ - | ~~~~^~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp: In member function ‘void rstbx::bandpass::use_case_bp3::picture_fast_slow_force()’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp:296:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] - 296 | for (int idx = 0; idx < P.indices.size(); ++idx){ - | ~~~~^~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp:462:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] - 462 | for ( int idx = 0; idx < P.indices.size(); ++idx){ - | ~~~~^~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp: In member function ‘scitbx::af::shared > rstbx::bandpass::use_case_bp3::spot_rectangles(rstbx::bandpass::vec3ref)’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp:477:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] - 477 | for (int idx = 0; idx < lo_E_limit.size(); ++idx){ - | ~~~~^~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp: In member function ‘scitbx::af::shared > rstbx::bandpass::use_case_bp3::spot_rectregions(rstbx::bandpass::vec3ref, const double&)’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp:511:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] - 511 | for (int idx = 0; idx < lo_E_limit.size(); ++idx){ - | ~~~~^~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp: In member function ‘scitbx::af::shared > rstbx::bandpass::use_case_bp3::enclosed_pixels() const’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp:543:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] - 543 | for (int idx = 0; idx < spot_rectangle_vertices.size(); idx+=5){ - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp: In member function ‘scitbx::af::shared > rstbx::bandpass::use_case_bp3::selected_hi_predictions() const’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp:752:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] - 752 | for (int idx = 0; idx < lo_E_limit.size(); ++idx){ - | ~~~~^~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp: In member function ‘scitbx::af::shared > rstbx::bandpass::use_case_bp3::selected_lo_predictions() const’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp:763:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] - 763 | for (int idx = 0; idx < lo_E_limit.size(); ++idx){ - | ~~~~^~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp: In member function ‘scitbx::af::shared > rstbx::bandpass::use_case_bp3::selected_predictions() const’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp:774:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] - 774 | for (int idx = 0; idx < lo_E_limit.size(); ++idx){ - | ~~~~^~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp: In member function ‘scitbx::af::shared > rstbx::bandpass::use_case_bp3::selected_predictions_labelit_format() const’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp:787:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] - 787 | for (int idx = 0; idx < lo_E_limit.size(); ++idx){ - | ~~~~^~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp: In member function ‘scitbx::af::shared > rstbx::bandpass::use_case_bp3::selected_hkls() const’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp:802:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] - 802 | for (int idx = 0; idx < lo_E_limit.size(); ++idx){ - | ~~~~^~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp: In member function ‘scitbx::af::shared > rstbx::bandpass::use_case_bp3::restricted_to_active_areas(scitbx::af::shared, scitbx::af::shared >) const’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp:815:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] - 815 | for (int idx = 0; idx < active_areas.size(); idx+=4){ - | ~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp: In member function ‘void rstbx::bandpass::use_case_bp3::set_subpixel(scitbx::af::shared, scitbx::af::shared)’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp:828:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] - 828 | for (int ixx=0; ixx< rotations_deg.size(); ++ixx){ //DEPRECATED - | ~~~^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp: In function ‘scitbx::af::shared > rstbx::bandpass::ext::use_case_bp2_picture_fast_slow(scitbx::af::shared >, const cctbx::crystal_orientation&, const scitbx::vec3&, const double&, const scitbx::vec3&, const scitbx::vec3&, const scitbx::vec3&, const scitbx::vec3&, const scitbx::vec3&, const double&, const scitbx::vec3&, const double&)’: -/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){ - | ~~~~^~~~~~~~~~~~~~~~ -/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] - 631 | for (int idx = 0; idx < spot_rectangle_vertices.size(); idx+=5){ - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/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 = unlimited_pixel_accept_policy]’: -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp:620:78: 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] -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 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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +Create symlinks for: 'lib/mmtbx_utils_ext.so.0.0.1' + 'lib/mmtbx_utils_ext.so.0'->'lib/mmtbx_utils_ext.so.0.0.1' + 'lib/mmtbx_utils_ext.so'->'lib/mmtbx_utils_ext.so.0.0.1' +Create symlinks for: 'lib/mmtbx_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' 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] @@ -13957,6 +14017,7 @@ /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/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 /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] @@ -13965,26 +14026,34 @@ /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] -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, +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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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 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 +/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/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/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("") - | ^~~~~~~~~~~~~~~~~~~~~~~ + from /usr/include/boost/python/object.hpp:9, + from /usr/include/boost/python/scope.hpp:9, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp:4: +/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()); + | ^~~~~~~~~~~~~ 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, @@ -14005,29 +14074,12 @@ /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/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/config/no_tr1/memory.hpp:21, - from /usr/include/boost/get_pointer.hpp:14, - from /usr/include/boost/python/object/pointer_holder.hpp:11, - from /usr/include/boost/python/to_python_indirect.hpp:10, - from /usr/include/boost/python/converter/arg_to_python.hpp:10, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/object.hpp:9, - from /usr/include/boost/python/scope.hpp:9, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/bandpass/ext.cpp:4: -/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 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 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/x86_64-linux-gnu -Llib -L/build/reproducible-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/x86_64-linux-gnu -Llib -L/build/reproducible-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 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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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/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, @@ -14070,10 +14122,7 @@ /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) { | ~~^~~~ -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 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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/indexing_api/ext.cpp: In member function ‘void indexing_api::rayleigh_cpp::estimate_parameters_from_cdf(scitbx::af::shared, scitbx::af::shared)’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/indexing_api/ext.cpp:59:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 59 | for (int i=0; i < x_data.size(); ++i){ @@ -14100,24 +14149,6 @@ 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/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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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' -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 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 -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 -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/x86_64-linux-gnu -Llib -L/build/reproducible-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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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/mmtbx_scaling_ext.so.0.0.1' - 'lib/mmtbx_scaling_ext.so.0'->'lib/mmtbx_scaling_ext.so.0.0.1' - 'lib/mmtbx_scaling_ext.so'->'lib/mmtbx_scaling_ext.so.0.0.1' -g++ -o 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 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, @@ -14138,6 +14169,12 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +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/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/x86_64-linux-gnu -Llib -L/build/reproducible-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_scaling_ext.so.0.0.1' + 'lib/mmtbx_scaling_ext.so.0'->'lib/mmtbx_scaling_ext.so.0.0.1' + 'lib/mmtbx_scaling_ext.so'->'lib/mmtbx_scaling_ext.so.0.0.1' +g++ -o 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 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, @@ -14225,6 +14262,16 @@ /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){ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/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) { + | ~~^~~~~~~~~~~ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_ext.cpp:375:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] + 375 | for(int n=0; n < n_repeats; ++n) { + | ~~^~~~~~~~~~~ +/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) { + | ~~^~~~~~~~~~~ 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] @@ -14241,21 +14288,6 @@ /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)) { \ | ^~~~~~~~~ -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/x86_64-linux-gnu -Llib -L/build/reproducible-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 -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_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 -/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) { - | ~~^~~~~~~~~~~ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_ext.cpp:375:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] - 375 | for(int n=0; n < n_repeats; ++n) { - | ~~^~~~~~~~~~~ -/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) { - | ~~^~~~~~~~~~~ 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, @@ -14676,439 +14708,46 @@ /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] -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_size_t.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 /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/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] - 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 = 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] - 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 unsigned int]’: -/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/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 = unsigned int]’: -/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/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 /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, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/flex_types.h:7, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/simulation/sim_xfel1.h:4: -/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::vec3]’: -/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()); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -/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/detail/push_back_etc.h:175:26: note: ‘’ declared here - 175 | resize(new_size, ElementType()); - | ^~~~~~~~~~~~~ -/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]’ -/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/flex_wrapper.h:616:41: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = equal_to; _Tp = long unsigned 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 = 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: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 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/boost_python/flex_wrapper.h:621:40: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = equal_to; _Tp = long unsigned 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 = unsigned char; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >; e_t = unsigned 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 = 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/boost_python/flex_wrapper.h:616:41: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = equal_to; _Tp = unsigned 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 = unsigned char; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >; e_t = unsigned 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 = 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/boost_python/flex_wrapper.h:621:40: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = equal_to; _Tp = unsigned 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) - | ^~~~~~~ -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_bool.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/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 unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >; e_t = short 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 = 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/boost_python/flex_wrapper.h:616:41: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = equal_to; _Tp = short unsigned 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 unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >; e_t = short 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 = 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/boost_python/flex_wrapper.h:621:40: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = equal_to; _Tp = short unsigned 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) - | ^~~~~~~ -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/x86_64-linux-gnu -Llib -L/build/reproducible-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 -/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 = 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: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 = 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/boost_python/flex_wrapper.h:616:41: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = equal_to; _Tp = unsigned 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 = 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]’ -/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/boost_python/flex_wrapper.h:621:40: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = equal_to; _Tp = unsigned 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 /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/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()); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -/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 cctbx::crystal_orientation&’ to ‘void scitbx::af::shared_plain::resize(const size_type&, const ElementType&) [with ElementType = cctbx::crystal_orientation]’ 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/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_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 -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 = 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/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 = 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/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_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]’ -/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/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 = 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/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_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 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/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 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/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/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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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 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/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 = 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/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 = 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]’ -/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 = 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:806:13: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = long unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ -/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:89:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 89 | for (int i=0;i >&, small, const const_ref >&) [with T = long unsigned int]’: -/build/reproducible-path/cctbx-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:114:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 114 | for (int i=0;i > scitbx::af::copy_slice(const const_ref >&, small) [with T = unsigned 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]’ -/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 = 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:89:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 89 | for (int i=0;i >&, small, const const_ref >&) [with T = unsigned char]’: -/build/reproducible-path/cctbx-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: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'lib/rstbx_indexing_api_ext.so.0.0.1' - 'lib/rstbx_indexing_api_ext.so'->'lib/rstbx_indexing_api_ext.so.0.0.1' -/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]’ -/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 = 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:89:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 89 | for (int i=0;i >&, small, const const_ref >&) [with T = short unsigned int]’: -/build/reproducible-path/cctbx-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:114:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 114 | for (int i=0;i > scitbx::af::copy_slice(const const_ref >&, small) [with T = unsigned int]’: -/build/reproducible-path/cctbx-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]’ -/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 = 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:89:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 89 | for (int i=0;i >&, small, const const_ref >&) [with T = unsigned int]’: -/build/reproducible-path/cctbx-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: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; -/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] +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/x86_64-linux-gnu -Llib -L/build/reproducible-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 +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_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 +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_bool.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 /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/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] @@ -15135,20 +14774,6 @@ /usr/include/c++/12/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -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_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 -/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] 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, @@ -15172,6 +14797,23 @@ /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/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, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/flex_types.h:7, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/rstbx/simulation/sim_xfel1.h:4: +/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::vec3]’: +/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()); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +/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/detail/push_back_etc.h:175:26: note: ‘’ declared here + 175 | resize(new_size, ElementType()); + | ^~~~~~~~~~~~~ +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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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/x86_64-linux-gnu -Llib -L/build/reproducible-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 /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]’ @@ -15189,6 +14831,16 @@ /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::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()); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +/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 cctbx::crystal_orientation&’ to ‘void scitbx::af::shared_plain::resize(const size_type&, const ElementType&) [with ElementType = cctbx::crystal_orientation]’ 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/detail/push_back_etc.h:175:26: note: ‘’ declared here + 175 | resize(new_size, ElementType()); + | ^~~~~~~~~~~~~ /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 = 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 >]’ @@ -15197,7 +14849,6 @@ /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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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 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, @@ -15236,13 +14887,11 @@ 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 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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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 -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 -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_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 +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 +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_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 /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] @@ -15283,7 +14932,41 @@ /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 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/x86_64-linux-gnu -Llib -L/build/reproducible-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 +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_size_t.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 /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/boost_python/flex_wrapper.h: In instantiation of ‘static boost::optional scitbx::af::boost_python::flex_wrapper::first_index_a_s(const f_t&, e_t) [with ElementType = int; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >; e_t = int]’: /build/reproducible-path/cctbx-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]’ @@ -15316,6 +14999,7 @@ /usr/include/c++/12/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ +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/x86_64-linux-gnu -Llib -L/build/reproducible-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 /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]’ @@ -15360,10 +15044,10 @@ /usr/include/c++/12/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -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_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 +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_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 = 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]’ @@ -15386,63 +15070,146 @@ /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/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] + 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/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("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -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]); - | ~~^~~~~~~~~~~~~ +/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 = 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] + 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 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/x86_64-linux-gnu -Llib -L/build/reproducible-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 +/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 unsigned int]’: +/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/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 = unsigned int]’: +/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/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); + | ^~~~~~~~~~~~~ +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_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 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]’ +/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/flex_wrapper.h:616:41: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = equal_to; _Tp = long unsigned 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 = 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: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 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/boost_python/flex_wrapper.h:621:40: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = equal_to; _Tp = long unsigned 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 = unsigned char; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >; e_t = unsigned 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 = 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/boost_python/flex_wrapper.h:616:41: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = equal_to; _Tp = unsigned 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 = unsigned char; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >; e_t = unsigned 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 = 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/boost_python/flex_wrapper.h:621:40: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = equal_to; _Tp = unsigned 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) + | ^~~~~~~ +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/x86_64-linux-gnu -Llib -L/build/reproducible-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 +/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 unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >; e_t = short 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 = 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/boost_python/flex_wrapper.h:616:41: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = equal_to; _Tp = short unsigned 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 unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >; e_t = short 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 = 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/boost_python/flex_wrapper.h:621:40: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = equal_to; _Tp = short unsigned 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 = 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: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 = 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/boost_python/flex_wrapper.h:616:41: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = equal_to; _Tp = unsigned 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 = 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]’ +/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/boost_python/flex_wrapper.h:621:40: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = equal_to; _Tp = unsigned 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) + | ^~~~~~~ +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_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 /usr/include/boost/assert.hpp:58, from /usr/include/boost/move/detail/type_traits.hpp:33, from /usr/include/boost/move/traits.hpp:31, @@ -15474,51 +15241,6 @@ /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 = 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] -/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]’ -/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/boost_python/flex_wrapper.h:616:41: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = equal_to; _Tp = float]’ 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 = 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: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 = 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]’ -/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/boost_python/flex_wrapper.h:621:40: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = equal_to; _Tp = float]’ 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_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); - | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ -/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/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]’ @@ -15528,23 +15250,6 @@ /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 /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( - | ^~~~~~~~~~~~~~~~~~~~ /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 = 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]’ @@ -15554,9 +15259,6 @@ /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] -/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/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 = 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]’ @@ -15575,36 +15277,6 @@ /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] -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/x86_64-linux-gnu -Llib -L/build/reproducible-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, - 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 = 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: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 = 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: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 = 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]’ -/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] - 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 = 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: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 = 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: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 = 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]’ -/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/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]’ @@ -15623,10 +15295,6 @@ /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] -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_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 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]’ @@ -15652,19 +15320,35 @@ /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}::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) { - | ^ +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 = 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/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 = 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/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 ‘scitbx::af::versa > scitbx::af::copy_slice(const const_ref >&, small) [with T = long 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 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 = long int; GetitemReturnValuePolicy = boost::python::return_value_policy]’ @@ -15689,36 +15373,6 @@ /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 = 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]’ -/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 = float; 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 = 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: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 = 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: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 = 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]’ -/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: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 = 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 >]’ -/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 = float; 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 = 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: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 = 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: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 = 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]’ -/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: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 >&)’: -/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 << ","; - | ~~^~~~~~~~~~~~~~~~~~~~~ /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 = 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]’ @@ -15767,12 +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::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]’ +/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/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 = 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/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_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 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/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 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/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 = 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 >]’ @@ -15785,17 +15465,22 @@ /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 = 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 >]’ -/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 = float; 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 = 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: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 = 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: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 = 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]’ -/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/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 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/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 = 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/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 = 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 >]’ @@ -15818,16 +15503,66 @@ /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] -/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); +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]’ +/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 = 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:806:13: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = long unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ +/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:89:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 89 | for (int i=0;i >&, small, const const_ref >&) [with T = long unsigned int]’: +/build/reproducible-path/cctbx-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:114:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 114 | for (int i=0;i > scitbx::af::copy_slice(const const_ref >&, small) [with T = unsigned 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]’ +/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 = 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:89:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 89 | for (int i=0;i >&, small, const const_ref >&) [with T = unsigned char]’: +/build/reproducible-path/cctbx-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: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 >]’ @@ -15839,6 +15574,343 @@ /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] +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( + | ^~~~~~~~~~~~~~~~~~~~ +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/x86_64-linux-gnu -Llib -L/build/reproducible-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 +/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 = 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]’ +/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 = 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:89:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 89 | for (int i=0;i >&, small, const const_ref >&) [with T = short unsigned int]’: +/build/reproducible-path/cctbx-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:114:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 114 | for (int i=0;i > scitbx::af::copy_slice(const const_ref >&, small) [with T = unsigned int]’: +/build/reproducible-path/cctbx-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]’ +/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 = 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:89:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 89 | for (int i=0;i >&, small, const const_ref >&) [with T = unsigned int]’: +/build/reproducible-path/cctbx-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: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'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_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 +/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; +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]); + | ~~^~~~~~~~~~~~~ +/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]’ +/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/boost_python/flex_wrapper.h:616:41: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = equal_to; _Tp = float]’ 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 = 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: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 = 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]’ +/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/boost_python/flex_wrapper.h:621:40: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = equal_to; _Tp = float]’ 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] +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 = 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: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 = 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: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 = 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]’ +/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] + 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 = 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: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 = 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: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 = 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]’ +/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/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] +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]’ +/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 = float; 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 = 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: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 = 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: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 = 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]’ +/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: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 = 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 >]’ +/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 = float; 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 = 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: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 = 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: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 = 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]’ +/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: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 = 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/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 >]’ +/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 = float; 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 = 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: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 = 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: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 = 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]’ +/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; +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_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_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 +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_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); + | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ +/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/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/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 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); + | ^~~~~~~~~~~~~ +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: +/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/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/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]’ @@ -15869,23 +15941,6 @@ /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_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] - 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 /usr/include/boost/assert.hpp:58, from /usr/include/boost/move/detail/type_traits.hpp:33, from /usr/include/boost/move/traits.hpp:31, @@ -15915,6 +15970,31 @@ /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] +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] 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]’ @@ -15938,7 +16018,6 @@ /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 = 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 >]’ @@ -15950,6 +16029,51 @@ /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 /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 = 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 /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] + 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/boost_python/flex_std_string.cpp:1: /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 = std::__cxx11::basic_string; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa, scitbx::af::flex_grid<> >; e_t = std::__cxx11::basic_string]’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_wrapper.h:885:12: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::ordered(const std::string&, const boost::python::api::object&) [with ElementType = std::__cxx11::basic_string; 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]’ @@ -15983,10 +16107,6 @@ /usr/include/c++/12/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -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 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, @@ -16014,41 +16134,6 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_wrapper.h:888:19: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::ordered(const std::string&, const boost::python::api::object&) [with ElementType = std::__cxx11::basic_string; 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_std_string.cpp:132:16: 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_complex_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); - | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ -/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/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("") - | ^~~~~~~~~~~~~~~~~~~~~~~ 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::__cxx11::basic_string]’: /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::__cxx11::basic_string; GetitemReturnValuePolicy = boost::python::return_value_policy]’ @@ -16077,76 +16162,21 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/flex_std_string.cpp:132:16: 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] -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 = 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; 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_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 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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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_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 lib/rstbx_array_family_flex_ext.so.0.0.1 -shared -rdynamic -std=c++11 -Wl,-soname=rstbx_array_family_flex_ext.so.0 rstbx/array_family/ext.o rstbx/array_family/flex_rstbx_arrays.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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_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 -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_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 +g++ -o lib/rstbx_array_family_flex_ext.so.0.0.1 -shared -rdynamic -std=c++11 -Wl,-soname=rstbx_array_family_flex_ext.so.0 rstbx/array_family/ext.o rstbx/array_family/flex_rstbx_arrays.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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 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]’ @@ -16155,6 +16185,12 @@ /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) { | ~~^~~~~~~~~~~~~ +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_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, @@ -16170,26 +16206,7 @@ /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/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 /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 /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]’ @@ -16245,6 +16247,50 @@ /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::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<> >]’ +/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]’ +/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::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/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 +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 >&, 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<> >]’ -/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]’ -/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::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/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::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]’ @@ -16333,13 +16371,12 @@ /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::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<> >]’ -/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]’ -/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::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/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<> >]’ +/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]’ +/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::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/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::vec2]’: @@ -16365,6 +16402,7 @@ /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/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 /usr/include/boost/assert.hpp:58, from /usr/include/boost/move/detail/type_traits.hpp:33, from /usr/include/boost/move/traits.hpp:31, @@ -16413,7 +16451,6 @@ /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; -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 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, @@ -16439,6 +16476,54 @@ 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::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] + 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::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, + 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, 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, @@ -16480,56 +16565,8 @@ /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; -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::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] - 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::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; -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 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 +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 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: @@ -16556,93 +16593,6 @@ /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/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 -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::sym_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()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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::sym_mat3&’ to ‘_ForwardIterator std::uninitialized_fill_n(_ForwardIterator, _Size, const _Tp&) [with _ForwardIterator = scitbx::sym_mat3*; _Size = long unsigned int; _Tp = scitbx::sym_mat3]’ declared here - 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::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()); - | ^~~~~~~~~~~~~ -/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: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::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()); - | ^~~~~~~~~~~~~ -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 -/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 /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, @@ -16665,33 +16615,19 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +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 -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: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::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 - 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::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()); + | ^~~~~~~~~~~~~ /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] @@ -16972,17 +16908,96 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/boost_python/numpy_bridge.cpp:138:5: note: in expansion of macro ‘SCITBX_ASSERT’ 138 | SCITBX_ASSERT(grid.size_1d() == PyArray_Size(obj_ptr)); | ^~~~~~~~~~~~~ -/build/reproducible-path/cctbx-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<>]’: +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::sym_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()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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::sym_mat3&’ to ‘_ForwardIterator std::uninitialized_fill_n(_ForwardIterator, _Size, const _Tp&) [with _ForwardIterator = scitbx::sym_mat3*; _Size = long unsigned int; _Tp = scitbx::sym_mat3]’ declared here + 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/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()); + | ^~~~~~~~~~~~~ +/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::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::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::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()); + | ^~~~~~~~~~~~~ +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 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, @@ -17007,6 +17022,17 @@ /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::vector; GetitemReturnValuePolicy = boost::python::return_internal_reference<>; 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:41:51: 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/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()); + | ^~~~~~~~~~~~~ /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::set; GetitemReturnValuePolicy = boost::python::return_internal_reference<>; std::string = std::__cxx11::basic_string]’ @@ -17027,6 +17053,17 @@ /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:50:40: 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] +/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()); + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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::vec2&’ to ‘void scitbx::af::shared_plain::resize(const size_type&, const ElementType&) [with ElementType = scitbx::vec2]’ declared here + 165 | void resize(size_type const& new_size, ElementType const& x) { + | ^~~~~~ +/build/reproducible-path/cctbx-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/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 = scitbx::af::tiny; GetitemReturnValuePolicy = boost::python::return_value_policy; std::string = std::__cxx11::basic_string]’ @@ -17035,7 +17072,7 @@ 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::vec3]’: +/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()); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -17052,7 +17089,7 @@ 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::vec3&’ to ‘_ForwardIterator std::uninitialized_fill_n(_ForwardIterator, _Size, const _Tp&) [with _ForwardIterator = scitbx::vec3*; _Size = long unsigned int; _Tp = scitbx::vec3]’ 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 @@ -17061,7 +17098,7 @@ 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::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::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()); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -17078,44 +17115,12 @@ 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::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 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::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()); - | ^~~~~~~~~~~~~ -/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()); - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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::vec2&’ to ‘void scitbx::af::shared_plain::resize(const size_type&, const ElementType&) [with ElementType = scitbx::vec2]’ declared here - 165 | void resize(size_type const& new_size, ElementType const& x) { - | ^~~~~~ -/build/reproducible-path/cctbx-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++) { - | ~~^~~~~~~~~~~~~~~~~~~~ -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 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, @@ -17136,27 +17141,37 @@ /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/scitbx/glmtbx/boost_python/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 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 +/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/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++) { + | ~~^~~~~~~~~~~~~~~~~~~~ +/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 /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 @@ -17166,6 +17181,7 @@ 63 | if (i_cub[1] < 0 || i_cub[1] >= n_cubicles[1]) continue; /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/cubicle_neighbors.hpp:65:40: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare] 65 | if (i_cub[2] < 0 || i_cub[2] >= n_cubicles[2]) continue; +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 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]’ @@ -17182,9 +17198,28 @@ /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 /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/scitbx/glmtbx/boost_python/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 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 -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 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, @@ -17197,7 +17232,6 @@ /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; | ~~^~~~ -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 /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()) { @@ -17223,12 +17257,18 @@ /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/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 +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 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 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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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_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/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 +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/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 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 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, @@ -17237,8 +17277,13 @@ /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 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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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 +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/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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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/serialization/base_256.h:2, from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/math/floating_point_epsilon.h:4, @@ -17301,6 +17346,11 @@ /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'lib/scitbx_glmtbx_ext.so.0.0.1' + 'lib/scitbx_glmtbx_ext.so'->'lib/scitbx_glmtbx_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 /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/lbfgsb.h: In instantiation of ‘scitbx::lbfgsb::minimizer::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&]’ @@ -17337,25 +17387,12 @@ /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/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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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 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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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/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 -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/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 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 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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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 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/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 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, @@ -17376,7 +17413,6 @@ /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/x86_64-linux-gnu -Llib -L/build/reproducible-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, @@ -17391,48 +17427,48 @@ /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/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 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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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 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 Create symlinks for: 'lib/scitbx_fftpack_ext.so.0.0.1' 'lib/scitbx_fftpack_ext.so.0'->'lib/scitbx_fftpack_ext.so.0.0.1' 'lib/scitbx_fftpack_ext.so'->'lib/scitbx_fftpack_ext.so.0.0.1' -g++ -o scitbx/math/boost_python/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 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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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 +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/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 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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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/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 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/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 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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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/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 g++ -o scitbx/math/boost_python/resample.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-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/resample.cpp g++ -o scitbx/math/boost_python/quadrature.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-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/quadrature.cpp +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 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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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 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/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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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 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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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 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/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 g++ -o scitbx/math/boost_python/zernike.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-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/zernike.cpp g++ -o scitbx/math/boost_python/zernike_moments.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-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/zernike_moments.cpp g++ -o scitbx/math/boost_python/2d_zernike_moments.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-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/2d_zernike_moments.cpp @@ -17460,6 +17496,7 @@ /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/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 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, @@ -17480,7 +17517,6 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -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 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 /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, @@ -17523,6 +17559,7 @@ /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/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 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, @@ -17535,6 +17572,7 @@ /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/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 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]’: @@ -17593,20 +17631,19 @@ /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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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 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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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 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 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 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 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&)’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/stl/set_wrapper.h:52:28: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] @@ -17643,6 +17680,37 @@ /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/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 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 +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/class.hpp:9, + from /usr/include/boost/python/class.hpp:13, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/stl/vector_wrapper.h:4, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/stl/vector_ext.cpp:2: +/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/stl/vector_wrapper.h:121:52: required from ‘static void scitbx::stl::boost_python::vector_wrapper::wrap(const std::string&) [with ElementType = unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; std::string = std::__cxx11::basic_string]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/stl/vector_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] + 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::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/stl/vector_wrapper.h:121:52: required from ‘static void scitbx::stl::boost_python::vector_wrapper::wrap(const std::string&) [with ElementType = double; GetitemReturnValuePolicy = boost::python::return_value_policy; std::string = std::__cxx11::basic_string]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/stl/vector_ext.cpp:11:33: 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/boost_python/container_conversions.h: In instantiation of ‘static void* scitbx::boost_python::container_conversions::from_python_sequence::convertible(PyObject*) [with ContainerType = std::vector, std::allocator > >; 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, std::allocator > >; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/stl/vector_wrapper.h:121:52: required from ‘static void scitbx::stl::boost_python::vector_wrapper::wrap(const std::string&) [with ElementType = std::set; GetitemReturnValuePolicy = boost::python::return_internal_reference<>; std::string = std::__cxx11::basic_string]’ +/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/stl/vector_ext.cpp:14:50: 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/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/versa_matrix.h:4: @@ -17677,59 +17745,7 @@ /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/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 /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/class.hpp:9, - from /usr/include/boost/python/class.hpp:13, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/stl/vector_wrapper.h:4, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/stl/vector_ext.cpp:2: -/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/stl/vector_wrapper.h:121:52: required from ‘static void scitbx::stl::boost_python::vector_wrapper::wrap(const std::string&) [with ElementType = unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; std::string = std::__cxx11::basic_string]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/stl/vector_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] - 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::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/stl/vector_wrapper.h:121:52: required from ‘static void scitbx::stl::boost_python::vector_wrapper::wrap(const std::string&) [with ElementType = double; GetitemReturnValuePolicy = boost::python::return_value_policy; std::string = std::__cxx11::basic_string]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/stl/vector_ext.cpp:11:33: 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/boost_python/container_conversions.h: In instantiation of ‘static void* scitbx::boost_python::container_conversions::from_python_sequence::convertible(PyObject*) [with ContainerType = std::vector, std::allocator > >; 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, std::allocator > >; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/stl/vector_wrapper.h:121:52: required from ‘static void scitbx::stl::boost_python::vector_wrapper::wrap(const std::string&) [with ElementType = std::set; GetitemReturnValuePolicy = boost::python::return_internal_reference<>; std::string = std::__cxx11::basic_string]’ -/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/stl/vector_ext.cpp:14:50: 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 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 -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] - 175 | resize(new_size, ElementType()); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -/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/detail/push_back_etc.h:175:26: note: ‘’ declared here - 175 | resize(new_size, ElementType()); - | ^~~~~~~~~~~~~ -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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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 lib/scitbx_suffixtree_shared_ext.so.0.0.1 -shared -rdynamic -std=c++11 -Wl,-soname=scitbx_suffixtree_shared_ext.so.0 scitbx/suffixtree/boost_python/suffixtree_shared_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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_shared_ext.so.0.0.1' - 'lib/scitbx_suffixtree_shared_ext.so.0'->'lib/scitbx_suffixtree_shared_ext.so.0.0.1' - 'lib/scitbx_suffixtree_shared_ext.so'->'lib/scitbx_suffixtree_shared_ext.so.0.0.1' g++ -o smtbx/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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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 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, @@ -17750,70 +17766,90 @@ /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/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/x86_64-linux-gnu -Llib -L/build/reproducible-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_suffixtree_shared_ext.so.0.0.1 -shared -rdynamic -std=c++11 -Wl,-soname=scitbx_suffixtree_shared_ext.so.0 scitbx/suffixtree/boost_python/suffixtree_shared_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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/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] + 175 | resize(new_size, ElementType()); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +/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/detail/push_back_etc.h:175:26: note: ‘’ declared here + 175 | resize(new_size, ElementType()); + | ^~~~~~~~~~~~~ +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/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 +Create symlinks for: 'lib/scitbx_suffixtree_shared_ext.so.0.0.1' + 'lib/scitbx_suffixtree_shared_ext.so.0'->'lib/scitbx_suffixtree_shared_ext.so.0.0.1' + 'lib/scitbx_suffixtree_shared_ext.so'->'lib/scitbx_suffixtree_shared_ext.so.0.0.1' g++ -o smtbx/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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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 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/x86_64-linux-gnu -Llib -L/build/reproducible-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 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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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 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/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 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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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 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 +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/x86_64-linux-gnu -Llib -L/build/reproducible-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' -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/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 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/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/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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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 -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/scaled_adp.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/x86_64-linux-gnu -Llib -L/build/reproducible-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 +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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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' +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/scatterer_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/scatterer_parameters.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/x86_64-linux-gnu -Llib -L/build/reproducible-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 -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/x86_64-linux-gnu -Llib -L/build/reproducible-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' - 'lib/scitbx_rigid_body_ext.so.0'->'lib/scitbx_rigid_body_ext.so.0.0.1' - 'lib/scitbx_rigid_body_ext.so'->'lib/scitbx_rigid_body_ext.so.0.0.1' g++ -o smtbx/refinement/constraints/boost_python/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 Create symlinks for: 'lib/scitbx_math_ext.so.0.0.1' 'lib/scitbx_math_ext.so.0'->'lib/scitbx_math_ext.so.0.0.1' 'lib/scitbx_math_ext.so'->'lib/scitbx_math_ext.so.0.0.1' g++ -o smtbx/refinement/constraints/boost_python/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 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/x86_64-linux-gnu -Llib -L/build/reproducible-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' + 'lib/scitbx_rigid_body_ext.so.0'->'lib/scitbx_rigid_body_ext.so.0.0.1' + 'lib/scitbx_rigid_body_ext.so'->'lib/scitbx_rigid_body_ext.so.0.0.1' g++ -o smtbx/refinement/constraints/boost_python/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_stl_vector_ext.so.0.0.1 -shared -rdynamic -std=c++11 -Wl,-soname=scitbx_stl_vector_ext.so.0 scitbx/stl/vector_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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_vector_ext.so.0.0.1' 'lib/scitbx_stl_vector_ext.so.0'->'lib/scitbx_stl_vector_ext.so.0.0.1' 'lib/scitbx_stl_vector_ext.so'->'lib/scitbx_stl_vector_ext.so.0.0.1' -g++ -o smtbx/refinement/constraints/boost_python/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/x86_64-linux-gnu -Llib -L/build/reproducible-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 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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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/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 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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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 +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/structure_factors/direct/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/smtbx/structure_factors/direct/boost_python/ext.cpp g++ -o smtbx/structure_factors/direct/boost_python/standard_xray.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-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/structure_factors/direct/boost_python/standard_xray.cpp g++ -o spotfinder/array_family/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 -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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/array_family/src -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/spotfinder/array_family/src -Ispotfinder/array_family/include -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/spotfinder/array_family/include /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/spotfinder/array_family/flex_ext.cpp @@ -17830,6 +17866,7 @@ g++ -o scitbx/array_family/boost_python/regression_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 -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/regression_test_ext.cpp 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 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/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, @@ -17942,10 +17979,30 @@ /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 /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/spotfinder/diffraction/geometry.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( + | ^~~~~~~~~~~~~~~~~~~~ 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, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_af_1.cpp:1: + 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/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, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_af_2.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]; \ @@ -17972,6 +18029,36 @@ /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) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/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/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] /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]; \ @@ -18050,39 +18137,62 @@ /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/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] -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: -/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/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] +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, + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_af_1.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/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, @@ -18096,13 +18206,71 @@ 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/diffraction/geometry.cpp:1: + 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( | ^~~~~~~~~~~~~~~~~~~~ +/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, + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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 ‘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]; \ + | ^~ +/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/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/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/versa_plain.h: In member function ‘const ElementType& scitbx::af::versa_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/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/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/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 /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: +/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/scitbx/array_family/tst_af_1.cpp: In instantiation of ‘static void {anonymous}::array_exercise::run_2() [with ArrayType = scitbx::af::small_plain]’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_af_1.cpp:29:12: required from ‘static void {anonymous}::array_exercise::run() [with ArrayType = scitbx::af::small_plain]’ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_af_1.cpp:619:52: required from here @@ -18186,6 +18354,28 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +g++ -o scitbx/array_family/tst_af_2 -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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/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( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +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, @@ -18220,58 +18410,9 @@ /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/smtbx_stl_map_ext.so.0.0.1 -shared -rdynamic -std=c++11 -Wl,-soname=smtbx_stl_map_ext.so.0 smtbx/stl/map_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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_stl_map_ext.so.0.0.1' - 'lib/smtbx_stl_map_ext.so.0'->'lib/smtbx_stl_map_ext.so.0.0.1' - 'lib/smtbx_stl_map_ext.so'->'lib/smtbx_stl_map_ext.so.0.0.1' -g++ -o scitbx/array_family/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/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/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( - | ^~~~~~~~~~~~~~~~~~~~ -/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/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( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -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 /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/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, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_af_2.cpp:1: + 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: /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]; \ @@ -18298,6 +18439,9 @@ /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_stl_map_ext.so.0.0.1' + 'lib/smtbx_stl_map_ext.so.0'->'lib/smtbx_stl_map_ext.so.0.0.1' + 'lib/smtbx_stl_map_ext.so'->'lib/smtbx_stl_map_ext.so.0.0.1' /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]; \ @@ -18350,6 +18494,7 @@ /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/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 /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]; \ @@ -18376,9 +18521,11 @@ /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_accessors -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -pthread scitbx/array_family/tst_accessors.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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 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: + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_af_4.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]; \ @@ -18405,6 +18552,7 @@ /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 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 /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]; \ @@ -18483,16 +18631,10 @@ /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, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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_accessors -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -pthread scitbx/array_family/tst_accessors.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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_2 -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-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/x86_64-linux-gnu -Llib -L/build/reproducible-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 mmtbx/masks/tst_mask -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -pthread mmtbx/masks/tst_mask.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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 -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_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 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/simple_io.h:5, - from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_af_4.cpp:1: + from /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_af_5.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]; \ @@ -18519,88 +18661,12 @@ /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, - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/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, - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/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]; \ - | ^~ -/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/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/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/versa_plain.h: In member function ‘const ElementType& scitbx::af::versa_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/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/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/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_1 -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-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/x86_64-linux-gnu -Llib -L/build/reproducible-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 /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: + 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/array_family/tst_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]; \ @@ -18653,39 +18719,9 @@ /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/array_family/tst_af_3 -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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 -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/array_family/tst_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) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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/x86_64-linux-gnu -Llib -L/build/reproducible-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, @@ -18719,7 +18755,6 @@ /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 scitbx/array_family/tst_af_3 -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-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/x86_64-linux-gnu -Llib -L/build/reproducible-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 /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]; \ @@ -18798,11 +18833,11 @@ /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_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 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/x86_64-linux-gnu -Llib -L/build/reproducible-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 +g++ -o scitbx/array_family/tst_af_1 -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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_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 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, @@ -18912,6 +18947,7 @@ /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_5 -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-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/x86_64-linux-gnu -Llib -L/build/reproducible-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/tst_rectangular_full_packed.cpp: In function ‘int main()’: /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/array_family/tst_rectangular_full_packed.cpp:52:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 52 | for(int i=0; i::at(size_type)’: @@ -18974,7 +19011,6 @@ /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/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 /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]; \ @@ -19027,6 +19063,8 @@ /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_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/array_family/tst_rectangular_full_packed -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-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/x86_64-linux-gnu -Llib -L/build/reproducible-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 /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, @@ -19060,19 +19098,9 @@ /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/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/x86_64-linux-gnu -Llib -L/build/reproducible-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_af_5 -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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 g++ -o scitbx/array_family/tst_mat3 -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -pthread scitbx/array_family/tst_mat3.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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/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_optional_copy -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-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/x86_64-linux-gnu -Llib -L/build/reproducible-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/array_family/tst_ref_matrix_facet -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-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/x86_64-linux-gnu -Llib -L/build/reproducible-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/x86_64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -pthread scitbx/error/tst_error.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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 /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, @@ -19104,8 +19132,10 @@ /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/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/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/array_family/tst_unsigned_float_arithmetic -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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/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, @@ -19137,6 +19167,10 @@ /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/x86_64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -pthread scitbx/error/tst_error.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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/array_family/tst_ref_matrix_facet -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-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/x86_64-linux-gnu -Llib -L/build/reproducible-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/x86_64-linux-gnu -Llib -L/build/reproducible-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 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, @@ -19203,7 +19237,21 @@ /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_unsigned_float_arithmetic -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-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/x86_64-linux-gnu -Llib -L/build/reproducible-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: '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' +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; + | ~~^~~~ 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 g++ -o scitbx/array_family/tst_sym_mat3 -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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 @@ -19241,18 +19289,27 @@ /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/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()) { + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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) { + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o scitbx/array_family/tst_vec3 -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -pthread scitbx/array_family/tst_vec3.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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/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) { + | ~~~~~~~^~~~~ /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]; \ @@ -19286,21 +19343,11 @@ /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/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) { - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o scitbx/array_family/tst_vec3 -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -pthread scitbx/array_family/tst_vec3.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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/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/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/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]; \ @@ -19327,12 +19374,7 @@ /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/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) { - | ~~~~~~~^~~~~ +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 /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]; \ @@ -19359,11 +19401,7 @@ /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, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 scitbx/math/tests/tst.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/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/math/tests -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/math/tests /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/math/tests/tst.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: @@ -19393,7 +19431,6 @@ /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 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 /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]; \ @@ -19427,6 +19464,35 @@ /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 " ) | ^~~~~~~~~~~~~~~~~~~~~~~ +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] + 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]; \ @@ -19453,6 +19519,7 @@ /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/lbfgs/sdrive_fem -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -pthread scitbx/lbfgs/sdrive_fem.o scitbx/lbfgs/lbfgs_fem.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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/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, @@ -19512,38 +19579,6 @@ /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::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/lbfgs/sdrive_fem -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -pthread scitbx/lbfgs/sdrive_fem.o scitbx/lbfgs/lbfgs_fem.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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/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]; \ @@ -19570,6 +19605,7 @@ /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/x86_64-linux-gnu -Llib -L/build/reproducible-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 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: @@ -19577,9 +19613,7 @@ /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 " ) | ^~~~~~~~~~~~~~~~~~~~~~~ -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 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/x86_64-linux-gnu -Llib -L/build/reproducible-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 /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]; \ @@ -19637,6 +19671,7 @@ /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/lbfgsb/raw.h:3672:5: note: in expansion of macro ‘SCITBX_ASSERT’ 3672 | SCITBX_ASSERT(l.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:3673:28: warning: comparison of integer expressions of different signedness: ‘scitbx::af::const_ref::size_type’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare] 3673 | SCITBX_ASSERT(u.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’ @@ -19661,8 +19696,6 @@ /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/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 -g++ -o scitbx/matrix/tests/tst_givens.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/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_givens.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/driver3.cpp:1: @@ -19692,6 +19725,13 @@ /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/matrix/tests/tst_givens.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/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_givens.cpp +Create symlinks for: 'lib/smtbx_refinement_restraints_ext.so.0.0.1' + 'lib/smtbx_refinement_restraints_ext.so.0'->'lib/smtbx_refinement_restraints_ext.so.0.0.1' + 'lib/smtbx_refinement_restraints_ext.so'->'lib/smtbx_refinement_restraints_ext.so.0.0.1' +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' /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]; \ @@ -19718,7 +19758,7 @@ /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/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/x86_64-linux-gnu -Llib -L/build/reproducible-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 +g++ -o scitbx/matrix/tests/tst_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 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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_householder.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: @@ -19726,6 +19766,7 @@ /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/matrix/tests/tst_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 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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_svd.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]; \ @@ -19807,55 +19848,50 @@ /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/fftpack/timing/fftpack_timer -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -pthread scitbx/fftpack/timing/fftpack_timer.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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 -lomptbx -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/matrix/tests/tst_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 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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_householder.cpp -g++ -o scitbx/matrix/tests/tst_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 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1 -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+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_svd.cpp g++ -o scitbx/math/tests/tst -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -pthread scitbx/math/tests/tst.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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/serialization/tst_base_256.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/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/serialization -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/serialization /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/serialization/tst_base_256.cpp -g++ -o scitbx/matrix/tests/tst_givens -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -pthread scitbx/matrix/tests/tst_givens.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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 -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -pthread scitbx/fftpack/timing/fftpack_timer.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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 -lomptbx -lm g++ -o scitbx/sparse/tests/tst_sparse.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/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/sparse/tests -I/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/sparse/tests /build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/scitbx/sparse/tests/tst_sparse.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/x86_64-linux-gnu -Llib -L/build/reproducible-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/lbfgsb/dev/driver1 -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -pthread scitbx/lbfgsb/dev/driver1.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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/serialization/tst_base_256 -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -pthread scitbx/serialization/tst_base_256.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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/matrix/tests/tst_givens -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -pthread scitbx/matrix/tests/tst_givens.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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/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 smtbx/refinement/constraints/tests/tst_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/tests/tst_geometrical_hydrogens.cpp -g++ -o scitbx/lbfgsb/dev/driver2 -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -pthread scitbx/lbfgsb/dev/driver2.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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_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/x86_64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -pthread scitbx/serialization/tst_base_256.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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/lbfgsb/dev/driver1 -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -pthread scitbx/lbfgsb/dev/driver1.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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/fftpack/timing/test0 -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -pthread scitbx/fftpack/timing/test0.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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 -lomptbx -lm +g++ -o scitbx/lbfgsb/dev/driver2 -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -pthread scitbx/lbfgsb/dev/driver2.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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/lbfgsb/dev/driver3 -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -pthread scitbx/lbfgsb/dev/driver3.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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: '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/matrix/tests/tst_cholesky -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -pthread scitbx/matrix/tests/tst_cholesky.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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/x86_64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -pthread scitbx/matrix/tests/tst_svd.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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_cholesky -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -pthread scitbx/matrix/tests/tst_cholesky.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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/x86_64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -pthread scitbx/matrix/tests/tst_householder.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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/x86_64-linux-gnu/hdf5/serial -lhdf5 -std=c++11 -pthread scitbx/sparse/tests/tst_sparse.o -L/usr/lib -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -Llib -L/build/reproducible-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 smtbx/refinement/constraints/tests/tst_reparametrisation -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-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/x86_64-linux-gnu -Llib -L/build/reproducible-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/x86_64-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/x86_64-linux-gnu -Llib -L/build/reproducible-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/x86_64-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/x86_64-linux-gnu -Llib -L/build/reproducible-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/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/x86_64-linux-gnu -Llib -L/build/reproducible-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 smtbx/refinement/constraints/tests/tst_geometrical_hydrogens -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-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/x86_64-linux-gnu -Llib -L/build/reproducible-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_reparametrisation -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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/x86_64-linux-gnu -Llib -L/build/reproducible-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_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 scitbx/array_family/tst_af_4 -rdynamic -Wl,-z,relro -L/usr/lib/x86_64-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/x86_64-linux-gnu -Llib -L/build/reproducible-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/x86_64-linux-gnu -Llib -L/build/reproducible-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 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/x86_64-linux-gnu -Llib -L/build/reproducible-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 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/x86_64-linux-gnu -Llib -L/build/reproducible-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: 71.63 seconds -wall clock time: 46 minutes 59.86 seconds (2819.86 seconds total) +usr+sys time: 67.76 seconds +wall clock time: 10 minutes 56.54 seconds (656.54 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 @@ -34654,39 +34690,7 @@ {'_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/samosa.scale"): 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/samosa_scale.py"), - relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/samosa.join"): 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/samosa_join.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.precession_view"): 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/precession_view.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.form_factor_query"): 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/form_factor_query.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.find_reticular_twin_laws"): 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/find_reticular_twin_laws.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.euclidean_model_matching"): 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/euclidean_model_matching.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.eltbx.show_fp_fdp"): 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/eltbx.show_fp_fdp.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.diffuse"): 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/diffuse.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.diffuse"): 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/diffuse.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.cod_select_and_pickle"): 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/cod_select_and_pickle.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_regression.test_nightly"): 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/cctbx_test_nightly.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.brehm_diederichs"): 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/brehm_diederichs.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.auto_sharpen"): 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/auto_sharpen.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.visualize_r_factors"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../crys3d/command_line/visualize_r_factors.py"), - relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/crys3d.qttbx.view_structure"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../crys3d/command_line/qttbx.view_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.multiplicity_viewer"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../crys3d/command_line/multiplicity_viewer.py"), - relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/crys3d.model_viewer"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../crys3d/command_line/model_viewer.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.make_install_HKLviewer_ChimeraX"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../crys3d/command_line/make_install_HKLviewer_ChimeraX.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.data_viewer"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../crys3d/command_line/hklview.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.data_viewer"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../crys3d/command_line/hklview.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.compare_datasets"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../crys3d/command_line/compare_datasets.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.HKLviewer"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../crys3d/command_line/HKLviewer.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.HKLviewer"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../crys3d/command_line/HKLviewer.py"), - relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/phasertng.HKLviewer"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../crys3d/command_line/HKLviewer.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.HKLinfo"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../crys3d/command_line/HKLinfo.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.HKLinfo"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../crys3d/command_line/HKLinfo.py"), - relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/smtbx.refine"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../smtbx/command_line/refine.py"), - relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/smtbx.masks"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../smtbx/command_line/masks.py"), - relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/smtbx.benchmark_refinement"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../smtbx/command_line/benchmark_refinement.py"), - relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/smtbx.anom_refine"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../smtbx/command_line/anom_refine.py"), - relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/smtbx.absolute_structure"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../smtbx/command_line/absolute_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/iotbx.xplor.map.show_summary"): 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/xplor.map.show_summary.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.unique_with_biomt"): 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/unique_with_biomt.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.unique_with_biomt"): 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/unique_with_biomt.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.unique_with_biomt"): 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/unique_with_biomt.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"): 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/symmetry_search.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.split_data_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/split_data_cif.py"), @@ -34784,10 +34788,9 @@ relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/mmtbx.superpose"): 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/superpose.py"), relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/mmtbx.super"): 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/super.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.suitename"): 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/suitename.py"), - relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/molprobity.suitename"): 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/suitename.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.suitename"): 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/suitename.py"), - relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/mmtbx.strip_model"): 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/strip_model.py"), - relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/mmtbx.ssm_rmsd_for_chains"): 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/ssm_rmsd_for_chains.py"), + relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/wxtbx.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"), + relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/scitbx.show_build_path"): 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_build_path.py"), + relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/annlib.show_build_path"): 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_build_path.py"), relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/cbflib.show_build_path"): 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_build_path.py"), relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/ccp4io.show_build_path"): 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_build_path.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.show_build_path"): 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_build_path.py"), @@ -34818,7 +34821,8 @@ relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/mmtbx.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"), relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/spotfinder.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"), relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/rstbx.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"), - relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/wxtbx.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"), + relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/wxtbx.anomalous_differences_histogram"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../wxtbx/command_line/anomalous_differences_histogram.py"), + relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/dxtbx.show_registry"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../dxtbx/src/dxtbx/command_line/show_registry.py"), relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/dxtbx.show_matching_formats"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../dxtbx/src/dxtbx/command_line/show_matching_formats.py"), relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/dxtbx.show_mask_info"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../dxtbx/src/dxtbx/command_line/show_mask_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/dxtbx.saturation"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../dxtbx/src/dxtbx/command_line/saturation.py"), @@ -34859,8 +34863,8 @@ relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/boost.show_build_path"): 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_build_path.py"), relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/omptbx.show_build_path"): 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_build_path.py"), relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/fable.show_build_path"): 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_build_path.py"), - relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/scitbx.show_build_path"): 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_build_path.py"), - relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/annlib.show_build_path"): 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_build_path.py"), + relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/mmtbx.anneal_real_space"): 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/anneal_real_space.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.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/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/mmtbx.analyze_static_disorder"): 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/analyze_static_disorder.py"), relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/mmtbx.analyze_peptides"): 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/analyze_peptides.py"), relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/mmtbx.altloc_remediate"): 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/altloc_remediate.py"), @@ -34891,8 +34895,8 @@ relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/cctbx.loggraph"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../wxtbx/command_line/loggraph.py"), relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/wxtbx.inspect_r_free_flags"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../wxtbx/command_line/inspect_r_free_flags.py"), relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/mmtbx.bfactor_plot"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../wxtbx/command_line/b_plot.py"), - relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/wxtbx.anomalous_differences_histogram"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../wxtbx/command_line/anomalous_differences_histogram.py"), - relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/dxtbx.show_registry"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../dxtbx/src/dxtbx/command_line/show_registry.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/mmtbx.extend_sidechains"): 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/extend_sidechains.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.evalurama"): 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/evalurama.py"), relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/mmtbx.estimate_bijvoet_ratio"): 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/estimate_bijvoet_ratio.py"), @@ -34925,8 +34929,8 @@ relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/mmtbx.build_alternate_conformations"): 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/build_alternate_conformations.py"), relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/mmtbx.simple_build_alt_confs"): 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/build_alt_confs_simple.py"), relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/mmtbx.apply_ncs_to_ligand"): 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/apply_ncs_to_ligand.py"), - relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/mmtbx.anneal_real_space"): 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/anneal_real_space.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.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/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.maximum_entropy_map"): 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/maximum_entropy_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/mmtbx.matthews"): 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/matthews.py"), relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/mmtbx.massage_data"): 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/massage_data.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.mask"): 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/mask.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.maps"): 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/maps.py"), @@ -34958,8 +34962,9 @@ relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/iotbx.fetch_pdb"): 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/fetch_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/phenix.fest"): 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/fest.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.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/mmtbx.prune_model"): 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/prune_model.py"), + relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/mmtbx.process_predicted_model"): 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/process_predicted_model.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.process_predicted_model"): 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/process_predicted_model.py"), relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/molprobity.probescore_ligand"): 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/probescore_ligand.py"), relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/mmtbx.probe2"): 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/probe2.py"), relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/mmtbx.prepare_pdb_deposition"): 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/prepare_pdb_deposition.py"), @@ -34992,8 +34997,10 @@ relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/phenix.model_model_distances"): 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/model_model_distances.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.model_map"): 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/model_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.model_idealization"): 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/model_idealization.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.maximum_entropy_map"): 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/maximum_entropy_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/mmtbx.matthews"): 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/matthews.py"), + relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/molprobity.suitename"): 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/suitename.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.suitename"): 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/suitename.py"), + relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/mmtbx.strip_model"): 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/strip_model.py"), + relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/mmtbx.ssm_rmsd_for_chains"): 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/ssm_rmsd_for_chains.py"), relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/mmtbx.ss_idealization"): 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/ss_idealization.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.sort_hetatms"): 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/sort_hetatms.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.sisa"): 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/sisa.py"), @@ -35025,9 +35032,44 @@ relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/phenix.rama_z"): 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/rama_z.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.r_factor_statistics"): 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/r_factor_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/mmtbx.quantum_interface"): 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/quantum_interface.py"), - relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/mmtbx.prune_model"): 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/prune_model.py"), - relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/mmtbx.process_predicted_model"): 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/process_predicted_model.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.process_predicted_model"): 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/process_predicted_model.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.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/samosa.scale"): 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/samosa_scale.py"), + relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/samosa.join"): 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/samosa_join.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.precession_view"): 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/precession_view.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.form_factor_query"): 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/form_factor_query.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.find_reticular_twin_laws"): 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/find_reticular_twin_laws.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.euclidean_model_matching"): 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/euclidean_model_matching.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.eltbx.show_fp_fdp"): 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/eltbx.show_fp_fdp.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.diffuse"): 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/diffuse.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.diffuse"): 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/diffuse.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.cod_select_and_pickle"): 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/cod_select_and_pickle.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_regression.test_nightly"): 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/cctbx_test_nightly.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.brehm_diederichs"): 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/brehm_diederichs.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.auto_sharpen"): 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/auto_sharpen.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.visualize_r_factors"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../crys3d/command_line/visualize_r_factors.py"), + relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/crys3d.qttbx.view_structure"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../crys3d/command_line/qttbx.view_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.multiplicity_viewer"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../crys3d/command_line/multiplicity_viewer.py"), + relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/crys3d.model_viewer"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../crys3d/command_line/model_viewer.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.make_install_HKLviewer_ChimeraX"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../crys3d/command_line/make_install_HKLviewer_ChimeraX.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.data_viewer"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../crys3d/command_line/hklview.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.data_viewer"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../crys3d/command_line/hklview.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.compare_datasets"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../crys3d/command_line/compare_datasets.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.HKLviewer"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../crys3d/command_line/HKLviewer.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.HKLviewer"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../crys3d/command_line/HKLviewer.py"), + relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/phasertng.HKLviewer"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../crys3d/command_line/HKLviewer.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.HKLinfo"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../crys3d/command_line/HKLinfo.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.HKLinfo"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../crys3d/command_line/HKLinfo.py"), + relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/smtbx.refine"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../smtbx/command_line/refine.py"), + relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/smtbx.masks"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../smtbx/command_line/masks.py"), + relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/smtbx.benchmark_refinement"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../smtbx/command_line/benchmark_refinement.py"), + relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/smtbx.anom_refine"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../smtbx/command_line/anom_refine.py"), + relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/smtbx.absolute_structure"): relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="../../../smtbx/command_line/absolute_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/iotbx.xplor.map.show_summary"): 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/xplor.map.show_summary.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/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"), @@ -35056,48 +35098,6 @@ relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/cctbx.wavelength_units"): 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/wavelength_units.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.version"): 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/version.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.subgroups"): 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/subgroups.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.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.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"), - 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_build_path"): 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_build_path.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_build_options"): 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_build_options.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_bin_path"): 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_bin_path.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_all_on_path"): 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_all_on_path.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.sh"): 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/sh.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.sge_qstat_counts"): 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/sge_qstat_counts.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.sge_available_slots"): 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/sge_available_slots.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.seconds_since_the_epoch"): 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/seconds_since_the_epoch.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.scons"): 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/scons.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.run_tests_parallel"): 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/run_tests_parallel.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.run_pickled_function"): 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/run_pickled_function.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.remove_tree"): 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/remove_tree.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.remote_processing"): 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/remote_processing.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.refresh"): 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/refresh.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.raise_exception_for_testing"): 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/raise_exception_for_testing.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.py_compile_all"): 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/py_compile_all.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.printenv"): 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/printenv.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.prime_factors_of"): 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/prime_factors_of.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.phil"): 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/phil.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.pdflatex"): 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/pdflatex.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.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"), - relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/libtbx.parallel_simple"): 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/parallel_simple.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.nequal"): 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/nequal.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.make_sphinx_html"): 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/make_sphinx_html.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.make_dist"): 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/make_dist.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.list_source_files_sorted_by_size"): 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/list_source_files_sorted_by_size.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.list_modules"): 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/list_modules.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.list_files"): 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/list_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/libtbx.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/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.latex"): 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/latex.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.install_conda"): 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/install_conda.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.install"): 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/install.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.import_all_python"): 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/import_all_python.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.import_all_ext"): 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/import_all_ext.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.help"): 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/help.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.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"), @@ -35138,9 +35138,48 @@ 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_stdin"): 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_stdin.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.assert_not_show_diff"): 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_not_show_diff.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.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_environ_usage"): 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_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/libtbx.show_env"): 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_env.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_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"), + 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"), + 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_build_path"): 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_build_path.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_build_options"): 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_build_options.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_bin_path"): 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_bin_path.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_all_on_path"): 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_all_on_path.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.sh"): 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/sh.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.sge_qstat_counts"): 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/sge_qstat_counts.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.sge_available_slots"): 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/sge_available_slots.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.seconds_since_the_epoch"): 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/seconds_since_the_epoch.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.scons"): 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/scons.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.run_tests_parallel"): 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/run_tests_parallel.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.run_pickled_function"): 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/run_pickled_function.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.remove_tree"): 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/remove_tree.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.remote_processing"): 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/remote_processing.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.refresh"): 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/refresh.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.raise_exception_for_testing"): 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/raise_exception_for_testing.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.py_compile_all"): 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/py_compile_all.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.printenv"): 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/printenv.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.prime_factors_of"): 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/prime_factors_of.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.phil"): 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/phil.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.pdflatex"): 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/pdflatex.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.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"), + relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/libtbx.parallel_simple"): 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/parallel_simple.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.nequal"): 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/nequal.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.make_sphinx_html"): 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/make_sphinx_html.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.make_dist"): 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/make_dist.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.list_source_files_sorted_by_size"): 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/list_source_files_sorted_by_size.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.list_modules"): 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/list_modules.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.list_files"): 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/list_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/libtbx.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/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.latex"): 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/latex.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.install_conda"): 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/install_conda.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.install"): 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/install.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.import_all_python"): 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/import_all_python.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.import_all_ext"): 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/import_all_ext.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.help"): 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/help.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.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.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.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"), relocatable_path(anchor="/build/reproducible-path/cctbx-2022.9+ds2+~3.11.2+ds1/debian/tmp/usr/lib/cctbx/python3.11", relocatable="bin/libtbx.unpack_in_sources"): 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/unpack_in_sources.csh"), @@ -35162,13 +35201,10 @@ 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_include_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_include_paths.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_host_and_user"): 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_host_and_user.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_full_command_path"): 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_full_command_path.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_environ_usage"): 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_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/libtbx.show_env"): 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_env.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_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"), 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")}, '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, @@ -35204,29 +35240,29 @@ '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': {'cbflib', 'docutils', 'king', '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': }, + 'missing_optional': {'cbflib', 'probe', 'reduce', 'docutils', 'king'}, + '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"), @@ -35252,28 +35288,28 @@ '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"), @@ -35293,40 +35329,7 @@ {'_dispatcher_include_at_start': [], '_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.split_data_cif"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/split_data_cif.py"), - relocatable_path(anchor="/usr", relocatable="bin/iotbx.pdb.sort_atoms"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/sort_atoms.py"), - relocatable_path(anchor="/usr", relocatable="bin/iotbx.simple_map_coefficients"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/simple_map_coefficients.py"), - relocatable_path(anchor="/usr", relocatable="bin/cctbx.show_systematic_absences"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/show_systematic_absences.py"), - relocatable_path(anchor="/usr", relocatable="bin/iotbx.show_distances"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/show_distances.py"), - relocatable_path(anchor="/usr", relocatable="bin/iotbx.shelx.dump_as_python"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/shelx.dump_as_python.py"), - relocatable_path(anchor="/usr", relocatable="bin/iotbx.shelx.as_xray_structure"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/shelx.as_xray_structure.py"), - relocatable_path(anchor="/usr", relocatable="bin/iotbx.shelx.as_cif"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/shelx.as_cif.py"), - relocatable_path(anchor="/usr", relocatable="bin/phenix.reindex"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/reindex.py"), - relocatable_path(anchor="/usr", relocatable="bin/phenix.reflection_statistics"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/reflection_statistics.py"), - relocatable_path(anchor="/usr", relocatable="bin/iotbx.reflection_file_reader"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/reflection_file_reader.py"), - relocatable_path(anchor="/usr", relocatable="bin/iotbx.reflection_file_editor"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/reflection_file_editor.py"), - relocatable_path(anchor="/usr", relocatable="bin/phenix.reflection_file_converter"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/reflection_file_converter.py"), - relocatable_path(anchor="/usr", relocatable="bin/iotbx.reflection_file_converter"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/reflection_file_converter.py"), - relocatable_path(anchor="/usr", relocatable="bin/iotbx.r_free_flags_completion_simple"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/r_free_flags_completion_simple.py"), - relocatable_path(anchor="/usr", relocatable="bin/iotbx.r_free_flags_as_cns"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/r_free_flags_as_cns.py"), - relocatable_path(anchor="/usr", relocatable="bin/iotbx.r_free_flags_accumulation"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/r_free_flags_accumulation.py"), - relocatable_path(anchor="/usr", relocatable="bin/iotbx.poscar_as_xray_structure"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/poscar_as_xray_structure.py"), - relocatable_path(anchor="/usr", relocatable="bin/iotbx.phil"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/phil.py"), - relocatable_path(anchor="/usr", relocatable="bin/iotbx.pdb.split_models"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/pdb_split_models.py"), - relocatable_path(anchor="/usr", relocatable="bin/iotbx.pdb.show_connectivity"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/pdb_show_connectivity.py"), - relocatable_path(anchor="/usr", relocatable="bin/iotbx.pdb_remediator"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/pdb_remediator.py"), - relocatable_path(anchor="/usr", relocatable="bin/iotbx.pdb_labels_diff"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/pdb_labels_diff.py"), - relocatable_path(anchor="/usr", relocatable="bin/iotbx.pdb_labels_comparison"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/pdb_labels_comparison.py"), - relocatable_path(anchor="/usr", relocatable="bin/iotbx.pdb.get_citation"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/pdb_get_citation.py"), - relocatable_path(anchor="/usr", relocatable="bin/iotbx.pdb_as_fasta"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/pdb_as_fasta.py"), - relocatable_path(anchor="/usr", relocatable="bin/phenix.pdb_as_cif"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/pdb_as_cif.py"), - relocatable_path(anchor="/usr", relocatable="bin/iotbx.pdb.add_conformations"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/pdb_add_conformations.py"), - relocatable_path(anchor="/usr", relocatable="bin/iotbx.pdb.superpose_centers_of_mass"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/pdb.superpose_centers_of_mass.py"), - relocatable_path(anchor="/usr", relocatable="bin/iotbx.pdb.superpose_atoms_by_name"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/pdb.superpose_atoms_by_name.py"), - relocatable_path(anchor="/usr", relocatable="bin/iotbx.pdb.print_sequence"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/pdb.print_sequence.py"), + '_dispatcher_registry': {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.pdb.link_as_geometry_restraints_edits"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/pdb.link_as_geometry_restraints_edits.py"), relocatable_path(anchor="/usr", relocatable="bin/iotbx.pdb.join_fragment_files"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/pdb.join_fragment_files.py"), relocatable_path(anchor="/usr", relocatable="bin/iotbx.pdb.insert_scale_records"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/pdb.insert_scale_records.py"), @@ -35422,7 +35425,7 @@ relocatable_path(anchor="/usr", relocatable="bin/phenix.rank_scale_map"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/mmtbx/command_line/rank_scale_map.py"), relocatable_path(anchor="/usr", relocatable="bin/phenix.ramalyze"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/mmtbx/command_line/ramalyze.py"), relocatable_path(anchor="/usr", relocatable="bin/molprobity.ramalyze"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/mmtbx/command_line/ramalyze.py"), - relocatable_path(anchor="/usr", relocatable="bin/mmtbx.rama_z"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/mmtbx/command_line/rama_z.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/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"), @@ -35457,9 +35460,8 @@ 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/boost.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/omptbx.python"): relocatable_path(anchor="/usr", relocatable="bin/python3.11"), relocatable_path(anchor="/usr", relocatable="bin/fable.python"): relocatable_path(anchor="/usr", relocatable="bin/python3.11"), relocatable_path(anchor="/usr", relocatable="bin/scitbx.python"): relocatable_path(anchor="/usr", relocatable="bin/python3.11"), @@ -35475,6 +35477,8 @@ 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/dev.dxtbx.debug_memory"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/dxtbx/src/dxtbx/command_line/debug_memory.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"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/wxtbx/command_line/wxpython.py"), @@ -35506,7 +35510,7 @@ relocatable_path(anchor="/usr", relocatable="bin/dxtbx.display_parallax_correction"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/dxtbx/src/dxtbx/command_line/display_parallax_correction.py"), 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/dxtbx.depends_on"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/dxtbx/src/dxtbx/command_line/depends_on.py"), - relocatable_path(anchor="/usr", relocatable="bin/dev.dxtbx.debug_memory"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/dxtbx/src/dxtbx/command_line/debug_memory.py"), + relocatable_path(anchor="/usr", relocatable="bin/phenix.cc_star"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/mmtbx/command_line/cc_star.py"), relocatable_path(anchor="/usr", relocatable="bin/phenix.cbetadev"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/mmtbx/command_line/cbetadev.py"), relocatable_path(anchor="/usr", relocatable="bin/molprobity.cbetadev"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/mmtbx/command_line/cbetadev.py"), relocatable_path(anchor="/usr", relocatable="bin/phenix.cablam_validate"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/mmtbx/command_line/cablam_validate.py"), @@ -35569,7 +35573,7 @@ relocatable_path(anchor="/usr", relocatable="bin/iotbx.cif_as_mtz"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/mmtbx/command_line/cif_as_mtz.py"), relocatable_path(anchor="/usr", relocatable="bin/phenix.chains_as_models"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/mmtbx/command_line/chains_as_models.py"), relocatable_path(anchor="/usr", relocatable="bin/mmtbx.cdl_lookup"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/mmtbx/command_line/cdl_lookup.py"), - relocatable_path(anchor="/usr", relocatable="bin/phenix.cc_star"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/mmtbx/command_line/cc_star.py"), + relocatable_path(anchor="/usr", relocatable="bin/phenix.models_as_chains"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/mmtbx/command_line/models_as_chains.py"), relocatable_path(anchor="/usr", relocatable="bin/phenix.model_vs_sequence"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/mmtbx/command_line/model_vs_sequence.py"), relocatable_path(anchor="/usr", relocatable="bin/phenix.model_vs_map"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/mmtbx/command_line/model_vs_map.py"), relocatable_path(anchor="/usr", relocatable="bin/mmtbx.model_vs_data"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/mmtbx/command_line/model_vs_data.py"), @@ -35601,6 +35605,7 @@ relocatable_path(anchor="/usr", relocatable="bin/mmtbx.flipbase"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/mmtbx/command_line/flipbase.py"), relocatable_path(anchor="/usr", relocatable="bin/mmtbx.fix_rotamer_outliers"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/mmtbx/command_line/fix_rotamer_outliers.py"), relocatable_path(anchor="/usr", relocatable="bin/mmtbx.fix_rama_outliers"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/mmtbx/command_line/fix_rama_outliers.py"), + relocatable_path(anchor="/usr", relocatable="bin/mmtbx.rama_z"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/mmtbx/command_line/rama_z.py"), relocatable_path(anchor="/usr", relocatable="bin/phenix.rama_z"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/mmtbx/command_line/rama_z.py"), relocatable_path(anchor="/usr", relocatable="bin/phenix.r_factor_statistics"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/mmtbx/command_line/r_factor_statistics.py"), relocatable_path(anchor="/usr", relocatable="bin/mmtbx.quantum_interface"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/mmtbx/command_line/quantum_interface.py"), @@ -35632,7 +35637,38 @@ relocatable_path(anchor="/usr", relocatable="bin/mmtbx.mon_lib_cif_triage"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/mmtbx/command_line/mon_lib_cif_triage.py"), relocatable_path(anchor="/usr", relocatable="bin/phenix.molprobity"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/mmtbx/command_line/molprobity.py"), relocatable_path(anchor="/usr", relocatable="bin/molprobity.molprobity"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/mmtbx/command_line/molprobity.py"), - relocatable_path(anchor="/usr", relocatable="bin/phenix.models_as_chains"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/mmtbx/command_line/models_as_chains.py"), + relocatable_path(anchor="/usr", relocatable="bin/libtbx.python"): relocatable_path(anchor="/usr", relocatable="bin/python3.11"), + relocatable_path(anchor="/usr", relocatable="bin/iotbx.split_data_cif"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/split_data_cif.py"), + relocatable_path(anchor="/usr", relocatable="bin/iotbx.pdb.sort_atoms"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/sort_atoms.py"), + relocatable_path(anchor="/usr", relocatable="bin/iotbx.simple_map_coefficients"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/simple_map_coefficients.py"), + relocatable_path(anchor="/usr", relocatable="bin/cctbx.show_systematic_absences"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/show_systematic_absences.py"), + relocatable_path(anchor="/usr", relocatable="bin/iotbx.show_distances"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/show_distances.py"), + relocatable_path(anchor="/usr", relocatable="bin/iotbx.shelx.dump_as_python"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/shelx.dump_as_python.py"), + relocatable_path(anchor="/usr", relocatable="bin/iotbx.shelx.as_xray_structure"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/shelx.as_xray_structure.py"), + relocatable_path(anchor="/usr", relocatable="bin/iotbx.shelx.as_cif"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/shelx.as_cif.py"), + relocatable_path(anchor="/usr", relocatable="bin/phenix.reindex"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/reindex.py"), + relocatable_path(anchor="/usr", relocatable="bin/phenix.reflection_statistics"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/reflection_statistics.py"), + relocatable_path(anchor="/usr", relocatable="bin/iotbx.reflection_file_reader"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/reflection_file_reader.py"), + relocatable_path(anchor="/usr", relocatable="bin/iotbx.reflection_file_editor"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/reflection_file_editor.py"), + relocatable_path(anchor="/usr", relocatable="bin/phenix.reflection_file_converter"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/reflection_file_converter.py"), + relocatable_path(anchor="/usr", relocatable="bin/iotbx.reflection_file_converter"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/reflection_file_converter.py"), + relocatable_path(anchor="/usr", relocatable="bin/iotbx.r_free_flags_completion_simple"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/r_free_flags_completion_simple.py"), + relocatable_path(anchor="/usr", relocatable="bin/iotbx.r_free_flags_as_cns"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/r_free_flags_as_cns.py"), + relocatable_path(anchor="/usr", relocatable="bin/iotbx.r_free_flags_accumulation"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/r_free_flags_accumulation.py"), + relocatable_path(anchor="/usr", relocatable="bin/iotbx.poscar_as_xray_structure"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/poscar_as_xray_structure.py"), + relocatable_path(anchor="/usr", relocatable="bin/iotbx.phil"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/phil.py"), + relocatable_path(anchor="/usr", relocatable="bin/iotbx.pdb.split_models"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/pdb_split_models.py"), + relocatable_path(anchor="/usr", relocatable="bin/iotbx.pdb.show_connectivity"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/pdb_show_connectivity.py"), + relocatable_path(anchor="/usr", relocatable="bin/iotbx.pdb_remediator"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/pdb_remediator.py"), + relocatable_path(anchor="/usr", relocatable="bin/iotbx.pdb_labels_diff"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/pdb_labels_diff.py"), + relocatable_path(anchor="/usr", relocatable="bin/iotbx.pdb_labels_comparison"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/pdb_labels_comparison.py"), + relocatable_path(anchor="/usr", relocatable="bin/iotbx.pdb.get_citation"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/pdb_get_citation.py"), + relocatable_path(anchor="/usr", relocatable="bin/iotbx.pdb_as_fasta"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/pdb_as_fasta.py"), + relocatable_path(anchor="/usr", relocatable="bin/phenix.pdb_as_cif"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/pdb_as_cif.py"), + relocatable_path(anchor="/usr", relocatable="bin/iotbx.pdb.add_conformations"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/pdb_add_conformations.py"), + relocatable_path(anchor="/usr", relocatable="bin/iotbx.pdb.superpose_centers_of_mass"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/pdb.superpose_centers_of_mass.py"), + relocatable_path(anchor="/usr", relocatable="bin/iotbx.pdb.superpose_atoms_by_name"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/pdb.superpose_atoms_by_name.py"), + relocatable_path(anchor="/usr", relocatable="bin/iotbx.pdb.print_sequence"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/pdb.print_sequence.py"), relocatable_path(anchor="/usr", relocatable="bin/phenix.find_reticular_twin_laws"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/cctbx/command_line/find_reticular_twin_laws.py"), relocatable_path(anchor="/usr", relocatable="bin/cctbx.euclidean_model_matching"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/cctbx/command_line/euclidean_model_matching.py"), relocatable_path(anchor="/usr", relocatable="bin/cctbx.eltbx.show_fp_fdp"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/cctbx/command_line/eltbx.show_fp_fdp.py"), @@ -35664,6 +35700,47 @@ relocatable_path(anchor="/usr", relocatable="bin/iotbx.unique_with_biomt"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/unique_with_biomt.py"), relocatable_path(anchor="/usr", relocatable="bin/phenix.unique_with_biomt"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/unique_with_biomt.py"), relocatable_path(anchor="/usr", relocatable="bin/iotbx.symmetry_search"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/iotbx/command_line/symmetry_search.py"), + relocatable_path(anchor="/usr", relocatable="bin/libtbx.assert_not_show_diff"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/assert_not_show_diff.py"), + relocatable_path(anchor="/usr", relocatable="bin/libtbx.assert_line_count"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/assert_line_count.py"), + relocatable_path(anchor="/usr", relocatable="bin/libtbx.any2unix"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/any2unix.py"), + relocatable_path(anchor="/usr", relocatable="bin/libtbx.analyse_code_comments"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/analyse_code_comments.py"), + relocatable_path(anchor="/usr", relocatable="bin/libtbx.add_from_future_import_division"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/add_from_future_import_division.py"), + relocatable_path(anchor="/usr", relocatable="bin/boost_adaptbx.show_platform_info"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/boost_adaptbx/command_line/show_platform_info.py"), + relocatable_path(anchor="/usr", relocatable="bin/boost_adaptbx.show_environ_usage"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/boost_adaptbx/command_line/show_environ_usage.py"), + relocatable_path(anchor="/usr", relocatable="bin/boost_adaptbx.segmentation_fault"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/boost_adaptbx/command_line/segmentation_fault.py"), + relocatable_path(anchor="/usr", relocatable="bin/boost_adaptbx.nested_cpp_loops_with_check_signals"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/boost_adaptbx/command_line/nested_cpp_loops_with_check_signals.py"), + relocatable_path(anchor="/usr", relocatable="bin/boost.lcm"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/boost_adaptbx/command_line/lcm.py"), + relocatable_path(anchor="/usr", relocatable="bin/boost_adaptbx.int_overflow"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/boost_adaptbx/command_line/int_overflow.py"), + relocatable_path(anchor="/usr", relocatable="bin/boost_adaptbx.inexact"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/boost_adaptbx/command_line/inexact.py"), + relocatable_path(anchor="/usr", relocatable="bin/boost.gcd"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/boost_adaptbx/command_line/gcd.py"), + relocatable_path(anchor="/usr", relocatable="bin/boost_adaptbx.double_overflow"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/boost_adaptbx/command_line/double_overflow.py"), + relocatable_path(anchor="/usr", relocatable="bin/boost_adaptbx.divide_by_zero"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/boost_adaptbx/command_line/divide_by_zero.py"), + relocatable_path(anchor="/usr", relocatable="bin/fable.split"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/fable/command_line/split.py"), + relocatable_path(anchor="/usr", relocatable="bin/fable.show_calls"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/fable/command_line/show_calls.py"), + relocatable_path(anchor="/usr", relocatable="bin/fable.read"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/fable/command_line/read.py"), + relocatable_path(anchor="/usr", relocatable="bin/fable.insert_write_at_start_of_each_procedure"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/fable/command_line/insert_write_at_start_of_each_procedure.py"), + relocatable_path(anchor="/usr", relocatable="bin/fable.fem_include_search_paths"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/fable/command_line/fem_include_search_paths.py"), + relocatable_path(anchor="/usr", relocatable="bin/fable.cout"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/fable/command_line/cout.py"), + relocatable_path(anchor="/usr", relocatable="bin/scitbx.unicode_examples"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/scitbx/command_line/unicode_examples.py"), + relocatable_path(anchor="/usr", relocatable="bin/scitbx.show_sizes"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/scitbx/command_line/show_sizes.py"), + relocatable_path(anchor="/usr", relocatable="bin/scitbx.show_exp_times"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/scitbx/command_line/show_exp_times.py"), + relocatable_path(anchor="/usr", relocatable="bin/scitbx.histogram"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/scitbx/command_line/histogram.py"), + relocatable_path(anchor="/usr", relocatable="bin/scitbx.generate_error_h"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/scitbx/command_line/generate_error_h.py"), + relocatable_path(anchor="/usr", relocatable="bin/scitbx.apply_tapenade_hints"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/scitbx/command_line/apply_tapenade_hints.py"), + relocatable_path(anchor="/usr", relocatable="bin/cbf.dump"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/cbflib_adaptbx/command_line/dump.py"), + relocatable_path(anchor="/usr", relocatable="bin/cctbx.xray_structure.show"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/cctbx/command_line/xray_structure.show.py"), + relocatable_path(anchor="/usr", relocatable="bin/cctbx.web.install"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/cctbx/command_line/web.install.csh"), + relocatable_path(anchor="/usr", relocatable="bin/cctbx.wavelength_units"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/cctbx/command_line/wavelength_units.py"), + relocatable_path(anchor="/usr", relocatable="bin/cctbx.version"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/cctbx/command_line/version.py"), + relocatable_path(anchor="/usr", relocatable="bin/cctbx.subgroups"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/cctbx/command_line/subgroups.py"), + relocatable_path(anchor="/usr", relocatable="bin/cctbx.structure_factor_timings"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/cctbx/command_line/structure_factor_timings.py"), + relocatable_path(anchor="/usr", relocatable="bin/cctbx.space_group_info"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/cctbx/command_line/space_group_info.py"), + relocatable_path(anchor="/usr", relocatable="bin/phenix.segment_and_split_map"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/cctbx/command_line/segment_and_split_map.py"), + relocatable_path(anchor="/usr", relocatable="bin/samosa.scale"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/cctbx/command_line/samosa_scale.py"), + relocatable_path(anchor="/usr", relocatable="bin/samosa.join"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/cctbx/command_line/samosa_join.py"), + relocatable_path(anchor="/usr", relocatable="bin/cctbx.precession_view"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/cctbx/command_line/precession_view.py"), + relocatable_path(anchor="/usr", relocatable="bin/phenix.form_factor_query"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/cctbx/command_line/form_factor_query.py"), + relocatable_path(anchor="/usr", relocatable="bin/libtbx.import_all_python"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/import_all_python.py"), relocatable_path(anchor="/usr", relocatable="bin/libtbx.import_all_ext"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/import_all_ext.py"), relocatable_path(anchor="/usr", relocatable="bin/libtbx.help"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/help.py"), relocatable_path(anchor="/usr", relocatable="bin/libtbx.git_avoid_merges"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/git_avoid_merges.py"), @@ -35705,59 +35782,20 @@ relocatable_path(anchor="/usr", relocatable="bin/libtbx.assert_stdin_contains_strings"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/assert_stdin_contains_strings.py"), relocatable_path(anchor="/usr", relocatable="bin/libtbx.assert_stdin_does_not_contain_strings"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/assert_stdin_contains_strings.py"), relocatable_path(anchor="/usr", relocatable="bin/libtbx.assert_stdin"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/assert_stdin.py"), - relocatable_path(anchor="/usr", relocatable="bin/libtbx.assert_not_show_diff"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/assert_not_show_diff.py"), - relocatable_path(anchor="/usr", relocatable="bin/libtbx.assert_line_count"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/assert_line_count.py"), - relocatable_path(anchor="/usr", relocatable="bin/libtbx.any2unix"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/any2unix.py"), - relocatable_path(anchor="/usr", relocatable="bin/libtbx.analyse_code_comments"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/analyse_code_comments.py"), - relocatable_path(anchor="/usr", relocatable="bin/libtbx.add_from_future_import_division"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/add_from_future_import_division.py"), - relocatable_path(anchor="/usr", relocatable="bin/boost_adaptbx.show_platform_info"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/boost_adaptbx/command_line/show_platform_info.py"), - relocatable_path(anchor="/usr", relocatable="bin/boost_adaptbx.show_environ_usage"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/boost_adaptbx/command_line/show_environ_usage.py"), - relocatable_path(anchor="/usr", relocatable="bin/boost_adaptbx.segmentation_fault"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/boost_adaptbx/command_line/segmentation_fault.py"), - relocatable_path(anchor="/usr", relocatable="bin/boost_adaptbx.nested_cpp_loops_with_check_signals"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/boost_adaptbx/command_line/nested_cpp_loops_with_check_signals.py"), - relocatable_path(anchor="/usr", relocatable="bin/boost.lcm"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/boost_adaptbx/command_line/lcm.py"), - relocatable_path(anchor="/usr", relocatable="bin/boost_adaptbx.int_overflow"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/boost_adaptbx/command_line/int_overflow.py"), - relocatable_path(anchor="/usr", relocatable="bin/boost_adaptbx.inexact"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/boost_adaptbx/command_line/inexact.py"), - relocatable_path(anchor="/usr", relocatable="bin/boost.gcd"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/boost_adaptbx/command_line/gcd.py"), - relocatable_path(anchor="/usr", relocatable="bin/boost_adaptbx.double_overflow"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/boost_adaptbx/command_line/double_overflow.py"), - relocatable_path(anchor="/usr", relocatable="bin/boost_adaptbx.divide_by_zero"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/boost_adaptbx/command_line/divide_by_zero.py"), - relocatable_path(anchor="/usr", relocatable="bin/fable.split"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/fable/command_line/split.py"), - relocatable_path(anchor="/usr", relocatable="bin/fable.show_calls"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/fable/command_line/show_calls.py"), - relocatable_path(anchor="/usr", relocatable="bin/fable.read"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/fable/command_line/read.py"), - relocatable_path(anchor="/usr", relocatable="bin/fable.insert_write_at_start_of_each_procedure"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/fable/command_line/insert_write_at_start_of_each_procedure.py"), - relocatable_path(anchor="/usr", relocatable="bin/fable.fem_include_search_paths"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/fable/command_line/fem_include_search_paths.py"), - relocatable_path(anchor="/usr", relocatable="bin/fable.cout"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/fable/command_line/cout.py"), - relocatable_path(anchor="/usr", relocatable="bin/scitbx.unicode_examples"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/scitbx/command_line/unicode_examples.py"), - relocatable_path(anchor="/usr", relocatable="bin/scitbx.show_sizes"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/scitbx/command_line/show_sizes.py"), - relocatable_path(anchor="/usr", relocatable="bin/scitbx.show_exp_times"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/scitbx/command_line/show_exp_times.py"), - relocatable_path(anchor="/usr", relocatable="bin/scitbx.histogram"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/scitbx/command_line/histogram.py"), - relocatable_path(anchor="/usr", relocatable="bin/scitbx.generate_error_h"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/scitbx/command_line/generate_error_h.py"), - relocatable_path(anchor="/usr", relocatable="bin/scitbx.apply_tapenade_hints"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/scitbx/command_line/apply_tapenade_hints.py"), - relocatable_path(anchor="/usr", relocatable="bin/cbf.dump"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/cbflib_adaptbx/command_line/dump.py"), - relocatable_path(anchor="/usr", relocatable="bin/cctbx.xray_structure.show"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/cctbx/command_line/xray_structure.show.py"), - relocatable_path(anchor="/usr", relocatable="bin/cctbx.web.install"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/cctbx/command_line/web.install.csh"), - relocatable_path(anchor="/usr", relocatable="bin/cctbx.wavelength_units"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/cctbx/command_line/wavelength_units.py"), - relocatable_path(anchor="/usr", relocatable="bin/cctbx.version"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/cctbx/command_line/version.py"), - relocatable_path(anchor="/usr", relocatable="bin/cctbx.subgroups"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/cctbx/command_line/subgroups.py"), - relocatable_path(anchor="/usr", relocatable="bin/cctbx.structure_factor_timings"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/cctbx/command_line/structure_factor_timings.py"), - relocatable_path(anchor="/usr", relocatable="bin/cctbx.space_group_info"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/cctbx/command_line/space_group_info.py"), - relocatable_path(anchor="/usr", relocatable="bin/phenix.segment_and_split_map"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/cctbx/command_line/segment_and_split_map.py"), - relocatable_path(anchor="/usr", relocatable="bin/samosa.scale"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/cctbx/command_line/samosa_scale.py"), - relocatable_path(anchor="/usr", relocatable="bin/samosa.join"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/cctbx/command_line/samosa_join.py"), - relocatable_path(anchor="/usr", relocatable="bin/cctbx.precession_view"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/cctbx/command_line/precession_view.py"), - relocatable_path(anchor="/usr", relocatable="bin/phenix.form_factor_query"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/cctbx/command_line/form_factor_query.py"), + relocatable_path(anchor="/usr", relocatable="bin/libtbx.show_all_on_path"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/show_all_on_path.py"), relocatable_path(anchor="/usr", relocatable="bin/libtbx.sh"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/sh.sh"), - relocatable_path(anchor="/usr", relocatable="bin/libtbx.sge_qstat_counts"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/sge_qstat_counts.py"), - relocatable_path(anchor="/usr", relocatable="bin/libtbx.scons"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/scons.py"), - relocatable_path(anchor="/usr", relocatable="bin/libtbx.seconds_since_the_epoch"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/seconds_since_the_epoch.py"), relocatable_path(anchor="/usr", relocatable="bin/libtbx.run_tests_parallel"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/run_tests_parallel.py"), + relocatable_path(anchor="/usr", relocatable="bin/libtbx.sge_qstat_counts"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/sge_qstat_counts.py"), + relocatable_path(anchor="/usr", relocatable="bin/libtbx.sge_available_slots"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/sge_available_slots.py"), relocatable_path(anchor="/usr", relocatable="bin/libtbx.run_pickled_function"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/run_pickled_function.py"), + relocatable_path(anchor="/usr", relocatable="bin/libtbx.scons"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/scons.py"), relocatable_path(anchor="/usr", relocatable="bin/libtbx.remove_tree"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/remove_tree.py"), relocatable_path(anchor="/usr", relocatable="bin/libtbx.remote_processing"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/remote_processing.py"), relocatable_path(anchor="/usr", relocatable="bin/libtbx.refresh"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/refresh.sh"), relocatable_path(anchor="/usr", relocatable="bin/libtbx.raise_exception_for_testing"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/raise_exception_for_testing.py"), - relocatable_path(anchor="/usr", relocatable="bin/libtbx.sge_available_slots"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/sge_available_slots.py"), relocatable_path(anchor="/usr", relocatable="bin/libtbx.py_compile_all"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/py_compile_all.py"), relocatable_path(anchor="/usr", relocatable="bin/libtbx.printenv"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/printenv.py"), + relocatable_path(anchor="/usr", relocatable="bin/libtbx.seconds_since_the_epoch"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/seconds_since_the_epoch.py"), relocatable_path(anchor="/usr", relocatable="bin/libtbx.prime_factors_of"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/prime_factors_of.py"), relocatable_path(anchor="/usr", relocatable="bin/libtbx.phil"): relocatable_path(anchor="/usr", 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"), @@ -35773,41 +35811,39 @@ relocatable_path(anchor="/usr", relocatable="bin/libtbx.latex"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/latex.sh"), relocatable_path(anchor="/usr", relocatable="bin/libtbx.install_conda"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/install_conda.py"), relocatable_path(anchor="/usr", relocatable="bin/libtbx.install"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/install.py"), - relocatable_path(anchor="/usr", relocatable="bin/libtbx.import_all_python"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/import_all_python.py"), relocatable_path(anchor="/usr", relocatable="bin/libtbx.show_but_no_repr"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/show_but_no_repr.py"), - relocatable_path(anchor="/usr", relocatable="bin/libtbx.show_commands"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/show_commands.py"), relocatable_path(anchor="/usr", relocatable="bin/libtbx.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/libtbx.show_lib_path"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/show_lib_path.py"), - relocatable_path(anchor="/usr", relocatable="bin/libtbx.show_build_options"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/show_build_options.py"), - relocatable_path(anchor="/usr", relocatable="bin/libtbx.show_full_command_path"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/show_full_command_path.py"), relocatable_path(anchor="/usr", relocatable="bin/libtbx.show_host_and_user"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/show_host_and_user.py"), + relocatable_path(anchor="/usr", relocatable="bin/libtbx.show_commands"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/show_commands.py"), + relocatable_path(anchor="/usr", relocatable="bin/libtbx.show_full_command_path"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/show_full_command_path.py"), + relocatable_path(anchor="/usr", relocatable="bin/libtbx.show_build_options"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/show_build_options.py"), relocatable_path(anchor="/usr", relocatable="bin/libtbx.show_environ_usage"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/show_environ_usage.py"), relocatable_path(anchor="/usr", relocatable="bin/libtbx.show_env"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/show_env.py"), relocatable_path(anchor="/usr", relocatable="bin/libtbx.show_bin_path"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/show_bin_path.py"), relocatable_path(anchor="/usr", relocatable="bin/libtbx.show_dist_paths"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/show_dist_paths.py"), - relocatable_path(anchor="/usr", relocatable="bin/libtbx.show_include_paths"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/show_include_paths.py"), relocatable_path(anchor="/usr", relocatable="bin/libtbx.show_date_and_time"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/show_date_and_time.py"), - relocatable_path(anchor="/usr", relocatable="bin/libtbx.show_all_on_path"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/show_all_on_path.py"), - relocatable_path(anchor="/usr", relocatable="bin/libtbx.show_python_dependencies"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/show_python_dependencies.py"), relocatable_path(anchor="/usr", relocatable="bin/libtbx.show_numpy_version"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/show_numpy_version.py"), relocatable_path(anchor="/usr", relocatable="bin/libtbx.show_numeric_version"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/show_numeric_version.py"), relocatable_path(anchor="/usr", relocatable="bin/libtbx.show_number_of_processors"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/show_number_of_processors.py"), relocatable_path(anchor="/usr", relocatable="bin/libtbx.show_module_dependencies"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/show_module_dependencies.py"), - relocatable_path(anchor="/usr", relocatable="bin/libtbx.show_tests"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/show_tests.py"), + relocatable_path(anchor="/usr", relocatable="bin/libtbx.show_lib_path"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/show_lib_path.py"), + relocatable_path(anchor="/usr", relocatable="bin/libtbx.show_include_paths"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/show_include_paths.py"), relocatable_path(anchor="/usr", relocatable="bin/libtbx.show_repository_paths"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/show_repository_paths.py"), relocatable_path(anchor="/usr", relocatable="bin/libtbx.show_pythonpath"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/show_pythonpath.py"), relocatable_path(anchor="/usr", relocatable="bin/libtbx.show_python_sys_executable"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/show_python_sys_executable.py"), + relocatable_path(anchor="/usr", relocatable="bin/libtbx.show_python_dependencies"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/show_python_dependencies.py"), + relocatable_path(anchor="/usr", relocatable="bin/libtbx.valgrind"): relocatable_path(anchor="/usr", 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/sphinx.build"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/sphinx_build.py"), relocatable_path(anchor="/usr", relocatable="bin/libtbx.show_variable_names"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/show_variable_names.py"), - relocatable_path(anchor="/usr", relocatable="bin/wxtbx.python"): relocatable_path(anchor="/usr", relocatable="bin/python3.11"), + relocatable_path(anchor="/usr", relocatable="bin/libtbx.show_tests"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/show_tests.py"), relocatable_path(anchor="/usr", relocatable="bin/boost.show_build_path"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/show_build_path.py")}, '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, @@ -35843,29 +35879,29 @@ 'lib_path': relocatable_path(anchor="/usr", relocatable="lib"), 'missing_for_build': set(), 'missing_for_use': set(), - 'missing_optional': {'cbflib', 'docutils', 'king', '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': }, + 'missing_optional': {'cbflib', 'probe', 'reduce', 'docutils', 'king'}, + '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"), @@ -35891,28 +35927,28 @@ '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"), @@ -35967,7 +36003,7 @@ smtbx/refinement/constraints/tests/tst_reparametrisation smtbx/refinement/constraints/tests/tst_special_position -sent 15,728,163 bytes received 568 bytes 6,291,492.40 bytes/sec +sent 15,728,158 bytes received 568 bytes 31,457,452.00 bytes/sec total size is 15,716,704 speedup is 1.00 building file list ... done ./ @@ -36029,13 +36065,13 @@ libspotfinder.so.0 -> libspotfinder.so.0.0.1 libspotfinder.so.0.0.1 -sent 56,668,181 bytes received 494 bytes 5,965,123.68 bytes/sec +sent 56,668,151 bytes received 494 bytes 113,337,290.00 bytes/sec total size is 56,652,034 speedup is 1.00 building file list ... done annlib_adaptbx/ annlib_adaptbx/ann_adaptor.h -sent 2,232 bytes received 38 bytes 4,540.00 bytes/sec +sent 2,234 bytes received 38 bytes 4,544.00 bytes/sec total size is 2,068 speedup is 0.91 building file list ... done boost_adaptbx/ @@ -36061,7 +36097,7 @@ 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/ @@ -36097,7 +36133,7 @@ ccp4io_adaptbx/dev/ ccp4io_adaptbx/dev/fftlib.hpp -sent 87,916 bytes received 326 bytes 176,484.00 bytes/sec +sent 87,940 bytes received 326 bytes 176,532.00 bytes/sec total size is 86,683 speedup is 0.98 building file list ... done cctbx/ @@ -36356,7 +36392,7 @@ cctbx/xray/targets/mli.h cctbx/xray/targets/shelxl_wght_ls.hpp -sent 1,895,073 bytes received 4,401 bytes 1,266,316.00 bytes/sec +sent 1,895,099 bytes received 4,401 bytes 3,799,000.00 bytes/sec total size is 1,878,555 speedup is 0.99 building file list ... done cma_es/ @@ -36364,7 +36400,7 @@ 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 @@ -36409,7 +36445,7 @@ dxtbx/model/boost_python/pickle_suite.h dxtbx/model/boost_python/to_from_dict.h -sent 362,409 bytes received 591 bytes 726,000.00 bytes/sec +sent 362,413 bytes received 591 bytes 242,002.67 bytes/sec total size is 360,079 speedup is 0.99 building file list ... done ./ @@ -36463,7 +36499,7 @@ fem/utils/string_to_double_fmt.hpp fem/utils/token.hpp -sent 203,744 bytes received 918 bytes 136,441.33 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/ @@ -36477,7 +36513,7 @@ gltbx/special_wrapper_support.h gltbx/util.h -sent 598,769 bytes received 190 bytes 1,197,918.00 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/ @@ -36520,11 +36556,11 @@ iotbx/xplor/map_reader.h iotbx/xplor/map_writer.h -sent 268,349 bytes received 629 bytes 179,318.67 bytes/sec +sent 268,353 bytes received 629 bytes 537,964.00 bytes/sec total size is 265,547 speedup is 0.99 building file list ... done -sent 467 bytes received 12 bytes 958.00 bytes/sec +sent 495 bytes received 12 bytes 1,014.00 bytes/sec total size is 0 speedup is 0.00 building file list ... done mmtbx/ @@ -36615,7 +36651,7 @@ 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/ @@ -36623,8 +36659,8 @@ omptbx/omp_or_stubs.h omptbx/stubs.h -sent 2,115 bytes received 76 bytes 4,382.00 bytes/sec -total size is 1,850 speedup is 0.84 +sent 2,111 bytes received 76 bytes 4,374.00 bytes/sec +total size is 1,850 speedup is 0.85 building file list ... done rstbx/ rstbx/backplane.h @@ -36659,7 +36695,7 @@ rstbx/symmetry/constraints/ rstbx/symmetry/constraints/a_g_conversion.h -sent 111,333 bytes received 400 bytes 223,466.00 bytes/sec +sent 111,337 bytes received 400 bytes 223,474.00 bytes/sec total size is 109,476 speedup is 0.98 building file list ... done scitbx/ @@ -36982,7 +37018,7 @@ scitbx/wigner/ scitbx/wigner/wigner3j.h -sent 1,904,482 bytes received 5,521 bytes 1,273,335.33 bytes/sec +sent 1,904,504 bytes received 5,521 bytes 3,820,050.00 bytes/sec total size is 1,884,752 speedup is 0.99 building file list ... done smtbx/ @@ -37018,7 +37054,7 @@ 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 182,133 bytes received 512 bytes 365,290.00 bytes/sec total size is 179,686 speedup is 0.98 building file list ... done spotfinder/ @@ -37037,7 +37073,7 @@ spotfinder/dxtbx_toolbox/distl.h spotfinder/dxtbx_toolbox/libdistl.h -sent 42,922 bytes received 221 bytes 86,286.00 bytes/sec +sent 42,926 bytes received 221 bytes 86,294.00 bytes/sec total size is 41,955 speedup is 0.97 building file list ... done tbxx/ @@ -37048,7 +37084,7 @@ 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 @@ -37088,38 +37124,39 @@ scitbx/array_family/detail/ scitbx/array_family/detail/operator_functors.h scitbx/array_family/detail/std_imports.h +smtbx/ smtbx/boost_python/ smtbx/boost_python/flex_fwd.h -sent 347,311 bytes received 537 bytes 695,696.00 bytes/sec +sent 347,313 bytes received 540 bytes 695,706.00 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 256 bytes received 12 bytes 536.00 bytes/sec total size is 0 speedup is 0.00 building file list ... done boost_adaptbx/ boost_adaptbx/command_line/ -sent 517 bytes received 22 bytes 1,078.00 bytes/sec -total size is 6,883 speedup is 12.77 +sent 558 bytes received 55 bytes 1,226.00 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 240 bytes received 28 bytes 536.00 bytes/sec +total size is 1,215 speedup is 4.53 building file list ... done -sent 145 bytes received 12 bytes 314.00 bytes/sec +sent 149 bytes received 12 bytes 322.00 bytes/sec total size is 0 speedup is 0.00 building file list ... done cctbx/ cctbx/command_line/ cctbx/command_line/web.install.csh -sent 2,941 bytes received 41 bytes 5,964.00 bytes/sec -total size is 39,547 speedup is 13.26 +sent 3,028 bytes received 101 bytes 6,258.00 bytes/sec +total size is 39,547 speedup is 12.64 building file list ... done sent 87 bytes received 12 bytes 198.00 bytes/sec @@ -37128,32 +37165,32 @@ 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 886 bytes received 79 bytes 1,930.00 bytes/sec +total size is 79,884 speedup is 82.78 building file list ... done fable/ fable/command_line/ -sent 451 bytes received 22 bytes 315.33 bytes/sec -total size is 15,542 speedup is 32.86 +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 180 bytes received 22 bytes 404.00 bytes/sec -total size is 606 speedup is 3.00 +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 5,308.00 bytes/sec -total size is 216,768 speedup is 81.68 +sent 2,858 bytes received 244 bytes 6,204.00 bytes/sec +total size is 216,768 speedup is 69.88 building file list ... done libtbx/ libtbx/command_line/ @@ -37174,8 +37211,8 @@ libtbx/command_line/unpack_in_sources.csh libtbx/command_line/valgrind.sh -sent 6,809 bytes received 326 bytes 14,270.00 bytes/sec -total size is 155,965 speedup is 21.86 +sent 7,116 bytes received 605 bytes 15,442.00 bytes/sec +total size is 155,965 speedup is 20.20 building file list ... done mmtbx/ mmtbx/command_line/ @@ -37183,8 +37220,8 @@ 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 @@ -37193,8 +37230,8 @@ 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 782 bytes received 49 bytes 1,662.00 bytes/sec +total size is 11,092 speedup is 13.35 building file list ... done scitbx/ scitbx/command_line/ @@ -37205,20 +37242,20 @@ scitbx/command_line/show_sizes.py scitbx/command_line/unicode_examples.py -sent 11,669 bytes received 136 bytes 7,870.00 bytes/sec +sent 11,707 bytes received 136 bytes 23,686.00 bytes/sec total size is 9,958 speedup is 0.84 building file list ... done 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 906 bytes received 40 bytes 1,892.00 bytes/sec +total size is 37,436 speedup is 39.57 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 543 bytes received 43 bytes 1,172.00 bytes/sec +total size is 22,750 speedup is 38.82 building file list ... done sent 87 bytes received 12 bytes 198.00 bytes/sec @@ -37227,11 +37264,11 @@ 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 520.00 bytes/sec +sent 256 bytes received 12 bytes 536.00 bytes/sec total size is 0 speedup is 0.00 building file list ... done boost_adaptbx/graph/ @@ -37264,7 +37301,7 @@ 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/ @@ -37277,8 +37314,8 @@ ccp4io_adaptbx/dev/ ccp4io_adaptbx/dev/tst_fftlib.py -sent 7,590 bytes received 44 bytes 15,268.00 bytes/sec -total size is 9,205 speedup is 1.21 +sent 7,600 bytes received 44 bytes 15,288.00 bytes/sec +total size is 9,205 speedup is 1.20 building file list ... done cctbx/adp_restraints/ cctbx/adptbx/ @@ -37361,21 +37398,21 @@ cctbx/xray/observations/ cctbx/xray/targets/ -sent 417,465 bytes received 816 bytes 836,562.00 bytes/sec -total size is 1,932,392 speedup is 4.62 +sent 417,853 bytes received 1,185 bytes 838,076.00 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 651 bytes received 12 bytes 1,326.00 bytes/sec total size is 0 speedup is 0.00 building file list ... done fable/test/ @@ -37384,12 +37421,12 @@ fable/test/tst_separate_files.py fable/test/tst_show_calls.py -sent 12,829 bytes received 91 bytes 25,840.00 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 209 bytes received 12 bytes 442.00 bytes/sec -total size is 8,108 speedup is 36.69 +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/ @@ -37437,14 +37474,14 @@ 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 240,859 bytes received 829 bytes 483,376.00 bytes/sec +total size is 2,112,818 speedup is 8.74 building file list ... done libtbx/phil/ libtbx/queuing_system_utils/ -sent 1,102 bytes received 18 bytes 2,240.00 bytes/sec -total size is 242,792 speedup is 216.78 +sent 1,205 bytes received 105 bytes 2,620.00 bytes/sec +total size is 242,792 speedup is 185.34 building file list ... done mmtbx/atomic_environment_vectors/ mmtbx/building/ @@ -37533,13 +37570,13 @@ mmtbx/validation/regression/ mmtbx/wwpdb/ -sent 747,030 bytes received 854 bytes 498,589.33 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/ @@ -37553,8 +37590,8 @@ 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 1,049 bytes received 87 bytes 2,272.00 bytes/sec +total size is 179,407 speedup is 157.93 building file list ... done scitbx/array_family/ scitbx/array_family/tst_accessors.cpp @@ -37660,7 +37697,7 @@ scitbx/tests/tst_smoothing.py scitbx/wigner/ -sent 674,726 bytes received 1,349 bytes 1,352,150.00 bytes/sec +sent 674,946 bytes received 1,547 bytes 1,352,986.00 bytes/sec total size is 1,108,176 speedup is 1.64 building file list ... done smtbx/ab_initio/ @@ -37689,7 +37726,7 @@ 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 130,396 bytes received 252 bytes 261,296.00 bytes/sec total size is 208,160 speedup is 1.59 building file list ... done spotfinder/core_toolbox/ @@ -37703,7 +37740,7 @@ 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/ @@ -38177,7 +38214,7 @@ smtbx/regression/test_data/thpp.hkl smtbx/regression/test_data/thpp.ins -sent 4,045,008 bytes received 8,672 bytes 737,032.73 bytes/sec +sent 4,046,170 bytes received 8,672 bytes 2,703,228.00 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 @@ -38199,12 +38236,12 @@ 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/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/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/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 @@ -38948,7 +38985,7 @@ 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-matplotlib', 'python3-tqdm', 'python3-six', 'python3-h5py (>= 3)', 'python3-procrunner', 'python3-numpy', 'python3-wxgtk4.0', 'python3-pint', 'python3-scipy', 'python3-pymol', 'python3:any', 'python3 (>= 3.11~)', 'python3 (<< 3.12)', 'python3-pil', 'python3-mrcfile', 'python3-requests'}; R=[]; S=[]; E=[], B=[]; RT=[] +D: dh_python3 depends:281: D={'python3-pint', 'python3:any', 'python3-numpy', 'python3-procrunner', 'python3-pymol', 'python3 (>= 3.11~)', 'python3-mrcfile', 'python3-scipy', 'python3 (<< 3.12)', 'python3-matplotlib', 'python3-six', 'python3-tqdm', 'python3-pil', 'python3-h5py (>= 3)', 'python3-wxgtk4.0', 'python3-requests'}; 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 @@ -39007,33 +39044,33 @@ 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/python3-cctbx - cd debian/libcctbx-dev cd debian/libcctbx0 - chmod a-x usr/share/doc/python3-cctbx/changelog usr/share/doc/python3-cctbx/changelog.Debian - chmod a-x usr/share/doc/libcctbx-dev/changelog usr/share/doc/libcctbx-dev/changelog.Debian + cd debian/libcctbx-dev + cd debian/python3-cctbx chmod a-x 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 + 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 gzip -9nf usr/share/doc/libcctbx-dev/changelog usr/share/doc/libcctbx-dev/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/python3-cctbx ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/libcctbx0 ! -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/libcctbx-dev/usr/include -type f -a -true -a -true -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/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 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 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/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/python3-cctbx/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x @@ -39066,31 +39103,36 @@ chmod 0644 -- debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/2a/cc55783bf1a7b57854330de851a6500e52fe7d.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libcctbx0/usr/lib/x86_64-linux-gnu/libsmtbx_refinement_constraints.so.0.0.1 objcopy --add-gnu-debuglink debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/2a/cc55783bf1a7b57854330de851a6500e52fe7d.debug debian/libcctbx0/usr/lib/x86_64-linux-gnu/libsmtbx_refinement_constraints.so.0.0.1 - install -m0755 -d debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/db - objcopy --only-keep-debug --compress-debug-sections debian/libcctbx0/usr/lib/x86_64-linux-gnu/libspotfinder.so.0.0.1 debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/db/382071e6a2037dcee62f96f5e3eddc28905bed.debug - chmod 0644 -- debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/db/382071e6a2037dcee62f96f5e3eddc28905bed.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libcctbx0/usr/lib/x86_64-linux-gnu/libspotfinder.so.0.0.1 - objcopy --add-gnu-debuglink debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/db/382071e6a2037dcee62f96f5e3eddc28905bed.debug debian/libcctbx0/usr/lib/x86_64-linux-gnu/libspotfinder.so.0.0.1 install -m0755 -d debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/9e objcopy --only-keep-debug --compress-debug-sections debian/libcctbx0/usr/lib/x86_64-linux-gnu/libcctbx_sgtbx_asu.so.0.0.1 debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/9e/97a2697cdd8a0b0b059456d0f0f6c14ca21fa1.debug chmod 0644 -- debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/9e/97a2697cdd8a0b0b059456d0f0f6c14ca21fa1.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libcctbx0/usr/lib/x86_64-linux-gnu/libcctbx_sgtbx_asu.so.0.0.1 objcopy --add-gnu-debuglink debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/9e/97a2697cdd8a0b0b059456d0f0f6c14ca21fa1.debug debian/libcctbx0/usr/lib/x86_64-linux-gnu/libcctbx_sgtbx_asu.so.0.0.1 - install -m0755 -d debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/13 - objcopy --only-keep-debug --compress-debug-sections debian/libcctbx0/usr/lib/x86_64-linux-gnu/libasymmetric_map.so.0.0.1 debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/13/c13e4215dab022c78ea194fde76f5218c2bfb3.debug - chmod 0644 -- debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/13/c13e4215dab022c78ea194fde76f5218c2bfb3.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libcctbx0/usr/lib/x86_64-linux-gnu/libasymmetric_map.so.0.0.1 - objcopy --add-gnu-debuglink debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/13/c13e4215dab022c78ea194fde76f5218c2bfb3.debug debian/libcctbx0/usr/lib/x86_64-linux-gnu/libasymmetric_map.so.0.0.1 + install -m0755 -d debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/db + objcopy --only-keep-debug --compress-debug-sections debian/libcctbx0/usr/lib/x86_64-linux-gnu/libspotfinder.so.0.0.1 debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/db/382071e6a2037dcee62f96f5e3eddc28905bed.debug + chmod 0644 -- debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/db/382071e6a2037dcee62f96f5e3eddc28905bed.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libcctbx0/usr/lib/x86_64-linux-gnu/libspotfinder.so.0.0.1 + objcopy --add-gnu-debuglink debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/db/382071e6a2037dcee62f96f5e3eddc28905bed.debug debian/libcctbx0/usr/lib/x86_64-linux-gnu/libspotfinder.so.0.0.1 install -m0755 -d debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/98 objcopy --only-keep-debug --compress-debug-sections debian/libcctbx0/usr/lib/x86_64-linux-gnu/librstbx.so.0.0.1 debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/98/baa098940028adeb4fc84ba0c1f5c3cad26cb8.debug chmod 0644 -- debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/98/baa098940028adeb4fc84ba0c1f5c3cad26cb8.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libcctbx0/usr/lib/x86_64-linux-gnu/librstbx.so.0.0.1 objcopy --add-gnu-debuglink debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/98/baa098940028adeb4fc84ba0c1f5c3cad26cb8.debug debian/libcctbx0/usr/lib/x86_64-linux-gnu/librstbx.so.0.0.1 + install -m0755 -d debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/13 + objcopy --only-keep-debug --compress-debug-sections debian/libcctbx0/usr/lib/x86_64-linux-gnu/libasymmetric_map.so.0.0.1 debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/13/c13e4215dab022c78ea194fde76f5218c2bfb3.debug + chmod 0644 -- debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/13/c13e4215dab022c78ea194fde76f5218c2bfb3.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libcctbx0/usr/lib/x86_64-linux-gnu/libasymmetric_map.so.0.0.1 + objcopy --add-gnu-debuglink debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/13/c13e4215dab022c78ea194fde76f5218c2bfb3.debug debian/libcctbx0/usr/lib/x86_64-linux-gnu/libasymmetric_map.so.0.0.1 install -m0755 -d debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/9a objcopy --only-keep-debug --compress-debug-sections debian/libcctbx0/usr/lib/x86_64-linux-gnu/libmmtbx_masks.so.0.0.1 debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/9a/388c5bfe68a69674ea465c91d72ad36dec6e88.debug chmod 0644 -- debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/9a/388c5bfe68a69674ea465c91d72ad36dec6e88.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libcctbx0/usr/lib/x86_64-linux-gnu/libmmtbx_masks.so.0.0.1 objcopy --add-gnu-debuglink debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/9a/388c5bfe68a69674ea465c91d72ad36dec6e88.debug debian/libcctbx0/usr/lib/x86_64-linux-gnu/libmmtbx_masks.so.0.0.1 + install -m0755 -d debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/78 + objcopy --only-keep-debug --compress-debug-sections debian/libcctbx0/usr/lib/x86_64-linux-gnu/libscitbx_boost_python.so.0.0.1 debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/78/d0f1cddef4727da37689ebaa72d1d0adc2ba1e.debug + chmod 0644 -- debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/78/d0f1cddef4727da37689ebaa72d1d0adc2ba1e.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libcctbx0/usr/lib/x86_64-linux-gnu/libscitbx_boost_python.so.0.0.1 + objcopy --add-gnu-debuglink debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/78/d0f1cddef4727da37689ebaa72d1d0adc2ba1e.debug debian/libcctbx0/usr/lib/x86_64-linux-gnu/libscitbx_boost_python.so.0.0.1 install -m0755 -d debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/65 objcopy --only-keep-debug --compress-debug-sections debian/libcctbx0/usr/lib/x86_64-linux-gnu/libscitbx_slatec.so.0.0.1 debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/65/14d95ea89054f3114ee0ea74a455d099c5974b.debug chmod 0644 -- debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/65/14d95ea89054f3114ee0ea74a455d099c5974b.debug @@ -39101,36 +39143,31 @@ chmod 0644 -- debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/0a/2f275febbc6951e6020e3141cdef5fcb6ec196.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libcctbx0/usr/lib/x86_64-linux-gnu/libscitbx_minpack.so.0.0.1 objcopy --add-gnu-debuglink debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/0a/2f275febbc6951e6020e3141cdef5fcb6ec196.debug debian/libcctbx0/usr/lib/x86_64-linux-gnu/libscitbx_minpack.so.0.0.1 - install -m0755 -d debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/78 - objcopy --only-keep-debug --compress-debug-sections debian/libcctbx0/usr/lib/x86_64-linux-gnu/libscitbx_boost_python.so.0.0.1 debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/78/d0f1cddef4727da37689ebaa72d1d0adc2ba1e.debug - chmod 0644 -- debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/78/d0f1cddef4727da37689ebaa72d1d0adc2ba1e.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libcctbx0/usr/lib/x86_64-linux-gnu/libscitbx_boost_python.so.0.0.1 - objcopy --add-gnu-debuglink debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/78/d0f1cddef4727da37689ebaa72d1d0adc2ba1e.debug debian/libcctbx0/usr/lib/x86_64-linux-gnu/libscitbx_boost_python.so.0.0.1 install -m0755 -d debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/27 objcopy --only-keep-debug --compress-debug-sections debian/libcctbx0/usr/lib/x86_64-linux-gnu/libiotbx_mtz.so.0.0.1 debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/27/7ab65c7fe1c2f5be9c08819d7f8df0fc82ad3c.debug chmod 0644 -- debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/27/7ab65c7fe1c2f5be9c08819d7f8df0fc82ad3c.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libcctbx0/usr/lib/x86_64-linux-gnu/libiotbx_mtz.so.0.0.1 objcopy --add-gnu-debuglink debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/27/7ab65c7fe1c2f5be9c08819d7f8df0fc82ad3c.debug debian/libcctbx0/usr/lib/x86_64-linux-gnu/libiotbx_mtz.so.0.0.1 - install -m0755 -d debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/5e - objcopy --only-keep-debug --compress-debug-sections debian/libcctbx0/usr/lib/x86_64-linux-gnu/libomptbx.so.0.0.1 debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/5e/9fb1988db97c930a20601f44e281da3811ec21.debug - chmod 0644 -- debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/5e/9fb1988db97c930a20601f44e281da3811ec21.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libcctbx0/usr/lib/x86_64-linux-gnu/libomptbx.so.0.0.1 - objcopy --add-gnu-debuglink debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/5e/9fb1988db97c930a20601f44e281da3811ec21.debug debian/libcctbx0/usr/lib/x86_64-linux-gnu/libomptbx.so.0.0.1 install -m0755 -d debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/f6 objcopy --only-keep-debug --compress-debug-sections debian/libcctbx0/usr/lib/x86_64-linux-gnu/libmmtbx_tls.so.0.0.1 debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/f6/fe37f3a3f966f64d035e43789c5959965d8bab.debug chmod 0644 -- debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/f6/fe37f3a3f966f64d035e43789c5959965d8bab.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libcctbx0/usr/lib/x86_64-linux-gnu/libmmtbx_tls.so.0.0.1 objcopy --add-gnu-debuglink debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/f6/fe37f3a3f966f64d035e43789c5959965d8bab.debug debian/libcctbx0/usr/lib/x86_64-linux-gnu/libmmtbx_tls.so.0.0.1 - install -m0755 -d debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/c9 - objcopy --only-keep-debug --compress-debug-sections debian/libcctbx0/usr/lib/x86_64-linux-gnu/libiotbx_xplor.so.0.0.1 debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/c9/787b229213c169b5cba39568a0b7ca3cdc99bd.debug - chmod 0644 -- debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/c9/787b229213c169b5cba39568a0b7ca3cdc99bd.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libcctbx0/usr/lib/x86_64-linux-gnu/libiotbx_xplor.so.0.0.1 - objcopy --add-gnu-debuglink debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/c9/787b229213c169b5cba39568a0b7ca3cdc99bd.debug debian/libcctbx0/usr/lib/x86_64-linux-gnu/libiotbx_xplor.so.0.0.1 + install -m0755 -d debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/5e + objcopy --only-keep-debug --compress-debug-sections debian/libcctbx0/usr/lib/x86_64-linux-gnu/libomptbx.so.0.0.1 debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/5e/9fb1988db97c930a20601f44e281da3811ec21.debug + chmod 0644 -- debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/5e/9fb1988db97c930a20601f44e281da3811ec21.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libcctbx0/usr/lib/x86_64-linux-gnu/libomptbx.so.0.0.1 + objcopy --add-gnu-debuglink debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/5e/9fb1988db97c930a20601f44e281da3811ec21.debug debian/libcctbx0/usr/lib/x86_64-linux-gnu/libomptbx.so.0.0.1 install -m0755 -d debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/b8 objcopy --only-keep-debug --compress-debug-sections debian/libcctbx0/usr/lib/x86_64-linux-gnu/libdxtbxspotfinder.so.0.0.1 debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/b8/3e5da383ada23e9dd10de29ea2693284671d18.debug chmod 0644 -- debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/b8/3e5da383ada23e9dd10de29ea2693284671d18.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libcctbx0/usr/lib/x86_64-linux-gnu/libdxtbxspotfinder.so.0.0.1 objcopy --add-gnu-debuglink debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/b8/3e5da383ada23e9dd10de29ea2693284671d18.debug debian/libcctbx0/usr/lib/x86_64-linux-gnu/libdxtbxspotfinder.so.0.0.1 + install -m0755 -d debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/c9 + objcopy --only-keep-debug --compress-debug-sections debian/libcctbx0/usr/lib/x86_64-linux-gnu/libiotbx_xplor.so.0.0.1 debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/c9/787b229213c169b5cba39568a0b7ca3cdc99bd.debug + chmod 0644 -- debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/c9/787b229213c169b5cba39568a0b7ca3cdc99bd.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libcctbx0/usr/lib/x86_64-linux-gnu/libiotbx_xplor.so.0.0.1 + objcopy --add-gnu-debuglink debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/c9/787b229213c169b5cba39568a0b7ca3cdc99bd.debug debian/libcctbx0/usr/lib/x86_64-linux-gnu/libiotbx_xplor.so.0.0.1 install -m0755 -d debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/88 objcopy --only-keep-debug --compress-debug-sections debian/libcctbx0/usr/lib/x86_64-linux-gnu/libcbf-private.so.0.0.1 debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/88/84e1c6f27bd4f2122bb958099ca54baf00bd10.debug chmod 0644 -- debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/88/84e1c6f27bd4f2122bb958099ca54baf00bd10.debug @@ -39171,31 +39208,31 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/9e/d12bb29955b9ac6fcb95ea7757770d6f9f1e12.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-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/9e/d12bb29955b9ac6fcb95ea7757770d6f9f1e12.debug debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_array_family_flex_ext.cpython-311-x86_64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/9d - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_dxtbx_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/9d/20fd5a3d87887c70a2d97473eb94efcacabe1b.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/9d/20fd5a3d87887c70a2d97473eb94efcacabe1b.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_dxtbx_ext.cpython-311-x86_64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/9d/20fd5a3d87887c70a2d97473eb94efcacabe1b.debug debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_dxtbx_ext.cpython-311-x86_64-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/std_pair_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/39/00fd127ad13a64f3a9f326116380f0543d5391.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/39/00fd127ad13a64f3a9f326116380f0543d5391.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/std_pair_ext.cpython-311-x86_64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/39/00fd127ad13a64f3a9f326116380f0543d5391.debug debian/python3-cctbx/usr/lib/python3/dist-packages/std_pair_ext.cpython-311-x86_64-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/spotfinder_hough_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/5f/5a53da387c0b76af6b6af5b862c7530b03aa91.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/5f/5a53da387c0b76af6b6af5b862c7530b03aa91.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_hough_ext.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/5f/5a53da387c0b76af6b6af5b862c7530b03aa91.debug debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_hough_ext.cpython-311-x86_64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/89 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_distltbx_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/89/6453eb560f96efc4f0493a6f2ade67dec8ca38.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/89/6453eb560f96efc4f0493a6f2ade67dec8ca38.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_distltbx_ext.cpython-311-x86_64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/89/6453eb560f96efc4f0493a6f2ade67dec8ca38.debug debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_distltbx_ext.cpython-311-x86_64-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/smtbx_refinement_least_squares_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/bb/4c69b2ab7e3a5b7ae8ca06bd21cc991e77d559.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/bb/4c69b2ab7e3a5b7ae8ca06bd21cc991e77d559.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_refinement_least_squares_ext.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/bb/4c69b2ab7e3a5b7ae8ca06bd21cc991e77d559.debug debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_refinement_least_squares_ext.cpython-311-x86_64-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/std_pair_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/39/00fd127ad13a64f3a9f326116380f0543d5391.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/39/00fd127ad13a64f3a9f326116380f0543d5391.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/std_pair_ext.cpython-311-x86_64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/39/00fd127ad13a64f3a9f326116380f0543d5391.debug debian/python3-cctbx/usr/lib/python3/dist-packages/std_pair_ext.cpython-311-x86_64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/89 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_distltbx_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/89/6453eb560f96efc4f0493a6f2ade67dec8ca38.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/89/6453eb560f96efc4f0493a6f2ade67dec8ca38.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_distltbx_ext.cpython-311-x86_64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/89/6453eb560f96efc4f0493a6f2ade67dec8ca38.debug debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_distltbx_ext.cpython-311-x86_64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/9d + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_dxtbx_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/9d/20fd5a3d87887c70a2d97473eb94efcacabe1b.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/9d/20fd5a3d87887c70a2d97473eb94efcacabe1b.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_dxtbx_ext.cpython-311-x86_64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/9d/20fd5a3d87887c70a2d97473eb94efcacabe1b.debug debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_dxtbx_ext.cpython-311-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/3c objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_structure_factors_direct_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/3c/0258cf1e0a7be7157f2615ec0597a58af5b52c.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/3c/0258cf1e0a7be7157f2615ec0597a58af5b52c.debug @@ -39206,6 +39243,11 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/5b/90eb25350f373951068468c49f12e3da6e6bd6.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_refinement_restraints_ext.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/5b/90eb25350f373951068468c49f12e3da6e6bd6.debug debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_refinement_restraints_ext.cpython-311-x86_64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ac + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_sparse_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ac/12da77e633f047f69cc54ac1ff77122a1c1912.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ac/12da77e633f047f69cc54ac1ff77122a1c1912.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_sparse_ext.cpython-311-x86_64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ac/12da77e633f047f69cc54ac1ff77122a1c1912.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_sparse_ext.cpython-311-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/5c objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_stl_map_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/5c/97eda791ff5f9c8c45ff8c64fba7e1d5d882e7.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/5c/97eda791ff5f9c8c45ff8c64fba7e1d5d882e7.debug @@ -39216,26 +39258,6 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b5/93e5d1aa4081d5ca934129942c5fd39a3f0699.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_suffixtree_single_ext.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b5/93e5d1aa4081d5ca934129942c5fd39a3f0699.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_suffixtree_single_ext.cpython-311-x86_64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ac - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_sparse_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ac/12da77e633f047f69cc54ac1ff77122a1c1912.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ac/12da77e633f047f69cc54ac1ff77122a1c1912.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_sparse_ext.cpython-311-x86_64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ac/12da77e633f047f69cc54ac1ff77122a1c1912.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_sparse_ext.cpython-311-x86_64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/72 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_stl_map_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/72/94031d3f8a3a10b96334611afa497086878773.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/72/94031d3f8a3a10b96334611afa497086878773.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_stl_map_ext.cpython-311-x86_64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/72/94031d3f8a3a10b96334611afa497086878773.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_stl_map_ext.cpython-311-x86_64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/01 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_array_family_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/01/47043efcde5d2d5724d7849b21eb0ce9f0905b.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/01/47043efcde5d2d5724d7849b21eb0ce9f0905b.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_array_family_ext.cpython-311-x86_64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/01/47043efcde5d2d5724d7849b21eb0ce9f0905b.debug debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_array_family_ext.cpython-311-x86_64-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/scitbx_wigner_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/eb/f5f254a9fdca2dcdf3ec79eb412a0d0b079145.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/eb/f5f254a9fdca2dcdf3ec79eb412a0d0b079145.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_wigner_ext.cpython-311-x86_64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/eb/f5f254a9fdca2dcdf3ec79eb412a0d0b079145.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_wigner_ext.cpython-311-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/bc objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_ab_initio_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/bc/06c4dbc418fa8c35d3006c4839ffcbb9459ab2.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/bc/06c4dbc418fa8c35d3006c4839ffcbb9459ab2.debug @@ -39246,166 +39268,176 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/96/4bb92c95ccaaa39956b88ddde6e6d57f1c7e43.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_stl_vector_ext.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/96/4bb92c95ccaaa39956b88ddde6e6d57f1c7e43.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_stl_vector_ext.cpython-311-x86_64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/23 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_suffixtree_shared_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/23/250beba66fad5b2dd9480b53dab2f6b9851cd6.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/23/250beba66fad5b2dd9480b53dab2f6b9851cd6.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_suffixtree_shared_ext.cpython-311-x86_64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/23/250beba66fad5b2dd9480b53dab2f6b9851cd6.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_suffixtree_shared_ext.cpython-311-x86_64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/cc - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_stl_set_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/cc/091010ce49953ef47f171d3e082387fb5e6a3b.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/cc/091010ce49953ef47f171d3e082387fb5e6a3b.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_stl_set_ext.cpython-311-x86_64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/cc/091010ce49953ef47f171d3e082387fb5e6a3b.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_stl_set_ext.cpython-311-x86_64-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/scitbx_wigner_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/eb/f5f254a9fdca2dcdf3ec79eb412a0d0b079145.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/eb/f5f254a9fdca2dcdf3ec79eb412a0d0b079145.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_wigner_ext.cpython-311-x86_64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/eb/f5f254a9fdca2dcdf3ec79eb412a0d0b079145.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_wigner_ext.cpython-311-x86_64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/01 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_array_family_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/01/47043efcde5d2d5724d7849b21eb0ce9f0905b.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/01/47043efcde5d2d5724d7849b21eb0ce9f0905b.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_array_family_ext.cpython-311-x86_64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/01/47043efcde5d2d5724d7849b21eb0ce9f0905b.debug debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_array_family_ext.cpython-311-x86_64-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_linalg_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d2/e9f35f3e9b702f1f2a3feccec6286ec56b1592.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d2/e9f35f3e9b702f1f2a3feccec6286ec56b1592.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_linalg_ext.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d2/e9f35f3e9b702f1f2a3feccec6286ec56b1592.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_linalg_ext.cpython-311-x86_64-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/scitbx_random_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/bb/e3e70a9dd5ebf5f8b9af67aef27a0bd2a34833.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/bb/e3e70a9dd5ebf5f8b9af67aef27a0bd2a34833.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_random_ext.cpython-311-x86_64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/bb/e3e70a9dd5ebf5f8b9af67aef27a0bd2a34833.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_random_ext.cpython-311-x86_64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/72 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_stl_map_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/72/94031d3f8a3a10b96334611afa497086878773.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/72/94031d3f8a3a10b96334611afa497086878773.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_stl_map_ext.cpython-311-x86_64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/72/94031d3f8a3a10b96334611afa497086878773.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_stl_map_ext.cpython-311-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b6 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_rigid_body_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b6/ead1a4959b9d88cecc9c94e1df9404dbb13ea2.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b6/ead1a4959b9d88cecc9c94e1df9404dbb13ea2.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_rigid_body_ext.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b6/ead1a4959b9d88cecc9c94e1df9404dbb13ea2.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_rigid_body_ext.cpython-311-x86_64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/23 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_suffixtree_shared_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/23/250beba66fad5b2dd9480b53dab2f6b9851cd6.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/23/250beba66fad5b2dd9480b53dab2f6b9851cd6.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_suffixtree_shared_ext.cpython-311-x86_64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/23/250beba66fad5b2dd9480b53dab2f6b9851cd6.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_suffixtree_shared_ext.cpython-311-x86_64-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/scitbx_random_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/bb/e3e70a9dd5ebf5f8b9af67aef27a0bd2a34833.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/bb/e3e70a9dd5ebf5f8b9af67aef27a0bd2a34833.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_random_ext.cpython-311-x86_64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/bb/e3e70a9dd5ebf5f8b9af67aef27a0bd2a34833.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_random_ext.cpython-311-x86_64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/cc + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_stl_set_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/cc/091010ce49953ef47f171d3e082387fb5e6a3b.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/cc/091010ce49953ef47f171d3e082387fb5e6a3b.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_stl_set_ext.cpython-311-x86_64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/cc/091010ce49953ef47f171d3e082387fb5e6a3b.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_stl_set_ext.cpython-311-x86_64-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/scitbx_lstbx_normal_equations_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/35/520cdba460638b74f45b69d7d77acb2359d072.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/35/520cdba460638b74f45b69d7d77acb2359d072.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-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/35/520cdba460638b74f45b69d7d77acb2359d072.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_lstbx_normal_equations_ext.cpython-311-x86_64-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_r3_utils_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/cf/97029a38616c4d47503f5fa71786ac5d1d0f8f.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/cf/97029a38616c4d47503f5fa71786ac5d1d0f8f.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_r3_utils_ext.cpython-311-x86_64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/cf/97029a38616c4d47503f5fa71786ac5d1d0f8f.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_r3_utils_ext.cpython-311-x86_64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/c9 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_array_family_shared_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/c9/89a2065ac186e9b14f541c81baf663d6688fc6.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/c9/89a2065ac186e9b14f541c81baf663d6688fc6.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-x86_64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/c9/89a2065ac186e9b14f541c81baf663d6688fc6.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_array_family_shared_ext.cpython-311-x86_64-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-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/3a/c4ab8eec6c3766554d8f0e340f43bc2f7debaf.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/3a/c4ab8eec6c3766554d8f0e340f43bc2f7debaf.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_minpack_ext.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/3a/c4ab8eec6c3766554d8f0e340f43bc2f7debaf.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_minpack_ext.cpython-311-x86_64-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_r3_utils_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/cf/97029a38616c4d47503f5fa71786ac5d1d0f8f.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/cf/97029a38616c4d47503f5fa71786ac5d1d0f8f.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_r3_utils_ext.cpython-311-x86_64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/cf/97029a38616c4d47503f5fa71786ac5d1d0f8f.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_r3_utils_ext.cpython-311-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/9d objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_lbfgs_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/9d/e4b75883c3d7b669f23487fb8e2098d0943142.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/9d/e4b75883c3d7b669f23487fb8e2098d0943142.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_lbfgs_ext.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/9d/e4b75883c3d7b669f23487fb8e2098d0943142.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_lbfgs_ext.cpython-311-x86_64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/c9 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_array_family_shared_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/c9/89a2065ac186e9b14f541c81baf663d6688fc6.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/c9/89a2065ac186e9b14f541c81baf663d6688fc6.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-x86_64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/c9/89a2065ac186e9b14f541c81baf663d6688fc6.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_array_family_shared_ext.cpython-311-x86_64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/93 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_fftpack_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/93/a44292c57868f95569bc48451c60dd1c6c0938.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/93/a44292c57868f95569bc48451c60dd1c6c0938.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_fftpack_ext.cpython-311-x86_64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/93/a44292c57868f95569bc48451c60dd1c6c0938.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_fftpack_ext.cpython-311-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/76 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_lbfgsb_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/76/ec0b4f99fff3e91ad95e4b7055c2dcc08828f6.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/76/ec0b4f99fff3e91ad95e4b7055c2dcc08828f6.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_lbfgsb_ext.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/76/ec0b4f99fff3e91ad95e4b7055c2dcc08828f6.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_lbfgsb_ext.cpython-311-x86_64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/93 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_fftpack_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/93/a44292c57868f95569bc48451c60dd1c6c0938.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/93/a44292c57868f95569bc48451c60dd1c6c0938.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_fftpack_ext.cpython-311-x86_64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/93/a44292c57868f95569bc48451c60dd1c6c0938.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_fftpack_ext.cpython-311-x86_64-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_iso_surface_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/26/7fed1ea9fe51539dcbbe2e54ab362d86eaa90c.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/26/7fed1ea9fe51539dcbbe2e54ab362d86eaa90c.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_iso_surface_ext.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/26/7fed1ea9fe51539dcbbe2e54ab362d86eaa90c.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_iso_surface_ext.cpython-311-x86_64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/76 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_graphics_utils_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/76/d2bd0c1b4f34838bb7342dfd0fccb240abc336.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/76/d2bd0c1b4f34838bb7342dfd0fccb240abc336.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_graphics_utils_ext.cpython-311-x86_64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/76/d2bd0c1b4f34838bb7342dfd0fccb240abc336.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_graphics_utils_ext.cpython-311-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/06 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_glmtbx_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/06/534a655a7eda94ac150eb3e9ebf6cb7831ff20.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/06/534a655a7eda94ac150eb3e9ebf6cb7831ff20.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_glmtbx_ext.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/06/534a655a7eda94ac150eb3e9ebf6cb7831ff20.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_glmtbx_ext.cpython-311-x86_64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/93 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/93/bdf93b92bd3473edb7768ed5637100396ba4a6.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/93/bdf93b92bd3473edb7768ed5637100396ba4a6.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_ext.cpython-311-x86_64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/93/bdf93b92bd3473edb7768ed5637100396ba4a6.debug debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_ext.cpython-311-x86_64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/76 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_graphics_utils_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/76/d2bd0c1b4f34838bb7342dfd0fccb240abc336.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/76/d2bd0c1b4f34838bb7342dfd0fccb240abc336.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_graphics_utils_ext.cpython-311-x86_64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/76/d2bd0c1b4f34838bb7342dfd0fccb240abc336.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_graphics_utils_ext.cpython-311-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/3c objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_cubicle_neighbors_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/3c/73cb9e39f04c42d6b5690c919f72be39c2f72f.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/3c/73cb9e39f04c42d6b5690c919f72be39c2f72f.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_cubicle_neighbors_ext.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/3c/73cb9e39f04c42d6b5690c919f72be39c2f72f.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_cubicle_neighbors_ext.cpython-311-x86_64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/30 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_array_family_flex_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/30/586d7c70a3ce4de3c7855f491403ad65feb25e.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/30/586d7c70a3ce4de3c7855f491403ad65feb25e.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-x86_64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/30/586d7c70a3ce4de3c7855f491403ad65feb25e.debug debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_array_family_flex_ext.cpython-311-x86_64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/93 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/93/bdf93b92bd3473edb7768ed5637100396ba4a6.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/93/bdf93b92bd3473edb7768ed5637100396ba4a6.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_ext.cpython-311-x86_64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/93/bdf93b92bd3473edb7768ed5637100396ba4a6.debug debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_ext.cpython-311-x86_64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/12 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_simulation_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/12/946b64fd24a3f257c2cd6d0329c0388c99c146.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/12/946b64fd24a3f257c2cd6d0329c0388c99c146.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_simulation_ext.cpython-311-x86_64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/12/946b64fd24a3f257c2cd6d0329c0388c99c146.debug debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_simulation_ext.cpython-311-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/2d objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_symmetry_constraints_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/2d/52136508bc79a8115c4583eb724d94ca2c643c.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/2d/52136508bc79a8115c4583eb724d94ca2c643c.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_symmetry_constraints_ext.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/2d/52136508bc79a8115c4583eb724d94ca2c643c.debug debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_symmetry_constraints_ext.cpython-311-x86_64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/30 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_array_family_flex_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/30/586d7c70a3ce4de3c7855f491403ad65feb25e.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/30/586d7c70a3ce4de3c7855f491403ad65feb25e.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-x86_64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/30/586d7c70a3ce4de3c7855f491403ad65feb25e.debug debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_array_family_flex_ext.cpython-311-x86_64-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/mmtbx_scaling_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d8/05489c1ea0d359afa8a3f0a0cbe69199750937.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d8/05489c1ea0d359afa8a3f0a0cbe69199750937.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_scaling_ext.cpython-311-x86_64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d8/05489c1ea0d359afa8a3f0a0cbe69199750937.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_scaling_ext.cpython-311-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ee objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_integration_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ee/a8a7cf73a7745372e1623d9df94e291b62ef18.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ee/a8a7cf73a7745372e1623d9df94e291b62ef18.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_integration_ext.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ee/a8a7cf73a7745372e1623d9df94e291b62ef18.debug debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_integration_ext.cpython-311-x86_64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/44 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_simage_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/44/cdb5398f3a990d7da3ea0bb1eac31747bf19c1.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/44/cdb5398f3a990d7da3ea0bb1eac31747bf19c1.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_simage_ext.cpython-311-x86_64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/44/cdb5398f3a990d7da3ea0bb1eac31747bf19c1.debug debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_simage_ext.cpython-311-x86_64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/12 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_simulation_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/12/946b64fd24a3f257c2cd6d0329c0388c99c146.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/12/946b64fd24a3f257c2cd6d0329c0388c99c146.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_simulation_ext.cpython-311-x86_64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/12/946b64fd24a3f257c2cd6d0329c0388c99c146.debug debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_simulation_ext.cpython-311-x86_64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/78 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_utils_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/78/7648984faaeec5a954ddea262b38ed3825fd64.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/78/7648984faaeec5a954ddea262b38ed3825fd64.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_utils_ext.cpython-311-x86_64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/78/7648984faaeec5a954ddea262b38ed3825fd64.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_utils_ext.cpython-311-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/5b objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_indexing_api_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/5b/642be31ca8049ef07ebe226c77c5b10b193b10.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/5b/642be31ca8049ef07ebe226c77c5b10b193b10.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_indexing_api_ext.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/5b/642be31ca8049ef07ebe226c77c5b10b193b10.debug debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_indexing_api_ext.cpython-311-x86_64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/78 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_utils_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/78/7648984faaeec5a954ddea262b38ed3825fd64.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/78/7648984faaeec5a954ddea262b38ed3825fd64.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_utils_ext.cpython-311-x86_64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/78/7648984faaeec5a954ddea262b38ed3825fd64.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_utils_ext.cpython-311-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/6c objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_diffraction_fastbragg_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/6c/6f85f461613cc7b31ecbdde366c6f84a65d67b.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/6c/6f85f461613cc7b31ecbdde366c6f84a65d67b.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_diffraction_fastbragg_ext.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/6c/6f85f461613cc7b31ecbdde366c6f84a65d67b.debug debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_diffraction_fastbragg_ext.cpython-311-x86_64-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/mmtbx_tls_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/19/a01bcc9d6ea0f9fb8b7ffa7153c539ed9aac1f.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/19/a01bcc9d6ea0f9fb8b7ffa7153c539ed9aac1f.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_ext.cpython-311-x86_64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/19/a01bcc9d6ea0f9fb8b7ffa7153c539ed9aac1f.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_ext.cpython-311-x86_64-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/mmtbx_scaling_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d8/05489c1ea0d359afa8a3f0a0cbe69199750937.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d8/05489c1ea0d359afa8a3f0a0cbe69199750937.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_scaling_ext.cpython-311-x86_64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d8/05489c1ea0d359afa8a3f0a0cbe69199750937.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_scaling_ext.cpython-311-x86_64-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/rstbx_bpcx_detector_model_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e0/72e492ae4e34e006cedf485308aabb7e92466e.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e0/72e492ae4e34e006cedf485308aabb7e92466e.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_bpcx_detector_model_ext.cpython-311-x86_64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e0/72e492ae4e34e006cedf485308aabb7e92466e.debug debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_bpcx_detector_model_ext.cpython-311-x86_64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/44 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_simage_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/44/cdb5398f3a990d7da3ea0bb1eac31747bf19c1.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/44/cdb5398f3a990d7da3ea0bb1eac31747bf19c1.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_simage_ext.cpython-311-x86_64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/44/cdb5398f3a990d7da3ea0bb1eac31747bf19c1.debug debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_simage_ext.cpython-311-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/48 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_bandpass_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/48/db5e8a8752a8624f74ab74f814d17747d3688b.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/48/db5e8a8752a8624f74ab74f814d17747d3688b.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_bandpass_ext.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/48/db5e8a8752a8624f74ab74f814d17747d3688b.debug debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_bandpass_ext.cpython-311-x86_64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ee - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/regression_test_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ee/7ba253895444ce2079f96fdfb3b53e337fe80d.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ee/7ba253895444ce2079f96fdfb3b53e337fe80d.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/regression_test_ext.cpython-311-x86_64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ee/7ba253895444ce2079f96fdfb3b53e337fe80d.debug debian/python3-cctbx/usr/lib/python3/dist-packages/regression_test_ext.cpython-311-x86_64-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/mmtbx_tls_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/19/a01bcc9d6ea0f9fb8b7ffa7153c539ed9aac1f.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/19/a01bcc9d6ea0f9fb8b7ffa7153c539ed9aac1f.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_ext.cpython-311-x86_64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/19/a01bcc9d6ea0f9fb8b7ffa7153c539ed9aac1f.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_ext.cpython-311-x86_64-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_probe_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/0d/a7fcc02f2cbfaf3e9fbdf5b41934efaa2d0229.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/0d/a7fcc02f2cbfaf3e9fbdf5b41934efaa2d0229.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_probe_ext.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/0d/a7fcc02f2cbfaf3e9fbdf5b41934efaa2d0229.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_probe_ext.cpython-311-x86_64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/53 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/omptbx_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/53/402a9ebeb400536e099656f53a060d8c0fe3af.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/53/402a9ebeb400536e099656f53a060d8c0fe3af.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/omptbx_ext.cpython-311-x86_64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/53/402a9ebeb400536e099656f53a060d8c0fe3af.debug debian/python3-cctbx/usr/lib/python3/dist-packages/omptbx_ext.cpython-311-x86_64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ee + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/regression_test_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ee/7ba253895444ce2079f96fdfb3b53e337fe80d.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ee/7ba253895444ce2079f96fdfb3b53e337fe80d.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/regression_test_ext.cpython-311-x86_64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ee/7ba253895444ce2079f96fdfb3b53e337fe80d.debug debian/python3-cctbx/usr/lib/python3/dist-packages/regression_test_ext.cpython-311-x86_64-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/rstbx_bpcx_detector_model_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e0/72e492ae4e34e006cedf485308aabb7e92466e.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e0/72e492ae4e34e006cedf485308aabb7e92466e.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_bpcx_detector_model_ext.cpython-311-x86_64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e0/72e492ae4e34e006cedf485308aabb7e92466e.debug debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_bpcx_detector_model_ext.cpython-311-x86_64-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/mmtbx_validation_ramachandran_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/84/df5ccade6196d8e712d530b2873a2b1f5f0f25.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/84/df5ccade6196d8e712d530b2873a2b1f5f0f25.debug @@ -39421,6 +39453,11 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e0/2e4f42f05cd8728f6da683463e98099d50438f.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_utils_ext.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e0/2e4f42f05cd8728f6da683463e98099d50438f.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_utils_ext.cpython-311-x86_64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/53 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/omptbx_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/53/402a9ebeb400536e099656f53a060d8c0fe3af.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/53/402a9ebeb400536e099656f53a060d8c0fe3af.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/omptbx_ext.cpython-311-x86_64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/53/402a9ebeb400536e099656f53a060d8c0fe3af.debug debian/python3-cctbx/usr/lib/python3/dist-packages/omptbx_ext.cpython-311-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/99 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_ramachandran_restraints_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/99/241bb5de931db45a87c03ed325e7b553a2b218.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/99/241bb5de931db45a87c03ed325e7b553a2b218.debug @@ -39431,11 +39468,11 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8c/927761dbb8ec435d540dd243e5846f6237cb5a.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_decompose_ext.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8c/927761dbb8ec435d540dd243e5846f6237cb5a.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_decompose_ext.cpython-311-x86_64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/63 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_reference_coordinate_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/63/346548208a7c6f17e6a6e4a3042af89cba007a.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/63/346548208a7c6f17e6a6e4a3042af89cba007a.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_reference_coordinate_ext.cpython-311-x86_64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/63/346548208a7c6f17e6a6e4a3042af89cba007a.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_reference_coordinate_ext.cpython-311-x86_64-linux-gnu.so + 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/python3/dist-packages/mmtbx_rsr_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/80/8f7067937413b16b850a6591cab22bc6b60e8b.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/80/8f7067937413b16b850a6591cab22bc6b60e8b.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_rsr_ext.cpython-311-x86_64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/80/8f7067937413b16b850a6591cab22bc6b60e8b.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_rsr_ext.cpython-311-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/77 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_rotamer_fit_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/77/143e4d42d4cc4de6e97f61939698312fc1c939.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/77/143e4d42d4cc4de6e97f61939698312fc1c939.debug @@ -39446,71 +39483,71 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a7/bc41a5067aaf321f5170b4b8e1a1acce738238.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_secondary_structure_ext.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a7/bc41a5067aaf321f5170b4b8e1a1acce738238.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_secondary_structure_ext.cpython-311-x86_64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/63 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_reference_coordinate_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/63/346548208a7c6f17e6a6e4a3042af89cba007a.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/63/346548208a7c6f17e6a6e4a3042af89cba007a.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_reference_coordinate_ext.cpython-311-x86_64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/63/346548208a7c6f17e6a6e4a3042af89cba007a.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_reference_coordinate_ext.cpython-311-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/37 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_pair_interaction_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/37/32a026974b16a2862af3fdc7da060e03a3a36a.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/37/32a026974b16a2862af3fdc7da060e03a3a36a.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_pair_interaction_ext.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/37/32a026974b16a2862af3fdc7da060e03a3a36a.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_pair_interaction_ext.cpython-311-x86_64-linux-gnu.so - 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/python3/dist-packages/mmtbx_rsr_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/80/8f7067937413b16b850a6591cab22bc6b60e8b.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/80/8f7067937413b16b850a6591cab22bc6b60e8b.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_rsr_ext.cpython-311-x86_64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/80/8f7067937413b16b850a6591cab22bc6b60e8b.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_rsr_ext.cpython-311-x86_64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/cd - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_max_lik_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/cd/630bd430b866a14151704c87da8ce3a8638f57.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/cd/630bd430b866a14151704c87da8ce3a8638f57.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_max_lik_ext.cpython-311-x86_64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/cd/630bd430b866a14151704c87da8ce3a8638f57.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_max_lik_ext.cpython-311-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/3e objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_ncs_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/3e/10d2c36d6281fa3f3f0a84e3acf3bc453e7d87.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/3e/10d2c36d6281fa3f3f0a84e3acf3bc453e7d87.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_ncs_ext.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/3e/10d2c36d6281fa3f3f0a84e3acf3bc453e7d87.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_ncs_ext.cpython-311-x86_64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f5 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_model_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f5/63799e0a29e559f12d6daf85a503b81aad6a04.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f5/63799e0a29e559f12d6daf85a503b81aad6a04.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_model_ext.cpython-311-x86_64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f5/63799e0a29e559f12d6daf85a503b81aad6a04.debug debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_model_ext.cpython-311-x86_64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/77 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_ncs_cartesian_restraints_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/77/d9ef8d101a6662ada917ae7924bb9e06e82aa8.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/77/d9ef8d101a6662ada917ae7924bb9e06e82aa8.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-x86_64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/77/d9ef8d101a6662ada917ae7924bb9e06e82aa8.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_ncs_cartesian_restraints_ext.cpython-311-x86_64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/cd + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_max_lik_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/cd/630bd430b866a14151704c87da8ce3a8638f57.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/cd/630bd430b866a14151704c87da8ce3a8638f57.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_max_lik_ext.cpython-311-x86_64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/cd/630bd430b866a14151704c87da8ce3a8638f57.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_max_lik_ext.cpython-311-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/12 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_asa_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/12/76ef8ae7557ab34ac259400e7cee8f436f8aab.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/12/76ef8ae7557ab34ac259400e7cee8f436f8aab.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_asa_ext.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/12/76ef8ae7557ab34ac259400e7cee8f436f8aab.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_asa_ext.cpython-311-x86_64-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_masks_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f2/047b0e33a36d86acb4ffddcab97e46006f788a.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f2/047b0e33a36d86acb4ffddcab97e46006f788a.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_masks_ext.cpython-311-x86_64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f2/047b0e33a36d86acb4ffddcab97e46006f788a.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_masks_ext.cpython-311-x86_64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/77 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_ncs_cartesian_restraints_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/77/d9ef8d101a6662ada917ae7924bb9e06e82aa8.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/77/d9ef8d101a6662ada917ae7924bb9e06e82aa8.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-x86_64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/77/d9ef8d101a6662ada917ae7924bb9e06e82aa8.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_ncs_cartesian_restraints_ext.cpython-311-x86_64-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/mmtbx_mosaic_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/6a/445c92eccc60dbdafb87448fad76378ffdcae3.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/6a/445c92eccc60dbdafb87448fad76378ffdcae3.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_mosaic_ext.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/6a/445c92eccc60dbdafb87448fad76378ffdcae3.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_mosaic_ext.cpython-311-x86_64-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/python3/dist-packages/mmtbx_geometry_clash_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7b/b037ce17f876203a452734213dca33a5632a82.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7b/b037ce17f876203a452734213dca33a5632a82.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_clash_ext.cpython-311-x86_64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7b/b037ce17f876203a452734213dca33a5632a82.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_clash_ext.cpython-311-x86_64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f5 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_model_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f5/63799e0a29e559f12d6daf85a503b81aad6a04.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f5/63799e0a29e559f12d6daf85a503b81aad6a04.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_model_ext.cpython-311-x86_64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f5/63799e0a29e559f12d6daf85a503b81aad6a04.debug debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_model_ext.cpython-311-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f0 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_pdb_hierarchy_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f0/596be9a443264013c2df06ef26ca4e989d412d.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f0/596be9a443264013c2df06ef26ca4e989d412d.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_pdb_hierarchy_ext.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f0/596be9a443264013c2df06ef26ca4e989d412d.debug debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_pdb_hierarchy_ext.cpython-311-x86_64-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/mmtbx_hydrogens_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/4b/578b2860de29618eac05578db1d6ba3a6c364d.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/4b/578b2860de29618eac05578db1d6ba3a6c364d.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_hydrogens_ext.cpython-311-x86_64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/4b/578b2860de29618eac05578db1d6ba3a6c364d.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_hydrogens_ext.cpython-311-x86_64-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_masks_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f2/047b0e33a36d86acb4ffddcab97e46006f788a.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f2/047b0e33a36d86acb4ffddcab97e46006f788a.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_masks_ext.cpython-311-x86_64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f2/047b0e33a36d86acb4ffddcab97e46006f788a.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_masks_ext.cpython-311-x86_64-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/python3/dist-packages/mmtbx_geometry_clash_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7b/b037ce17f876203a452734213dca33a5632a82.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7b/b037ce17f876203a452734213dca33a5632a82.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_clash_ext.cpython-311-x86_64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7b/b037ce17f876203a452734213dca33a5632a82.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_clash_ext.cpython-311-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/52 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_indexing_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/52/fde7ecd396ca6cdecb26f91d5df6e83286b044.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/52/fde7ecd396ca6cdecb26f91d5df6e83286b044.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_indexing_ext.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/52/fde7ecd396ca6cdecb26f91d5df6e83286b044.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_indexing_ext.cpython-311-x86_64-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/mmtbx_hydrogens_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/4b/578b2860de29618eac05578db1d6ba3a6c364d.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/4b/578b2860de29618eac05578db1d6ba3a6c364d.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_hydrogens_ext.cpython-311-x86_64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/4b/578b2860de29618eac05578db1d6ba3a6c364d.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_hydrogens_ext.cpython-311-x86_64-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_geometry_sphere_surface_sampling_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/c3/de1d3e8b17ca258dfd3ac212fa4aab45837917.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/c3/de1d3e8b17ca258dfd3ac212fa4aab45837917.debug @@ -39521,26 +39558,26 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/43/b1ad405574251e20d8150d424e193e5eb4fa53.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-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/43/b1ad405574251e20d8150d424e193e5eb4fa53.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_shared_types_ext.cpython-311-x86_64-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_geometry_primitive_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f2/0cfd1034ccf557f67a1b6046b85a3fb760a068.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f2/0cfd1034ccf557f67a1b6046b85a3fb760a068.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_primitive_ext.cpython-311-x86_64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f2/0cfd1034ccf557f67a1b6046b85a3fb760a068.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_primitive_ext.cpython-311-x86_64-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/mmtbx_f_model_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/4e/38dd5d42b05750b996ae09d6140e3f94a25f44.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/4e/38dd5d42b05750b996ae09d6140e3f94a25f44.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_f_model_ext.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/4e/38dd5d42b05750b996ae09d6140e3f94a25f44.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_f_model_ext.cpython-311-x86_64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/c5 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_dynamics_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/c5/df911e39b786db6938093882a4b0ca91de9ba5.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/c5/df911e39b786db6938093882a4b0ca91de9ba5.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_dynamics_ext.cpython-311-x86_64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/c5/df911e39b786db6938093882a4b0ca91de9ba5.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_dynamics_ext.cpython-311-x86_64-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_geometry_primitive_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f2/0cfd1034ccf557f67a1b6046b85a3fb760a068.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f2/0cfd1034ccf557f67a1b6046b85a3fb760a068.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_primitive_ext.cpython-311-x86_64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f2/0cfd1034ccf557f67a1b6046b85a3fb760a068.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_primitive_ext.cpython-311-x86_64-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/mmtbx_den_restraints_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/4c/1843188046dc2642f5271b8bd6870bc2349906.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/4c/1843188046dc2642f5271b8bd6870bc2349906.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_den_restraints_ext.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/4c/1843188046dc2642f5271b8bd6870bc2349906.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_den_restraints_ext.cpython-311-x86_64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/c5 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_dynamics_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/c5/df911e39b786db6938093882a4b0ca91de9ba5.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/c5/df911e39b786db6938093882a4b0ca91de9ba5.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_dynamics_ext.cpython-311-x86_64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/c5/df911e39b786db6938093882a4b0ca91de9ba5.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_dynamics_ext.cpython-311-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/71 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_bulk_solvent_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/71/1f1700cbd092cecbf21692dbb8398595088cf5.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/71/1f1700cbd092cecbf21692dbb8398595088cf5.debug @@ -39551,26 +39588,31 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b2/f2edddf59e5abad947a4f360890d835868746b.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_mtz_ext.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b2/f2edddf59e5abad947a4f360890d835868746b.debug debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_mtz_ext.cpython-311-x86_64-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/mmtbx_dssp_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ae/1dd3c4fe42b907386f0142092479a16d43e3d6.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ae/1dd3c4fe42b907386f0142092479a16d43e3d6.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_dssp_ext.cpython-311-x86_64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ae/1dd3c4fe42b907386f0142092479a16d43e3d6.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_dssp_ext.cpython-311-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/46 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_geometry_restraints_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/46/fa36491b1200357ea557369856b311f2aa1023.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/46/fa36491b1200357ea557369856b311f2aa1023.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_geometry_restraints_ext.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/46/fa36491b1200357ea557369856b311f2aa1023.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_geometry_restraints_ext.cpython-311-x86_64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b7 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_building_loop_closure_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b7/301e0ccc8da6df9ea2c4762230194c40eb4eff.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b7/301e0ccc8da6df9ea2c4762230194c40eb4eff.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-x86_64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b7/301e0ccc8da6df9ea2c4762230194c40eb4eff.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_building_loop_closure_ext.cpython-311-x86_64-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/mmtbx_dssp_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ae/1dd3c4fe42b907386f0142092479a16d43e3d6.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ae/1dd3c4fe42b907386f0142092479a16d43e3d6.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_dssp_ext.cpython-311-x86_64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ae/1dd3c4fe42b907386f0142092479a16d43e3d6.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_dssp_ext.cpython-311-x86_64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/78 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_xray_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/78/cba49f211c9257ba43a2de67ac58f648193d28.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/78/cba49f211c9257ba43a2de67ac58f648193d28.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_xray_ext.cpython-311-x86_64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/78/cba49f211c9257ba43a2de67ac58f648193d28.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_xray_ext.cpython-311-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/aa objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_cablam_align_utils_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/aa/98caf4f7d490e707a079303766658989b8df12.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/aa/98caf4f7d490e707a079303766658989b8df12.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-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/aa/98caf4f7d490e707a079303766658989b8df12.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_cablam_align_utils_ext.cpython-311-x86_64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b7 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_building_loop_closure_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b7/301e0ccc8da6df9ea2c4762230194c40eb4eff.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b7/301e0ccc8da6df9ea2c4762230194c40eb4eff.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-x86_64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b7/301e0ccc8da6df9ea2c4762230194c40eb4eff.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_building_loop_closure_ext.cpython-311-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/18 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_alignment_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/18/0f33d47fe338a2c1deed4a0182f8172dc7540a.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/18/0f33d47fe338a2c1deed4a0182f8172dc7540a.debug @@ -39581,6 +39623,11 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e4/42713964f463e11e5542b965707d898e1a8be0.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_xplor_ext.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e4/42713964f463e11e5542b965707d898e1a8be0.debug debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_xplor_ext.cpython-311-x86_64-linux-gnu.so + 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/python3/dist-packages/iotbx_shelx_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ff/e8327bdd29124bd995feea0ba8072b884a67a0.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ff/e8327bdd29124bd995feea0ba8072b884a67a0.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_shelx_ext.cpython-311-x86_64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ff/e8327bdd29124bd995feea0ba8072b884a67a0.debug debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_shelx_ext.cpython-311-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/72 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_pdb_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/72/ee9183bdf665aaf96906c90cfdbdf638d621bd.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/72/ee9183bdf665aaf96906c90cfdbdf638d621bd.debug @@ -39591,31 +39638,26 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/27/e51ac376369456b9f1fa55d4997524d5786124.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_wildcard_ext.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/27/e51ac376369456b9f1fa55d4997524d5786124.debug debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_wildcard_ext.cpython-311-x86_64-linux-gnu.so - 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/python3/dist-packages/iotbx_shelx_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ff/e8327bdd29124bd995feea0ba8072b884a67a0.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ff/e8327bdd29124bd995feea0ba8072b884a67a0.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_shelx_ext.cpython-311-x86_64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ff/e8327bdd29124bd995feea0ba8072b884a67a0.debug debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_shelx_ext.cpython-311-x86_64-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/iotbx_detectors_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a2/a7bc0ec82a8e88e907b3449de4be9530640d00.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a2/a7bc0ec82a8e88e907b3449de4be9530640d00.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_detectors_ext.cpython-311-x86_64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a2/a7bc0ec82a8e88e907b3449de4be9530640d00.debug debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_detectors_ext.cpython-311-x86_64-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/iotbx_scalepack_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b1/99dda924160115ae76ff6dd0a5d9eb30fe3155.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b1/99dda924160115ae76ff6dd0a5d9eb30fe3155.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_scalepack_ext.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b1/99dda924160115ae76ff6dd0a5d9eb30fe3155.debug debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_scalepack_ext.cpython-311-x86_64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/78 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_xray_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/78/cba49f211c9257ba43a2de67ac58f648193d28.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/78/cba49f211c9257ba43a2de67ac58f648193d28.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_xray_ext.cpython-311-x86_64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/78/cba49f211c9257ba43a2de67ac58f648193d28.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_xray_ext.cpython-311-x86_64-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/cctbx_sgtbx_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f6/aaa5414033695916a664f464de422b28af3a00.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f6/aaa5414033695916a664f464de422b28af3a00.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_sgtbx_ext.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f6/aaa5414033695916a664f464de422b28af3a00.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_sgtbx_ext.cpython-311-x86_64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7e + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_gl_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7e/491e74803fbf911bd265a7b95e1131d4dc7b14.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7e/491e74803fbf911bd265a7b95e1131d4dc7b14.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_gl_ext.cpython-311-x86_64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7e/491e74803fbf911bd265a7b95e1131d4dc7b14.debug debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_gl_ext.cpython-311-x86_64-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/iotbx_detectors_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a2/a7bc0ec82a8e88e907b3449de4be9530640d00.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a2/a7bc0ec82a8e88e907b3449de4be9530640d00.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_detectors_ext.cpython-311-x86_64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a2/a7bc0ec82a8e88e907b3449de4be9530640d00.debug debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_detectors_ext.cpython-311-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/71 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_dtrek_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/71/c8cb097a794e41fd9f29da89b4d830ff775245.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/71/c8cb097a794e41fd9f29da89b4d830ff775245.debug @@ -39631,21 +39673,16 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/48/2c48065f3c943441230737ab1b94a2d1ac1e4e.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_detectors_bruker_ext.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/48/2c48065f3c943441230737ab1b94a2d1ac1e4e.debug debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_detectors_bruker_ext.cpython-311-x86_64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7e - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_gl_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7e/491e74803fbf911bd265a7b95e1131d4dc7b14.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7e/491e74803fbf911bd265a7b95e1131d4dc7b14.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_gl_ext.cpython-311-x86_64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7e/491e74803fbf911bd265a7b95e1131d4dc7b14.debug debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_gl_ext.cpython-311-x86_64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/9c - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_cif_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/9c/f1961688f66fa95e15b339e05cfecedba817de.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/9c/f1961688f66fa95e15b339e05cfecedba817de.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_cif_ext.cpython-311-x86_64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/9c/f1961688f66fa95e15b339e05cfecedba817de.debug debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_cif_ext.cpython-311-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/43 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_ccp4_map_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/43/fb1a6232206f6198348c466005566ce0fce604.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/43/fb1a6232206f6198348c466005566ce0fce604.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_ccp4_map_ext.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/43/fb1a6232206f6198348c466005566ce0fce604.debug debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_ccp4_map_ext.cpython-311-x86_64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/9c + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_cif_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/9c/f1961688f66fa95e15b339e05cfecedba817de.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/9c/f1961688f66fa95e15b339e05cfecedba817de.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_cif_ext.cpython-311-x86_64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/9c/f1961688f66fa95e15b339e05cfecedba817de.debug debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_cif_ext.cpython-311-x86_64-linux-gnu.so 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/python3/dist-packages/gltbx_viewer_utils_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/80/ba7a94f137adc14986bf8c108b8e4eb1ac4795.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/80/ba7a94f137adc14986bf8c108b8e4eb1ac4795.debug @@ -39671,71 +39708,71 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/aa/06b0745fa74be0af3bccf145971f3030f0e9d2.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_glu_ext.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/aa/06b0745fa74be0af3bccf145971f3030f0e9d2.debug debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_glu_ext.cpython-311-x86_64-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/dxtbx_masking_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/14/069acbdeae9c0efec1175b28c20726ece8604a.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/14/069acbdeae9c0efec1175b28c20726ece8604a.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_masking_ext.cpython-311-x86_64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/14/069acbdeae9c0efec1175b28c20726ece8604a.debug debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_masking_ext.cpython-311-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/34 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_fonts_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/34/cdc8191327beea4f7151da570738f3b169e639.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/34/cdc8191327beea4f7151da570738f3b169e639.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_fonts_ext.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/34/cdc8191327beea4f7151da570738f3b169e639.debug debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_fonts_ext.cpython-311-x86_64-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/dxtbx_masking_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/14/069acbdeae9c0efec1175b28c20726ece8604a.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/14/069acbdeae9c0efec1175b28c20726ece8604a.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_masking_ext.cpython-311-x86_64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/14/069acbdeae9c0efec1175b28c20726ece8604a.debug debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_masking_ext.cpython-311-x86_64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/5d + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_miller_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/5d/57ca26001de1188b32ee80136c9829460a874c.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/5d/57ca26001de1188b32ee80136c9829460a874c.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_miller_ext.cpython-311-x86_64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/5d/57ca26001de1188b32ee80136c9829460a874c.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_miller_ext.cpython-311-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/3e objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/fable_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/3e/3f83eea6874c9ad31583198e6d90707192be40.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/3e/3f83eea6874c9ad31583198e6d90707192be40.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/fable_ext.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/3e/3f83eea6874c9ad31583198e6d90707192be40.debug debian/python3-cctbx/usr/lib/python3/dist-packages/fable_ext.cpython-311-x86_64-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/dxtbx_flumpy.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a1/aedf81515c281ea19d538aa08e79fb21503f6d.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a1/aedf81515c281ea19d538aa08e79fb21503f6d.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_flumpy.cpython-311-x86_64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a1/aedf81515c281ea19d538aa08e79fb21503f6d.debug debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_flumpy.cpython-311-x86_64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/96 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_maptbx_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/96/63ef7fb7a215e02efae375459fea17b5f29b44.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/96/63ef7fb7a215e02efae375459fea17b5f29b44.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_maptbx_ext.cpython-311-x86_64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/96/63ef7fb7a215e02efae375459fea17b5f29b44.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_maptbx_ext.cpython-311-x86_64-linux-gnu.so 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/python3/dist-packages/dxtbx_format_image_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/80/e912715b14c594b79989273b7d915d15cb8a16.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/80/e912715b14c594b79989273b7d915d15cb8a16.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_format_image_ext.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/80/e912715b14c594b79989273b7d915d15cb8a16.debug debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_format_image_ext.cpython-311-x86_64-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/dxtbx_flumpy.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a1/aedf81515c281ea19d538aa08e79fb21503f6d.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a1/aedf81515c281ea19d538aa08e79fb21503f6d.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_flumpy.cpython-311-x86_64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a1/aedf81515c281ea19d538aa08e79fb21503f6d.debug debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_flumpy.cpython-311-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f0 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_format_nexus_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f0/eefbeff33649c233d018da6515a14a633461c7.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f0/eefbeff33649c233d018da6515a14a633461c7.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_format_nexus_ext.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f0/eefbeff33649c233d018da6515a14a633461c7.debug debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_format_nexus_ext.cpython-311-x86_64-linux-gnu.so - 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/python3/dist-packages/dxtbx_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ff/3800ffc694a579a39d7a9c4f571b63cecf2792.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ff/3800ffc694a579a39d7a9c4f571b63cecf2792.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_ext.cpython-311-x86_64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ff/3800ffc694a579a39d7a9c4f571b63cecf2792.debug debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_ext.cpython-311-x86_64-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/cctbx_xray_observations_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d7/d312b5a650f9d3c823b416ff106c0aff02b11e.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d7/d312b5a650f9d3c823b416ff106c0aff02b11e.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_xray_observations_ext.cpython-311-x86_64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d7/d312b5a650f9d3c823b416ff106c0aff02b11e.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_xray_observations_ext.cpython-311-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ea objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_crystal_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ea/0d28e022c89fd618629d09c61ae6b14e429628.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ea/0d28e022c89fd618629d09c61ae6b14e429628.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_crystal_ext.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ea/0d28e022c89fd618629d09c61ae6b14e429628.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_crystal_ext.cpython-311-x86_64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ee - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cma_es_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ee/04d67b4f30f0c318257c09811f87f27f862e9e.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ee/04d67b4f30f0c318257c09811f87f27f862e9e.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cma_es_ext.cpython-311-x86_64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ee/04d67b4f30f0c318257c09811f87f27f862e9e.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cma_es_ext.cpython-311-x86_64-linux-gnu.so + 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/python3/dist-packages/dxtbx_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ff/3800ffc694a579a39d7a9c4f571b63cecf2792.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ff/3800ffc694a579a39d7a9c4f571b63cecf2792.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_ext.cpython-311-x86_64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ff/3800ffc694a579a39d7a9c4f571b63cecf2792.debug debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_ext.cpython-311-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/63 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/determine_unit_cell_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/63/2b0286b117931b4c5acfbf43d69e5009737de1.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/63/2b0286b117931b4c5acfbf43d69e5009737de1.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/determine_unit_cell_ext.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/63/2b0286b117931b4c5acfbf43d69e5009737de1.debug debian/python3-cctbx/usr/lib/python3/dist-packages/determine_unit_cell_ext.cpython-311-x86_64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/5d - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_miller_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/5d/57ca26001de1188b32ee80136c9829460a874c.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/5d/57ca26001de1188b32ee80136c9829460a874c.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_miller_ext.cpython-311-x86_64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/5d/57ca26001de1188b32ee80136c9829460a874c.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_miller_ext.cpython-311-x86_64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/96 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_maptbx_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/96/63ef7fb7a215e02efae375459fea17b5f29b44.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/96/63ef7fb7a215e02efae375459fea17b5f29b44.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_maptbx_ext.cpython-311-x86_64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/96/63ef7fb7a215e02efae375459fea17b5f29b44.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_maptbx_ext.cpython-311-x86_64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ee + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cma_es_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ee/04d67b4f30f0c318257c09811f87f27f862e9e.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ee/04d67b4f30f0c318257c09811f87f27f862e9e.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cma_es_ext.cpython-311-x86_64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ee/04d67b4f30f0c318257c09811f87f27f862e9e.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cma_es_ext.cpython-311-x86_64-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/cctbx_xray_observations_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d7/d312b5a650f9d3c823b416ff106c0aff02b11e.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d7/d312b5a650f9d3c823b416ff106c0aff02b11e.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_xray_observations_ext.cpython-311-x86_64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d7/d312b5a650f9d3c823b416ff106c0aff02b11e.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_xray_observations_ext.cpython-311-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7a objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_uctbx_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7a/738a899762a5ed29ebf94d631831ba301a821c.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7a/738a899762a5ed29ebf94d631831ba301a821c.debug @@ -39746,31 +39783,36 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d9/abfa20ac8a32838d0b611abab7c7cbe42d7085.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_translation_search_ext.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d9/abfa20ac8a32838d0b611abab7c7cbe42d7085.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_translation_search_ext.cpython-311-x86_64-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_symmetry_search_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/dd/aba53591f0c116cef11576da22600237e4ea29.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/dd/aba53591f0c116cef11576da22600237e4ea29.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_symmetry_search_ext.cpython-311-x86_64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/dd/aba53591f0c116cef11576da22600237e4ea29.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_symmetry_search_ext.cpython-311-x86_64-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/cctbx_sgtbx_asu_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/6d/049dc551081e56f12d68c133b353aca4bf40bb.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/6d/049dc551081e56f12d68c133b353aca4bf40bb.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_sgtbx_asu_ext.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/6d/049dc551081e56f12d68c133b353aca4bf40bb.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_sgtbx_asu_ext.cpython-311-x86_64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/63 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_statistics_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/63/4703a41a15f93cfbf3a5c5681e9a46b88246fb.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/63/4703a41a15f93cfbf3a5c5681e9a46b88246fb.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_statistics_ext.cpython-311-x86_64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/63/4703a41a15f93cfbf3a5c5681e9a46b88246fb.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_statistics_ext.cpython-311-x86_64-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_symmetry_search_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/dd/aba53591f0c116cef11576da22600237e4ea29.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/dd/aba53591f0c116cef11576da22600237e4ea29.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_symmetry_search_ext.cpython-311-x86_64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/dd/aba53591f0c116cef11576da22600237e4ea29.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_symmetry_search_ext.cpython-311-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/51 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_adp_restraints_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/51/a5b59c889d47ace47d4fa7bb28d6458be6fd01.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/51/a5b59c889d47ace47d4fa7bb28d6458be6fd01.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_adp_restraints_ext.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/51/a5b59c889d47ace47d4fa7bb28d6458be6fd01.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_adp_restraints_ext.cpython-311-x86_64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/63 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_statistics_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/63/4703a41a15f93cfbf3a5c5681e9a46b88246fb.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/63/4703a41a15f93cfbf3a5c5681e9a46b88246fb.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_statistics_ext.cpython-311-x86_64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/63/4703a41a15f93cfbf3a5c5681e9a46b88246fb.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_statistics_ext.cpython-311-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/95 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_orientation_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/95/53e9d80eff266ed073c360c4c3a4ac78c8ba4d.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/95/53e9d80eff266ed073c360c4c3a4ac78c8ba4d.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_orientation_ext.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/95/53e9d80eff266ed073c360c4c3a4ac78c8ba4d.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_orientation_ext.cpython-311-x86_64-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/cctbx_array_family_flex_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/fe/6e28d0e5b32b71e3101b3bb60ce89de9eead5a.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/fe/6e28d0e5b32b71e3101b3bb60ce89de9eead5a.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-x86_64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/fe/6e28d0e5b32b71e3101b3bb60ce89de9eead5a.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_array_family_flex_ext.cpython-311-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/5e objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_multipolar_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/5e/3efcfc399597bc1f9bc6a1db4cbde0adcc144d.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/5e/3efcfc399597bc1f9bc6a1db4cbde0adcc144d.debug @@ -39781,16 +39823,6 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f4/bb7c5d519391620471f9c39769966f7d12140b.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_merging_ext.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f4/bb7c5d519391620471f9c39769966f7d12140b.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_merging_ext.cpython-311-x86_64-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/cctbx_array_family_flex_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/fe/6e28d0e5b32b71e3101b3bb60ce89de9eead5a.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/fe/6e28d0e5b32b71e3101b3bb60ce89de9eead5a.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-x86_64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/fe/6e28d0e5b32b71e3101b3bb60ce89de9eead5a.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_array_family_flex_ext.cpython-311-x86_64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/43 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_math_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/43/4621ee7337c5883b44edff81963c61e9e54384.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/43/4621ee7337c5883b44edff81963c61e9e54384.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_math_ext.cpython-311-x86_64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/43/4621ee7337c5883b44edff81963c61e9e54384.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_math_ext.cpython-311-x86_64-linux-gnu.so 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/python3/dist-packages/cctbx_masks_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ff/66448589f695f2e3c6bb74481225722f04149c.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ff/66448589f695f2e3c6bb74481225722f04149c.debug @@ -39801,21 +39833,26 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e2/3cc16518daf1046939ed1588034cec4df1664a.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-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e2/3cc16518daf1046939ed1588034cec4df1664a.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_maptbx_bcr_bcr_ext.cpython-311-x86_64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/43 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_math_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/43/4621ee7337c5883b44edff81963c61e9e54384.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/43/4621ee7337c5883b44edff81963c61e9e54384.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_math_ext.cpython-311-x86_64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/43/4621ee7337c5883b44edff81963c61e9e54384.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_math_ext.cpython-311-x86_64-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/cctbx_geometry_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/91/3d77bcd5aa72fd2bae67027b2d5c2d982f737d.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/91/3d77bcd5aa72fd2bae67027b2d5c2d982f737d.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_geometry_ext.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/91/3d77bcd5aa72fd2bae67027b2d5c2d982f737d.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_geometry_ext.cpython-311-x86_64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8d - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_xray_scattering_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8d/92dd1e67452676325f25aceb0ebf11db3f907f.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8d/92dd1e67452676325f25aceb0ebf11db3f907f.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-x86_64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8d/92dd1e67452676325f25aceb0ebf11db3f907f.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_xray_scattering_ext.cpython-311-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/9c objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_emma_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/9c/0b128e58e6846dbfef9a08948533e8fb6350ff.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/9c/0b128e58e6846dbfef9a08948533e8fb6350ff.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_emma_ext.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/9c/0b128e58e6846dbfef9a08948533e8fb6350ff.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_emma_ext.cpython-311-x86_64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8d + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_xray_scattering_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8d/92dd1e67452676325f25aceb0ebf11db3f907f.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8d/92dd1e67452676325f25aceb0ebf11db3f907f.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-x86_64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8d/92dd1e67452676325f25aceb0ebf11db3f907f.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_xray_scattering_ext.cpython-311-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/30 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_french_wilson_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/30/1c194a32802fcbba68f96d9c453ae10a6639ee.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/30/1c194a32802fcbba68f96d9c453ae10a6639ee.debug @@ -39836,6 +39873,11 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/0c/809850359f8a02e0f8b95b1c8ef2d54e94ec7a.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_sasaki_ext.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/0c/809850359f8a02e0f8b95b1c8ef2d54e94ec7a.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_sasaki_ext.cpython-311-x86_64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/0b + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_neutron_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/0b/5fabda34346e427138665b15eaf031ab170fce.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/0b/5fabda34346e427138665b15eaf031ab170fce.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_neutron_ext.cpython-311-x86_64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/0b/5fabda34346e427138665b15eaf031ab170fce.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_neutron_ext.cpython-311-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e9 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_icsd_radii_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e9/77fb74bb92e8d81ba3889cc1e37874d463fada.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e9/77fb74bb92e8d81ba3889cc1e37874d463fada.debug @@ -39846,16 +39888,6 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/5a/be77f9f7c29517d3eb4dc2c42724181fdfe3ba.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_henke_ext.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/5a/be77f9f7c29517d3eb4dc2c42724181fdfe3ba.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_henke_ext.cpython-311-x86_64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/0b - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_neutron_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/0b/5fabda34346e427138665b15eaf031ab170fce.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/0b/5fabda34346e427138665b15eaf031ab170fce.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_neutron_ext.cpython-311-x86_64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/0b/5fabda34346e427138665b15eaf031ab170fce.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_neutron_ext.cpython-311-x86_64-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/cctbx_eltbx_covalent_radii_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/16/13b9f7a2f2faecdf8bc25f35150d3da66f2386.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/16/13b9f7a2f2faecdf8bc25f35150d3da66f2386.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_covalent_radii_ext.cpython-311-x86_64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/16/13b9f7a2f2faecdf8bc25f35150d3da66f2386.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_covalent_radii_ext.cpython-311-x86_64-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/cctbx_eltbx_fp_fdp_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/3a/eab44d3bbf0aad5b35b878dbbc1ff4ff16a32e.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/3a/eab44d3bbf0aad5b35b878dbbc1ff4ff16a32e.debug @@ -39866,6 +39898,11 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8b/8d30ccd2ca7fc9239d5b48e09c0ae2e331bf90.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_dmtbx_ext.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8b/8d30ccd2ca7fc9239d5b48e09c0ae2e331bf90.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_dmtbx_ext.cpython-311-x86_64-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/cctbx_eltbx_covalent_radii_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/16/13b9f7a2f2faecdf8bc25f35150d3da66f2386.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/16/13b9f7a2f2faecdf8bc25f35150d3da66f2386.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_covalent_radii_ext.cpython-311-x86_64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/16/13b9f7a2f2faecdf8bc25f35150d3da66f2386.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_covalent_radii_ext.cpython-311-x86_64-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/cctbx_eltbx_attenuation_coefficient_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/c3/0223c1037ca2dc97e8aad82a06dde4094a6677.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/c3/0223c1037ca2dc97e8aad82a06dde4094a6677.debug @@ -39881,51 +39918,61 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/30/992d75517df9910c233a76da8bf1efe0b01f29.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_ext.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/30/992d75517df9910c233a76da8bf1efe0b01f29.debug debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_ext.cpython-311-x86_64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1f - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_adptbx_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1f/27de6773d077a739cd7115f64eb43dd2b0cd20.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1f/27de6773d077a739cd7115f64eb43dd2b0cd20.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_adptbx_ext.cpython-311-x86_64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1f/27de6773d077a739cd7115f64eb43dd2b0cd20.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_adptbx_ext.cpython-311-x86_64-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_asymmetric_map_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/39/49fe5f42c2f6c3ade823701d134f4fac453242.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/39/49fe5f42c2f6c3ade823701d134f4fac453242.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_asymmetric_map_ext.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/39/49fe5f42c2f6c3ade823701d134f4fac453242.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_asymmetric_map_ext.cpython-311-x86_64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1f + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_adptbx_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1f/27de6773d077a739cd7115f64eb43dd2b0cd20.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1f/27de6773d077a739cd7115f64eb43dd2b0cd20.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_adptbx_ext.cpython-311-x86_64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1f/27de6773d077a739cd7115f64eb43dd2b0cd20.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_adptbx_ext.cpython-311-x86_64-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/cctbx_covariance_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/cf/adaa60a6231f91d4a2c4353623f9793467ccfd.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/cf/adaa60a6231f91d4a2c4353623f9793467ccfd.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_covariance_ext.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/cf/adaa60a6231f91d4a2c4353623f9793467ccfd.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_covariance_ext.cpython-311-x86_64-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_graph_maximum_clique_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8f/c8de70c7f41b26188453b751bff36e499d257f.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8f/c8de70c7f41b26188453b751bff36e499d257f.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-x86_64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8f/c8de70c7f41b26188453b751bff36e499d257f.debug debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_maximum_clique_ext.cpython-311-x86_64-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/ccp4io_adaptbx_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/02/a74fc368e5f593782523bbfaf1f9135febb547.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/02/a74fc368e5f593782523bbfaf1f9135febb547.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/ccp4io_adaptbx_ext.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/02/a74fc368e5f593782523bbfaf1f9135febb547.debug debian/python3-cctbx/usr/lib/python3/dist-packages/ccp4io_adaptbx_ext.cpython-311-x86_64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d1 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cbflib_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d1/7d27ae9d0436656d9a49c4ea71d1790a558a23.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d1/7d27ae9d0436656d9a49c4ea71d1790a558a23.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cbflib_ext.cpython-311-x86_64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d1/7d27ae9d0436656d9a49c4ea71d1790a558a23.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cbflib_ext.cpython-311-x86_64-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_anharmonic_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/dd/7f3d18320903bef8f7d7e5ca522b2bce578677.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/dd/7f3d18320903bef8f7d7e5ca522b2bce578677.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_anharmonic_ext.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/dd/7f3d18320903bef8f7d7e5ca522b2bce578677.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_anharmonic_ext.cpython-311-x86_64-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_graph_maximum_clique_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8f/c8de70c7f41b26188453b751bff36e499d257f.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8f/c8de70c7f41b26188453b751bff36e499d257f.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-x86_64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8f/c8de70c7f41b26188453b751bff36e499d257f.debug debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_maximum_clique_ext.cpython-311-x86_64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/fa - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/boost_rational_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/fa/d824b8dc1cfeff6e01e9d83c32ec710df553bf.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/fa/d824b8dc1cfeff6e01e9d83c32ec710df553bf.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/boost_rational_ext.cpython-311-x86_64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/fa/d824b8dc1cfeff6e01e9d83c32ec710df553bf.debug debian/python3-cctbx/usr/lib/python3/dist-packages/boost_rational_ext.cpython-311-x86_64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d1 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cbflib_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d1/7d27ae9d0436656d9a49c4ea71d1790a558a23.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d1/7d27ae9d0436656d9a49c4ea71d1790a558a23.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cbflib_ext.cpython-311-x86_64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d1/7d27ae9d0436656d9a49c4ea71d1790a558a23.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cbflib_ext.cpython-311-x86_64-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/boost_adaptbx_graph_min_cut_max_flow_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/c4/bf7530c0b9ef6b172a8f4f09aa67dc137c6153.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/c4/bf7530c0b9ef6b172a8f4f09aa67dc137c6153.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-x86_64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/c4/bf7530c0b9ef6b172a8f4f09aa67dc137c6153.debug debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_min_cut_max_flow_ext.cpython-311-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e8 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/boost_python_meta_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e8/c1c6259c396055a17207f5b782cea2428afa3b.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e8/c1c6259c396055a17207f5b782cea2428afa3b.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/boost_python_meta_ext.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e8/c1c6259c396055a17207f5b782cea2428afa3b.debug debian/python3-cctbx/usr/lib/python3/dist-packages/boost_python_meta_ext.cpython-311-x86_64-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/boost_adaptbx_graph_metric_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/50/7912912423ad0bf870282030e6ed00989f1275.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/50/7912912423ad0bf870282030e6ed00989f1275.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-x86_64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/50/7912912423ad0bf870282030e6ed00989f1275.debug debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_metric_ext.cpython-311-x86_64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/fa + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/boost_rational_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/fa/d824b8dc1cfeff6e01e9d83c32ec710df553bf.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/fa/d824b8dc1cfeff6e01e9d83c32ec710df553bf.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/boost_rational_ext.cpython-311-x86_64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/fa/d824b8dc1cfeff6e01e9d83c32ec710df553bf.debug debian/python3-cctbx/usr/lib/python3/dist-packages/boost_rational_ext.cpython-311-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/5d objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/boost_tuple_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/5d/3681e57304165b9ed2bbe5de91504c425a1f1e.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/5d/3681e57304165b9ed2bbe5de91504c425a1f1e.debug @@ -39936,36 +39983,21 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f6/29f865937475cfb2f019cc555bd16026bf5d2a.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-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f6/29f865937475cfb2f019cc555bd16026bf5d2a.debug debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_utility_ext.cpython-311-x86_64-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/boost_adaptbx_graph_min_cut_max_flow_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/c4/bf7530c0b9ef6b172a8f4f09aa67dc137c6153.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/c4/bf7530c0b9ef6b172a8f4f09aa67dc137c6153.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-x86_64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/c4/bf7530c0b9ef6b172a8f4f09aa67dc137c6153.debug debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_min_cut_max_flow_ext.cpython-311-x86_64-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_python_hybrid_times_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/19/1bf9af4588df991a9b4a475cd6888fe04c59d1.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/19/1bf9af4588df991a9b4a475cd6888fe04c59d1.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-x86_64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/19/1bf9af4588df991a9b4a475cd6888fe04c59d1.debug debian/python3-cctbx/usr/lib/python3/dist-packages/boost_python_hybrid_times_ext.cpython-311-x86_64-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/boost_adaptbx_graph_metric_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/50/7912912423ad0bf870282030e6ed00989f1275.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/50/7912912423ad0bf870282030e6ed00989f1275.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-x86_64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/50/7912912423ad0bf870282030e6ed00989f1275.debug debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_metric_ext.cpython-311-x86_64-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_optional_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8f/dfa0d8f2688e6f8a5dbe86610f20be3a796ed3.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8f/dfa0d8f2688e6f8a5dbe86610f20be3a796ed3.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/boost_optional_ext.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8f/dfa0d8f2688e6f8a5dbe86610f20be3a796ed3.debug debian/python3-cctbx/usr/lib/python3/dist-packages/boost_optional_ext.cpython-311-x86_64-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_python_hybrid_times_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/19/1bf9af4588df991a9b4a475cd6888fe04c59d1.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/19/1bf9af4588df991a9b4a475cd6888fe04c59d1.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-x86_64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/19/1bf9af4588df991a9b4a475cd6888fe04c59d1.debug debian/python3-cctbx/usr/lib/python3/dist-packages/boost_python_hybrid_times_ext.cpython-311-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/54 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_python_streambuf_test_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/54/c69f9140b00e97376a823da2a15adeb906ae9a.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/54/c69f9140b00e97376a823da2a15adeb906ae9a.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_python_streambuf_test_ext.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/54/c69f9140b00e97376a823da2a15adeb906ae9a.debug debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_python_streambuf_test_ext.cpython-311-x86_64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8c - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_connected_component_algorithm_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8c/b09c91018865f235edbe38c0974163cb85e07e.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8c/b09c91018865f235edbe38c0974163cb85e07e.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-x86_64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8c/b09c91018865f235edbe38c0974163cb85e07e.debug debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_connected_component_algorithm_ext.cpython-311-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1b objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_graph_structure_comparison_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1b/811e2410bf400b3f9f2a7fe8bba936b981295d.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1b/811e2410bf400b3f9f2a7fe8bba936b981295d.debug @@ -39976,6 +40008,11 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/03/c1f65e5a27b0afecbb1f09e88da3fbb62be524.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-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/03/c1f65e5a27b0afecbb1f09e88da3fbb62be524.debug debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_clustering_algorithm_ext.cpython-311-x86_64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8c + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_connected_component_algorithm_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8c/b09c91018865f235edbe38c0974163cb85e07e.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8c/b09c91018865f235edbe38c0974163cb85e07e.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-x86_64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8c/b09c91018865f235edbe38c0974163cb85e07e.debug debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_connected_component_algorithm_ext.cpython-311-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/08 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_breadth_first_search_ext.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/08/5df047aef098ee9c0a9c80432d550fead64cbf.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/08/5df047aef098ee9c0a9c80432d550fead64cbf.debug @@ -39991,36 +40028,36 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/48/67ba51e623918fda7abc9c4b7ed518bacf329f.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/annlib_ext.cpython-311-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/48/67ba51e623918fda7abc9c4b7ed518bacf329f.debug debian/python3-cctbx/usr/lib/python3/dist-packages/annlib_ext.cpython-311-x86_64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/5c - 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/5c/95530567ec6521cf23a6102ab19cca81a21e01.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/5c/95530567ec6521cf23a6102ab19cca81a21e01.debug - strip --remove-section=.comment --remove-section=.note debian/python3-cctbx/usr/lib/cctbx/python3.11/smtbx/refinement/constraints/tests/tst_geometrical_hydrogens - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/5c/95530567ec6521cf23a6102ab19cca81a21e01.debug debian/python3-cctbx/usr/lib/cctbx/python3.11/smtbx/refinement/constraints/tests/tst_geometrical_hydrogens - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/0a - 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/0a/9f2677258476719ce242fa90698689f33b1469.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/0a/9f2677258476719ce242fa90698689f33b1469.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/0a/9f2677258476719ce242fa90698689f33b1469.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/5b 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/5b/86563df3bdcb6b583ed62456c379b26c6977a1.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/5b/86563df3bdcb6b583ed62456c379b26c6977a1.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/5b/86563df3bdcb6b583ed62456c379b26c6977a1.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/0a + 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/0a/9f2677258476719ce242fa90698689f33b1469.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/0a/9f2677258476719ce242fa90698689f33b1469.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/0a/9f2677258476719ce242fa90698689f33b1469.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/5c + 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/5c/95530567ec6521cf23a6102ab19cca81a21e01.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/5c/95530567ec6521cf23a6102ab19cca81a21e01.debug + strip --remove-section=.comment --remove-section=.note debian/python3-cctbx/usr/lib/cctbx/python3.11/smtbx/refinement/constraints/tests/tst_geometrical_hydrogens + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/5c/95530567ec6521cf23a6102ab19cca81a21e01.debug debian/python3-cctbx/usr/lib/cctbx/python3.11/smtbx/refinement/constraints/tests/tst_geometrical_hydrogens 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/serialization/tst_base_256 debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e0/f0534ee467ef3fd6afc36d7bcee01999af595a.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e0/f0534ee467ef3fd6afc36d7bcee01999af595a.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/e0/f0534ee467ef3fd6afc36d7bcee01999af595a.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/36 - 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/36/cc0e80b52a277cc056e9b43ac2b76f113c1c91.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/36/cc0e80b52a277cc056e9b43ac2b76f113c1c91.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/36/cc0e80b52a277cc056e9b43ac2b76f113c1c91.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/be 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/be/bfbf760d2f7de19e1fbf2f61506b90c982bdec.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/be/bfbf760d2f7de19e1fbf2f61506b90c982bdec.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/be/bfbf760d2f7de19e1fbf2f61506b90c982bdec.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/36 + 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/36/cc0e80b52a277cc056e9b43ac2b76f113c1c91.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/36/cc0e80b52a277cc056e9b43ac2b76f113c1c91.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/36/cc0e80b52a277cc056e9b43ac2b76f113c1c91.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/6d 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/6d/86564bb41348bb45b6527cb37f8c765ae7cfe0.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/6d/86564bb41348bb45b6527cb37f8c765ae7cfe0.debug @@ -40051,16 +40088,16 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/87/9e51aa2015eb60a1ffd1f51694ec9a1d607b7c.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/87/9e51aa2015eb60a1ffd1f51694ec9a1d607b7c.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/27 - 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/27/f5873f4438871f1461803e23f8f50de40f3085.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/27/f5873f4438871f1461803e23f8f50de40f3085.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/27/f5873f4438871f1461803e23f8f50de40f3085.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/57 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/57/3ef40226d9d3d2fd70cd1efe86ef09c7753ce3.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/57/3ef40226d9d3d2fd70cd1efe86ef09c7753ce3.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/57/3ef40226d9d3d2fd70cd1efe86ef09c7753ce3.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/27 + 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/27/f5873f4438871f1461803e23f8f50de40f3085.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/27/f5873f4438871f1461803e23f8f50de40f3085.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/27/f5873f4438871f1461803e23f8f50de40f3085.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/64 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_ref_matrix_facet debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/64/7724ae7566fb804342e52af1b0e9004a85bc8a.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/64/7724ae7566fb804342e52af1b0e9004a85bc8a.debug @@ -40076,41 +40113,41 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b9/3a14916bfce927af997091bcc9816622767f22.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/b9/3a14916bfce927af997091bcc9816622767f22.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/41 - 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/41/1d301a6374dfd521331a47eda37c558d9824de.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/41/1d301a6374dfd521331a47eda37c558d9824de.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/41/1d301a6374dfd521331a47eda37c558d9824de.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/72 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_optional_copy debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/72/ee48405427e7e538bee0e93dbdd20aeb76db33.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/72/ee48405427e7e538bee0e93dbdd20aeb76db33.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/72/ee48405427e7e538bee0e93dbdd20aeb76db33.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/6f + 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/6f/11efec972fa883ea131d28273a7894e208c786.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/6f/11efec972fa883ea131d28273a7894e208c786.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/6f/11efec972fa883ea131d28273a7894e208c786.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/0c 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/0c/f06bac2d8dbd9b0b8c4ad0a5c6ede5c6c5fb42.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/0c/f06bac2d8dbd9b0b8c4ad0a5c6ede5c6c5fb42.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/0c/f06bac2d8dbd9b0b8c4ad0a5c6ede5c6c5fb42.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/41 + 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/41/1d301a6374dfd521331a47eda37c558d9824de.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/41/1d301a6374dfd521331a47eda37c558d9824de.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/41/1d301a6374dfd521331a47eda37c558d9824de.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/db 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/db/5939864dfbb933eebd07ca7bcce74e1c5713ea.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/db/5939864dfbb933eebd07ca7bcce74e1c5713ea.debug strip --remove-section=.comment --remove-section=.note debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_af_1 objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/db/5939864dfbb933eebd07ca7bcce74e1c5713ea.debug debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_af_1 - 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/array_family/tst_af_3 debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/6f/11efec972fa883ea131d28273a7894e208c786.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/6f/11efec972fa883ea131d28273a7894e208c786.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/6f/11efec972fa883ea131d28273a7894e208c786.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/b5 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_af_2 debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b5/51d75e3fd88d64a65c4f9ab17ea4b9b77316ef.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b5/51d75e3fd88d64a65c4f9ab17ea4b9b77316ef.debug - strip --remove-section=.comment --remove-section=.note debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_af_2 - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b5/51d75e3fd88d64a65c4f9ab17ea4b9b77316ef.debug debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_af_2 install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8d objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_accessors debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8d/a6653419f9494f906f1a0bc4d496b1c6ba441d.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8d/a6653419f9494f906f1a0bc4d496b1c6ba441d.debug strip --remove-section=.comment --remove-section=.note debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_accessors objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8d/a6653419f9494f906f1a0bc4d496b1c6ba441d.debug debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_accessors + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b5 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_af_2 debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b5/51d75e3fd88d64a65c4f9ab17ea4b9b77316ef.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b5/51d75e3fd88d64a65c4f9ab17ea4b9b77316ef.debug + strip --remove-section=.comment --remove-section=.note debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_af_2 + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b5/51d75e3fd88d64a65c4f9ab17ea4b9b77316ef.debug debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_af_2 install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/9e objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/cctbx/python3.11/iotbx/pdb/hybrid_36_fem debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/9e/7e8669b6d2c75a8103d3e53d30bed20637869e.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/9e/7e8669b6d2c75a8103d3e53d30bed20637869e.debug @@ -40131,36 +40168,36 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b1/00a4368c8a1f7b512a0fd9f8097a06fd9487d9.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/b1/00a4368c8a1f7b512a0fd9f8097a06fd9487d9.debug debian/python3-cctbx/usr/bin/cctbx_blobs - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/66 - 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/66/f94ff4928102c0acc852cad02023243c3d8a57.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/66/f94ff4928102c0acc852cad02023243c3d8a57.debug - strip --remove-section=.comment --remove-section=.note debian/python3-cctbx/usr/bin/cctbx.lattice_symmetry - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/66/f94ff4928102c0acc852cad02023243c3d8a57.debug debian/python3-cctbx/usr/bin/cctbx.lattice_symmetry install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/63 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/bin/cctbx.sym_equiv_sites debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/63/51194c23277e809b9020e9a562782b7d06a113.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/63/51194c23277e809b9020e9a562782b7d06a113.debug strip --remove-section=.comment --remove-section=.note debian/python3-cctbx/usr/bin/cctbx.sym_equiv_sites objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/63/51194c23277e809b9020e9a562782b7d06a113.debug debian/python3-cctbx/usr/bin/cctbx.sym_equiv_sites - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/db - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/bin/cctbx.convert_ccp4_symop_lib debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/db/e76bafed4ee830b65dd5cceeb03915bc89ba26.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/db/e76bafed4ee830b65dd5cceeb03915bc89ba26.debug - strip --remove-section=.comment --remove-section=.note debian/python3-cctbx/usr/bin/cctbx.convert_ccp4_symop_lib - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/db/e76bafed4ee830b65dd5cceeb03915bc89ba26.debug debian/python3-cctbx/usr/bin/cctbx.convert_ccp4_symop_lib + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/66 + 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/66/f94ff4928102c0acc852cad02023243c3d8a57.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/66/f94ff4928102c0acc852cad02023243c3d8a57.debug + strip --remove-section=.comment --remove-section=.note debian/python3-cctbx/usr/bin/cctbx.lattice_symmetry + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/66/f94ff4928102c0acc852cad02023243c3d8a57.debug debian/python3-cctbx/usr/bin/cctbx.lattice_symmetry install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e5 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/bin/cctbx.getting_started debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e5/3551b48168e29ee3341b1f52983005bbf6b8e6.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e5/3551b48168e29ee3341b1f52983005bbf6b8e6.debug strip --remove-section=.comment --remove-section=.note debian/python3-cctbx/usr/bin/cctbx.getting_started objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e5/3551b48168e29ee3341b1f52983005bbf6b8e6.debug debian/python3-cctbx/usr/bin/cctbx.getting_started - 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/bin/cbflib.tst_memory debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7d/05e4b2b4ec131b37ff1e41a7c244d7ccdd284f.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7d/05e4b2b4ec131b37ff1e41a7c244d7ccdd284f.debug - strip --remove-section=.comment --remove-section=.note debian/python3-cctbx/usr/bin/cbflib.tst_memory - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7d/05e4b2b4ec131b37ff1e41a7c244d7ccdd284f.debug debian/python3-cctbx/usr/bin/cbflib.tst_memory + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/db + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/bin/cctbx.convert_ccp4_symop_lib debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/db/e76bafed4ee830b65dd5cceeb03915bc89ba26.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/db/e76bafed4ee830b65dd5cceeb03915bc89ba26.debug + strip --remove-section=.comment --remove-section=.note debian/python3-cctbx/usr/bin/cctbx.convert_ccp4_symop_lib + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/db/e76bafed4ee830b65dd5cceeb03915bc89ba26.debug debian/python3-cctbx/usr/bin/cctbx.convert_ccp4_symop_lib install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a6 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/bin/cctbx.sys_abs_equiv_space_groups debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a6/84b967ed77529d9d54d71d61835c184318efa5.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a6/84b967ed77529d9d54d71d61835c184318efa5.debug strip --remove-section=.comment --remove-section=.note debian/python3-cctbx/usr/bin/cctbx.sys_abs_equiv_space_groups objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a6/84b967ed77529d9d54d71d61835c184318efa5.debug debian/python3-cctbx/usr/bin/cctbx.sys_abs_equiv_space_groups + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7d + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/bin/cbflib.tst_memory debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7d/05e4b2b4ec131b37ff1e41a7c244d7ccdd284f.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7d/05e4b2b4ec131b37ff1e41a7c244d7ccdd284f.debug + strip --remove-section=.comment --remove-section=.note debian/python3-cctbx/usr/bin/cbflib.tst_memory + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7d/05e4b2b4ec131b37ff1e41a7c244d7ccdd284f.debug debian/python3-cctbx/usr/bin/cbflib.tst_memory install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/python3-cctbx/usr/lib/debug/.dwz/x86_64-linux-gnu debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/python3-cctbx/usr/lib/debug/.dwz @@ -40367,354 +40404,354 @@ 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/x86_64-linux-gnu/libcctbx.so.0.0.1 debian/libcctbx0/usr/lib/x86_64-linux-gnu/libiotbx_pdb.so.0.0.1 debian/libcctbx0/usr/lib/x86_64-linux-gnu/libsmtbx_refinement_constraints.so.0.0.1 debian/libcctbx0/usr/lib/x86_64-linux-gnu/libspotfinder.so.0.0.1 debian/libcctbx0/usr/lib/x86_64-linux-gnu/libcctbx_sgtbx_asu.so.0.0.1 debian/libcctbx0/usr/lib/x86_64-linux-gnu/libasymmetric_map.so.0.0.1 debian/libcctbx0/usr/lib/x86_64-linux-gnu/librstbx.so.0.0.1 debian/libcctbx0/usr/lib/x86_64-linux-gnu/libmmtbx_masks.so.0.0.1 debian/libcctbx0/usr/lib/x86_64-linux-gnu/libscitbx_slatec.so.0.0.1 debian/libcctbx0/usr/lib/x86_64-linux-gnu/libscitbx_minpack.so.0.0.1 debian/libcctbx0/usr/lib/x86_64-linux-gnu/libscitbx_boost_python.so.0.0.1 debian/libcctbx0/usr/lib/x86_64-linux-gnu/libiotbx_mtz.so.0.0.1 debian/libcctbx0/usr/lib/x86_64-linux-gnu/libomptbx.so.0.0.1 debian/libcctbx0/usr/lib/x86_64-linux-gnu/libmmtbx_tls.so.0.0.1 debian/libcctbx0/usr/lib/x86_64-linux-gnu/libiotbx_xplor.so.0.0.1 debian/libcctbx0/usr/lib/x86_64-linux-gnu/libdxtbxspotfinder.so.0.0.1 debian/libcctbx0/usr/lib/x86_64-linux-gnu/libcbf-private.so.0.0.1 debian/libcctbx0/usr/lib/x86_64-linux-gnu/libann_adaptor.so.0.0.1 debian/libcctbx0/usr/lib/x86_64-linux-gnu/libccp4io.so.0.0.1 + dpkg-shlibdeps -Tdebian/libcctbx0.substvars debian/libcctbx0/usr/lib/x86_64-linux-gnu/libcctbx.so.0.0.1 debian/libcctbx0/usr/lib/x86_64-linux-gnu/libiotbx_pdb.so.0.0.1 debian/libcctbx0/usr/lib/x86_64-linux-gnu/libsmtbx_refinement_constraints.so.0.0.1 debian/libcctbx0/usr/lib/x86_64-linux-gnu/libcctbx_sgtbx_asu.so.0.0.1 debian/libcctbx0/usr/lib/x86_64-linux-gnu/libspotfinder.so.0.0.1 debian/libcctbx0/usr/lib/x86_64-linux-gnu/librstbx.so.0.0.1 debian/libcctbx0/usr/lib/x86_64-linux-gnu/libasymmetric_map.so.0.0.1 debian/libcctbx0/usr/lib/x86_64-linux-gnu/libmmtbx_masks.so.0.0.1 debian/libcctbx0/usr/lib/x86_64-linux-gnu/libscitbx_boost_python.so.0.0.1 debian/libcctbx0/usr/lib/x86_64-linux-gnu/libscitbx_slatec.so.0.0.1 debian/libcctbx0/usr/lib/x86_64-linux-gnu/libscitbx_minpack.so.0.0.1 debian/libcctbx0/usr/lib/x86_64-linux-gnu/libiotbx_mtz.so.0.0.1 debian/libcctbx0/usr/lib/x86_64-linux-gnu/libmmtbx_tls.so.0.0.1 debian/libcctbx0/usr/lib/x86_64-linux-gnu/libomptbx.so.0.0.1 debian/libcctbx0/usr/lib/x86_64-linux-gnu/libdxtbxspotfinder.so.0.0.1 debian/libcctbx0/usr/lib/x86_64-linux-gnu/libiotbx_xplor.so.0.0.1 debian/libcctbx0/usr/lib/x86_64-linux-gnu/libcbf-private.so.0.0.1 debian/libcctbx0/usr/lib/x86_64-linux-gnu/libann_adaptor.so.0.0.1 debian/libcctbx0/usr/lib/x86_64-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-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_math_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_refinement_constraints_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_array_family_flex_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_dxtbx_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/std_pair_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_hough_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_distltbx_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_refinement_least_squares_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_structure_factors_direct_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_refinement_restraints_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_stl_map_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_suffixtree_single_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_sparse_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_stl_map_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_array_family_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_wigner_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_ab_initio_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_stl_vector_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_suffixtree_shared_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_stl_set_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_linalg_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_random_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_rigid_body_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_lstbx_normal_equations_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_r3_utils_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_minpack_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_lbfgs_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_array_family_shared_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_fftpack_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_lbfgsb_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_iso_surface_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_graphics_utils_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_glmtbx_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_cubicle_neighbors_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_array_family_flex_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_symmetry_constraints_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_integration_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_simage_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_simulation_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_utils_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_indexing_api_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_diffraction_fastbragg_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_scaling_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_bpcx_detector_model_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_bandpass_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/regression_test_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_probe_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/omptbx_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_validation_ramachandran_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_optimise_amplitudes_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_utils_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_ramachandran_restraints_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_decompose_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_reference_coordinate_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_rotamer_fit_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_secondary_structure_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_pair_interaction_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_rsr_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_max_lik_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_ncs_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_model_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_ncs_cartesian_restraints_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_asa_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_masks_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_mosaic_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_clash_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_pdb_hierarchy_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_hydrogens_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_indexing_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_sphere_surface_sampling_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_shared_types_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_primitive_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_f_model_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_dynamics_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_den_restraints_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_bulk_solvent_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_mtz_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_dssp_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_geometry_restraints_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_building_loop_closure_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_cablam_align_utils_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_alignment_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_xplor_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_pdb_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_wildcard_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_shelx_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_detectors_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_scalepack_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_xray_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_sgtbx_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_dtrek_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_dsn6_map_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_detectors_bruker_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_gl_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_cif_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_ccp4_map_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_viewer_utils_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_util_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_imageset_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_quadrics_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_glu_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_masking_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_fonts_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/fable_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_flumpy.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_format_image_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_format_nexus_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_xray_observations_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_crystal_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cma_es_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/determine_unit_cell_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_miller_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_maptbx_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_uctbx_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_translation_search_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_symmetry_search_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_sgtbx_asu_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_statistics_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_adp_restraints_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_orientation_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_multipolar_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_merging_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_array_family_flex_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_math_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_masks_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_maptbx_bcr_bcr_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_geometry_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_xray_scattering_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_emma_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_french_wilson_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_wavelengths_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_tiny_pse_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_sasaki_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_icsd_radii_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_henke_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_neutron_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_covalent_radii_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_fp_fdp_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_dmtbx_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_attenuation_coefficient_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_chemical_elements_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_adptbx_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_asymmetric_map_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_covariance_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/ccp4io_adaptbx_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cbflib_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_anharmonic_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_maximum_clique_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_rational_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_python_meta_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_tuple_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_utility_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_min_cut_max_flow_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_python_hybrid_times_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_metric_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_optional_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_python_streambuf_test_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_connected_component_algorithm_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_graph_structure_comparison_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_clustering_algorithm_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_breadth_first_search_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_boost_thread_test_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/annlib_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/cctbx/python3.11/smtbx/refinement/constraints/tests/tst_geometrical_hydrogens 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/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_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_ref_matrix_facet 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_rectangular_full_packed 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_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_1 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_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.convert_ccp4_symop_lib debian/python3-cctbx/usr/bin/cctbx.getting_started debian/python3-cctbx/usr/bin/cbflib.tst_memory debian/python3-cctbx/usr/bin/cctbx.sys_abs_equiv_space_groups -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_array_family_flex_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin + dpkg-shlibdeps -Tdebian/python3-cctbx.substvars debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_array_family_flex_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_math_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_refinement_constraints_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_array_family_flex_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_hough_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_refinement_least_squares_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/std_pair_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_distltbx_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_dxtbx_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_structure_factors_direct_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_refinement_restraints_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_sparse_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_stl_map_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_suffixtree_single_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_ab_initio_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_stl_vector_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_wigner_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_array_family_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_linalg_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_stl_map_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_rigid_body_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_suffixtree_shared_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_random_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_stl_set_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_lstbx_normal_equations_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_array_family_shared_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_minpack_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_r3_utils_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_lbfgs_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_lbfgsb_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_fftpack_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_iso_surface_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_glmtbx_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_graphics_utils_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_cubicle_neighbors_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_simulation_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_symmetry_constraints_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_array_family_flex_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_scaling_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_integration_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_indexing_api_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_utils_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_diffraction_fastbragg_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_simage_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_bandpass_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_probe_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/regression_test_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_bpcx_detector_model_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_validation_ramachandran_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_optimise_amplitudes_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_utils_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/omptbx_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_ramachandran_restraints_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_decompose_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_rsr_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_rotamer_fit_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_secondary_structure_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_reference_coordinate_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_pair_interaction_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_ncs_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_max_lik_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_asa_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_ncs_cartesian_restraints_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_mosaic_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_model_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_pdb_hierarchy_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_masks_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_clash_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_indexing_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_hydrogens_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_sphere_surface_sampling_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_shared_types_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_f_model_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_primitive_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_den_restraints_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_dynamics_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_bulk_solvent_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_mtz_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_geometry_restraints_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_dssp_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_xray_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_cablam_align_utils_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_building_loop_closure_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_alignment_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_xplor_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_shelx_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_pdb_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_wildcard_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_scalepack_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_sgtbx_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_gl_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_detectors_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_dtrek_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_dsn6_map_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_detectors_bruker_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_ccp4_map_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_cif_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_viewer_utils_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_util_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_imageset_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_quadrics_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_glu_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_fonts_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_masking_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_miller_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/fable_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_maptbx_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_format_image_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_flumpy.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_format_nexus_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_crystal_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/determine_unit_cell_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cma_es_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_xray_observations_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_uctbx_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_translation_search_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_sgtbx_asu_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_symmetry_search_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_adp_restraints_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_statistics_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_orientation_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_array_family_flex_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_multipolar_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_merging_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_masks_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_maptbx_bcr_bcr_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_math_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_geometry_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_emma_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_xray_scattering_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_french_wilson_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_wavelengths_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_tiny_pse_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_sasaki_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_neutron_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_icsd_radii_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_henke_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_fp_fdp_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_dmtbx_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_covalent_radii_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_attenuation_coefficient_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_chemical_elements_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_asymmetric_map_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_adptbx_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_covariance_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_maximum_clique_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/ccp4io_adaptbx_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_anharmonic_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cbflib_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_min_cut_max_flow_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_python_meta_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_metric_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_rational_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_tuple_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_utility_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_optional_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_python_hybrid_times_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_python_streambuf_test_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_graph_structure_comparison_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_clustering_algorithm_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_connected_component_algorithm_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_breadth_first_search_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_boost_thread_test_ext.cpython-311-x86_64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/annlib_ext.cpython-311-x86_64-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_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_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_ref_matrix_facet 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_rectangular_full_packed 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_3 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_1 debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_accessors debian/python3-cctbx/usr/lib/cctbx/python3.11/scitbx/array_family/tst_af_2 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.sym_equiv_sites debian/python3-cctbx/usr/bin/cctbx.lattice_symmetry debian/python3-cctbx/usr/bin/cctbx.getting_started debian/python3-cctbx/usr/bin/cctbx.convert_ccp4_symop_lib debian/python3-cctbx/usr/bin/cctbx.sys_abs_equiv_space_groups debian/python3-cctbx/usr/bin/cbflib.tst_memory +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_primitive_ext.cpython-311-x86_64-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/iotbx_pdb_hierarchy_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyLong_FromUnsignedLong: it's probably a plugin +dpkg-shlibdeps: warning: 33 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: symbol PyExc_IndexError used by debian/libcctbx0/usr/lib/x86_64-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/x86_64-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/x86_64-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/x86_64-linux-gnu/libscitbx_boost_python.so.0.0.1 found in none of the libraries +dpkg-shlibdeps: warning: symbol PyImport_ImportModule used by debian/libcctbx0/usr/lib/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-linux-gnu/libscitbx_boost_python.so.0.0.1 found in none of the libraries +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_crystal_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyBool_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_dmtbx_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyLong_FromUnsignedLong: it's probably a plugin +dpkg-shlibdeps: warning: 15 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_sasaki_ext.cpython-311-x86_64-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_hydrogens_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyLong_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_array_family_flex_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol _PyBytes_Resize: 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/dxtbx_format_image_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyTuple_GetItem: it's probably a plugin -dpkg-shlibdeps: warning: 23 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_detectors_bruker_ext.cpython-311-x86_64-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_tuple_ext.cpython-311-x86_64-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/gltbx_gl_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyBytes_AsString: it's probably a plugin +dpkg-shlibdeps: warning: 10 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_wildcard_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin +dpkg-shlibdeps: warning: 3 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_henke_ext.cpython-311-x86_64-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/spotfinder_dxtbx_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_FromDouble: it's probably a plugin +dpkg-shlibdeps: warning: 7 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_multipolar_ext.cpython-311-x86_64-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/rstbx_bpcx_detector_model_ext.cpython-311-x86_64-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_cablam_align_utils_ext.cpython-311-x86_64-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_maptbx_bcr_bcr_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyObject_Size: 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_sgtbx_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_FromDouble: 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_restraints_ext.cpython-311-x86_64-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/scitbx_lstbx_normal_equations_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyBool_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/scitbx_fftpack_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyLong_FromUnsignedLong: it's probably a plugin +dpkg-shlibdeps: warning: 6 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_utils_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyExc_IndexError: 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/dxtbx_format_image_ext.cpython-311-x86_64-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/scitbx_lbfgsb_ext.cpython-311-x86_64-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_eltbx_attenuation_coefficient_ext.cpython-311-x86_64-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_emma_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyBool_Type: it's probably a plugin +dpkg-shlibdeps: warning: 7 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_xray_observations_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyLong_FromLong: it's probably a plugin +dpkg-shlibdeps: warning: 7 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_attenuation_coefficient_ext.cpython-311-x86_64-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_array_family_shared_ext.cpython-311-x86_64-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/iotbx_ccp4_map_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_FromDouble: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/omptbx_ext.cpython-311-x86_64-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/mmtbx_building_loop_closure_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyBool_Type: it's probably a plugin dpkg-shlibdeps: warning: 7 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_integration_ext.cpython-311-x86_64-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_eltbx_henke_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyUnicode_Type: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_ncs_cartesian_restraints_ext.cpython-311-x86_64-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/spotfinder_distltbx_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyLong_Type: it's probably a plugin +dpkg-shlibdeps: warning: 7 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_viewer_utils_ext.cpython-311-x86_64-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/scitbx_r3_utils_ext.cpython-311-x86_64-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/boost_adaptbx_graph_clustering_algorithm_ext.cpython-311-x86_64-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_rsr_ext.cpython-311-x86_64-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/cctbx_eltbx_wavelengths_ext.cpython-311-x86_64-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/std_pair_ext.cpython-311-x86_64-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/rstbx_bandpass_ext.cpython-311-x86_64-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/iotbx_dsn6_map_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol _Py_NoneStruct: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_statistics_ext.cpython-311-x86_64-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/cbflib_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_Type: it's probably a plugin -dpkg-shlibdeps: warning: 10 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_scaling_ext.cpython-311-x86_64-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/determine_unit_cell_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin +dpkg-shlibdeps: warning: 3 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_alignment_ext.cpython-311-x86_64-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: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/x86_64-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/x86_64-linux-gnu/libscitbx_boost_python.so.0.0.1 found in none of the libraries -dpkg-shlibdeps: warning: symbol PyImport_ImportModule used by debian/libcctbx0/usr/lib/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/mmtbx_geometry_asa_ext.cpython-311-x86_64-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/smtbx_refinement_restraints_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyErr_SetString: it's probably a plugin -dpkg-shlibdeps: warning: 10 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_neutron_ext.cpython-311-x86_64-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/scitbx_sparse_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyTuple_New: 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_tls_utils_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyObject_Size: it's probably a plugin -dpkg-shlibdeps: warning: 17 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_model_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyObject_HasAttrString: 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/dxtbx_imageset_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyEval_CallFunction: it's probably a plugin -dpkg-shlibdeps: warning: 21 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_hydrogens_ext.cpython-311-x86_64-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_rigid_body_ext.cpython-311-x86_64-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_reference_coordinate_ext.cpython-311-x86_64-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/dxtbx_masking_ext.cpython-311-x86_64-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_tls_optimise_amplitudes_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_FromDouble: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_glu_ext.cpython-311-x86_64-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/cma_es_ext.cpython-311-x86_64-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/iotbx_detectors_ext.cpython-311-x86_64-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/regression_test_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyRange_Type: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_masking_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin +dpkg-shlibdeps: warning: 6 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_covariance_ext.cpython-311-x86_64-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/iotbx_pdb_ext.cpython-311-x86_64-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/cctbx_merging_ext.cpython-311-x86_64-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_geometry_ext.cpython-311-x86_64-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-x86_64-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/mmtbx_geometry_clash_ext.cpython-311-x86_64-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/mmtbx_dynamics_ext.cpython-311-x86_64-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/spotfinder_hough_ext.cpython-311-x86_64-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_python_hybrid_times_ext.cpython-311-x86_64-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_ncs_ext.cpython-311-x86_64-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/spotfinder_array_family_flex_ext.cpython-311-x86_64-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/iotbx_mtz_ext.cpython-311-x86_64-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/gltbx_glu_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyLong_Type: it's probably a plugin -dpkg-shlibdeps: warning: 11 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_f_model_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyIter_Check: 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_stl_set_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyErr_Clear: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_dtrek_ext.cpython-311-x86_64-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-x86_64-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/cbflib_ext.cpython-311-x86_64-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/scitbx_stl_set_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyBool_FromLong: it's probably a plugin dpkg-shlibdeps: warning: 17 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_pdb_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyDict_Type: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_graphics_utils_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyList_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/regression_test_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyExc_RuntimeError: it's probably a plugin dpkg-shlibdeps: warning: 13 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_xray_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PySlice_Type: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_mosaic_ext.cpython-311-x86_64-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/smtbx_array_family_ext.cpython-311-x86_64-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/cctbx_eltbx_covalent_radii_ext.cpython-311-x86_64-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/rstbx_symmetry_constraints_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin +dpkg-shlibdeps: warning: 3 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_xray_scattering_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyExc_StopIteration: 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_xray_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyIter_Next: it's probably a plugin dpkg-shlibdeps: warning: 28 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/ccp4io_adaptbx_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyImport_AddModule: 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_eltbx_sasaki_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_sparse_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyTuple_New: 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/smtbx_refinement_least_squares_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_Type: it's probably a plugin dpkg-shlibdeps: warning: 6 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_ab_initio_ext.cpython-311-x86_64-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_dsn6_map_ext.cpython-311-x86_64-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_sgtbx_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyErr_Occurred: 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/rstbx_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_FromDouble: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_mtz_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyIter_Check: 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_array_family_flex_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PySlice_Type: it's probably a plugin +dpkg-shlibdeps: warning: 18 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_diffraction_fastbragg_ext.cpython-311-x86_64-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_ext.cpython-311-x86_64-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/scitbx_math_ext.cpython-311-x86_64-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/cctbx_geometry_restraints_ext.cpython-311-x86_64-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/gltbx_fonts_ext.cpython-311-x86_64-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_scaling_ext.cpython-311-x86_64-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/scitbx_stl_map_ext.cpython-311-x86_64-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/ccp4io_adaptbx_ext.cpython-311-x86_64-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/scitbx_minpack_ext.cpython-311-x86_64-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/iotbx_shelx_ext.cpython-311-x86_64-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_eltbx_icsd_radii_ext.cpython-311-x86_64-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/scitbx_suffixtree_single_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyObject_IsTrue: 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_optional_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyLong_FromLong: it's probably a plugin +dpkg-shlibdeps: warning: 7 other similar warnings have been skipped (use -v to see them all) dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_chemical_elements_ext.cpython-311-x86_64-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/smtbx_array_family_ext.cpython-311-x86_64-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_shared_types_ext.cpython-311-x86_64-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/mmtbx_geometry_clash_ext.cpython-311-x86_64-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/scitbx_iso_surface_ext.cpython-311-x86_64-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_rigid_body_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyObject_Size: 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_lbfgs_ext.cpython-311-x86_64-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/mmtbx_tls_ext.cpython-311-x86_64-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/boost_adaptbx_graph_min_cut_max_flow_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyDict_Type: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_array_family_flex_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyIter_Next: 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_symmetry_search_ext.cpython-311-x86_64-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/mmtbx_probe_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyBool_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/smtbx_structure_factors_direct_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyComplex_FromDoubles: 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_covalent_radii_ext.cpython-311-x86_64-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/gltbx_util_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyLong_FromLong: 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_gl_ext.cpython-311-x86_64-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/scitbx_linalg_ext.cpython-311-x86_64-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_masks_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin +dpkg-shlibdeps: warning: 8 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_dssp_ext.cpython-311-x86_64-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/cctbx_eltbx_neutron_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_Type: it's probably a plugin +dpkg-shlibdeps: warning: 8 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_den_restraints_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol _Py_NoneStruct: 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_tls_ext.cpython-311-x86_64-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/iotbx_scalepack_ext.cpython-311-x86_64-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/iotbx_cif_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyEval_CallFunction: it's probably a plugin +dpkg-shlibdeps: warning: 5 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_imageset_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyLong_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/scitbx_math_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyExc_IndexError: 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_boost_thread_test_ext.cpython-311-x86_64-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/omptbx_ext.cpython-311-x86_64-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/iotbx_shelx_ext.cpython-311-x86_64-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/determine_unit_cell_ext.cpython-311-x86_64-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_python_meta_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyExc_OverflowError: 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_random_ext.cpython-311-x86_64-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/annlib_ext.cpython-311-x86_64-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_indexing_api_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyLong_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/cctbx_adp_restraints_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyObject_IsInstance: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_adp_restraints_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_FromDouble: 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/boost_adaptbx_graph_clustering_algorithm_ext.cpython-311-x86_64-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_geometry_indexing_ext.cpython-311-x86_64-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_merging_ext.cpython-311-x86_64-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/rstbx_simage_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyUnicode_FromStringAndSize: 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-x86_64-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-x86_64-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/gltbx_quadrics_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_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_distltbx_ext.cpython-311-x86_64-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_eltbx_fp_fdp_ext.cpython-311-x86_64-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_rational_ext.cpython-311-x86_64-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_math_ext.cpython-311-x86_64-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/boost_python_hybrid_times_ext.cpython-311-x86_64-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/iotbx_scalepack_ext.cpython-311-x86_64-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_anharmonic_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyComplex_Type: it's probably a plugin dpkg-shlibdeps: warning: 3 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_alignment_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyLong_FromLong: it's probably a plugin -dpkg-shlibdeps: warning: 4 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_pdb_hierarchy_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyUnicode_AsUTF8: 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/boost_python_meta_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyObject_IsTrue: 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_lbfgs_ext.cpython-311-x86_64-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/std_pair_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin +dpkg-shlibdeps: warning: 5 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_tiny_pse_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_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_eltbx_icsd_radii_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin -dpkg-shlibdeps: warning: 6 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_sgtbx_asu_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyTuple_GetItem: 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_array_family_shared_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyLong_Type: it's probably a plugin +dpkg-shlibdeps: warning: 16 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_secondary_structure_ext.cpython-311-x86_64-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_geometry_asa_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyLong_FromLong: it's probably a plugin +dpkg-shlibdeps: warning: 14 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_decompose_ext.cpython-311-x86_64-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_orientation_ext.cpython-311-x86_64-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/fable_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyList_Type: it's probably a plugin -dpkg-shlibdeps: warning: 11 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_french_wilson_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyBool_Type: it's probably a plugin -dpkg-shlibdeps: warning: 5 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_asymmetric_map_ext.cpython-311-x86_64-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_geometry_restraints_ext.cpython-311-x86_64-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/boost_adaptbx_python_streambuf_test_ext.cpython-311-x86_64-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_ext.cpython-311-x86_64-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/dxtbx_flumpy.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyErr_Format: 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/scitbx_wigner_ext.cpython-311-x86_64-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_integration_ext.cpython-311-x86_64-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-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyDict_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/rstbx_diffraction_fastbragg_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_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_uctbx_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyExc_IndexError: 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/smtbx_stl_map_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyErr_SetString: 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/gltbx_viewer_utils_ext.cpython-311-x86_64-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_multipolar_ext.cpython-311-x86_64-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_pair_interaction_ext.cpython-311-x86_64-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/rstbx_simulation_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol _Py_NoneStruct: it's probably a plugin dpkg-shlibdeps: warning: 1 similar warning has been skipped (use -v to see it) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/boost_tuple_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyTuple_New: it's probably a plugin -dpkg-shlibdeps: warning: 4 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_anharmonic_ext.cpython-311-x86_64-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/mmtbx_probe_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyRange_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/boost_adaptbx_graph_graph_structure_comparison_ext.cpython-311-x86_64-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_den_restraints_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyObject_HasAttrString: it's probably a plugin -dpkg-shlibdeps: warning: 20 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_wigner_ext.cpython-311-x86_64-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/fable_ext.cpython-311-x86_64-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_ccp4_map_ext.cpython-311-x86_64-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/boost_adaptbx_graph_utility_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin dpkg-shlibdeps: warning: 3 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_adptbx_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyTuple_Type: it's probably a plugin -dpkg-shlibdeps: warning: 18 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_translation_search_ext.cpython-311-x86_64-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_suffixtree_shared_ext.cpython-311-x86_64-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/gltbx_quadrics_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyErr_Occurred: it's probably a plugin +dpkg-shlibdeps: warning: 21 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_format_nexus_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyTuple_Type: it's probably a plugin +dpkg-shlibdeps: warning: 7 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_maptbx_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyBool_FromLong: it's probably a plugin +dpkg-shlibdeps: warning: 14 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_utils_ext.cpython-311-x86_64-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_geometry_shared_types_ext.cpython-311-x86_64-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/dxtbx_ext.cpython-311-x86_64-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_ramachandran_restraints_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyTuple_GetItem: it's probably a plugin -dpkg-shlibdeps: warning: 24 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_validation_ramachandran_ext.cpython-311-x86_64-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/scitbx_glmtbx_ext.cpython-311-x86_64-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/cctbx_statistics_ext.cpython-311-x86_64-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/iotbx_wildcard_ext.cpython-311-x86_64-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_dynamics_ext.cpython-311-x86_64-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/spotfinder_hough_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin dpkg-shlibdeps: warning: 3 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_primitive_ext.cpython-311-x86_64-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_uctbx_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_Type: it's probably a plugin +dpkg-shlibdeps: warning: 12 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_geometry_ext.cpython-311-x86_64-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/gltbx_util_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol _Py_NoneStruct: it's probably a plugin +dpkg-shlibdeps: warning: 17 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_masks_ext.cpython-311-x86_64-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/mmtbx_bulk_solvent_ext.cpython-311-x86_64-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/cctbx_eltbx_xray_scattering_ext.cpython-311-x86_64-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_adptbx_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyObject_GetIter: 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_linalg_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyObject_IsInstance: 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_cif_ext.cpython-311-x86_64-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_eltbx_tiny_pse_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyUnicode_Type: it's probably a plugin -dpkg-shlibdeps: warning: 8 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_stl_map_ext.cpython-311-x86_64-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/mmtbx_ncs_cartesian_restraints_ext.cpython-311-x86_64-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_minpack_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyBool_Type: it's probably a plugin -dpkg-shlibdeps: warning: 7 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_structure_factors_direct_ext.cpython-311-x86_64-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/scitbx_random_ext.cpython-311-x86_64-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/scitbx_lbfgsb_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyUnicode_FromStringAndSize: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_indexing_api_ext.cpython-311-x86_64-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/cctbx_eltbx_wavelengths_ext.cpython-311-x86_64-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_fftpack_ext.cpython-311-x86_64-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/dxtbx_flumpy.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyErr_Fetch: 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/scitbx_iso_surface_ext.cpython-311-x86_64-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_symmetry_constraints_ext.cpython-311-x86_64-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-x86_64-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/spotfinder_array_family_flex_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyObject_Size: it's probably a plugin +dpkg-shlibdeps: warning: 24 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_sgtbx_asu_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PySlice_Type: it's probably a plugin +dpkg-shlibdeps: warning: 19 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_asymmetric_map_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol _Py_NoneStruct: it's probably a plugin +dpkg-shlibdeps: warning: 1 similar warning has been skipped (use -v to see it) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_indexing_ext.cpython-311-x86_64-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/dxtbx_model_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyUnicode_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_metric_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin +dpkg-shlibdeps: warning: 5 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_graph_structure_comparison_ext.cpython-311-x86_64-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/cma_es_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol _Py_NoneStruct: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_ab_initio_ext.cpython-311-x86_64-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_graph_breadth_first_search_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin dpkg-shlibdeps: warning: 3 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_dssp_ext.cpython-311-x86_64-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_mosaic_ext.cpython-311-x86_64-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/mmtbx_geometry_sphere_surface_sampling_ext.cpython-311-x86_64-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/boost_adaptbx_graph_min_cut_max_flow_ext.cpython-311-x86_64-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_masks_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyLong_Type: it's probably a plugin -dpkg-shlibdeps: warning: 7 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_breadth_first_search_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyLong_FromUnsignedLong: 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_rotamer_fit_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_FromDouble: 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/boost_adaptbx_graph_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyEval_CallFunction: 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_tls_decompose_ext.cpython-311-x86_64-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_fp_fdp_ext.cpython-311-x86_64-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_symmetry_search_ext.cpython-311-x86_64-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_ncs_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyTuple_Type: it's probably a plugin +dpkg-shlibdeps: warning: 12 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_connected_component_algorithm_ext.cpython-311-x86_64-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_sphere_surface_sampling_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyLong_FromUnsignedLong: 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-x86_64-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_maptbx_bcr_bcr_ext.cpython-311-x86_64-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/boost_adaptbx_graph_metric_ext.cpython-311-x86_64-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/boost_adaptbx_graph_maximum_clique_ext.cpython-311-x86_64-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/scitbx_lstbx_normal_equations_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyExc_IndexError: it's probably a plugin -dpkg-shlibdeps: warning: 10 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_crystal_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyTuple_GetItem: 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-x86_64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin -dpkg-shlibdeps: warning: 6 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_emma_ext.cpython-311-x86_64-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_miller_ext.cpython-311-x86_64-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_miller_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyComplex_FromDoubles: 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/annlib_ext.cpython-311-x86_64-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/cctbx_dmtbx_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyIter_Check: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_stl_vector_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyObject_IsInstance: 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-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyLong_Type: it's probably a plugin +dpkg-shlibdeps: warning: 5 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_validation_ramachandran_ext.cpython-311-x86_64-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_f_model_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyRange_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/mmtbx_rsr_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyObject_IsInstance: 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_dtrek_ext.cpython-311-x86_64-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/boost_adaptbx_graph_connected_component_algorithm_ext.cpython-311-x86_64-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/smtbx_refinement_constraints_ext.cpython-311-x86_64-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/scitbx_suffixtree_single_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyExc_IndexError: 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/rstbx_bandpass_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_FromDouble: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_xplor_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyExc_IndexError: 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_utility_ext.cpython-311-x86_64-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/scitbx_cubicle_neighbors_ext.cpython-311-x86_64-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/mmtbx_max_lik_ext.cpython-311-x86_64-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/mmtbx_reference_coordinate_ext.cpython-311-x86_64-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/mmtbx_rotamer_fit_ext.cpython-311-x86_64-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/rstbx_array_family_flex_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyObject_GetIter: it's probably a plugin -dpkg-shlibdeps: warning: 18 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_detectors_ext.cpython-311-x86_64-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/cctbx_xray_observations_ext.cpython-311-x86_64-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_masks_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_Type: it's probably a plugin -dpkg-shlibdeps: warning: 8 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_secondary_structure_ext.cpython-311-x86_64-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_bpcx_detector_model_ext.cpython-311-x86_64-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_translation_search_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin dpkg-shlibdeps: warning: 5 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_stl_vector_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_FromDouble: it's probably a plugin -dpkg-shlibdeps: warning: 19 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/boost_optional_ext.cpython-311-x86_64-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_simulation_ext.cpython-311-x86_64-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-x86_64-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_adaptbx_python_streambuf_test_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin -dpkg-shlibdeps: warning: 3 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_covariance_ext.cpython-311-x86_64-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_french_wilson_ext.cpython-311-x86_64-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_max_lik_ext.cpython-311-x86_64-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_suffixtree_shared_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyLong_FromUnsignedLong: it's probably a plugin dpkg-shlibdeps: warning: 3 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_maximum_clique_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyList_Type: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_ramachandran_restraints_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_Type: it's probably a plugin +dpkg-shlibdeps: warning: 24 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_math_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyLong_Type: it's probably a plugin dpkg-shlibdeps: warning: 5 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_pair_interaction_ext.cpython-311-x86_64-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_graphics_utils_ext.cpython-311-x86_64-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/mmtbx_building_loop_closure_ext.cpython-311-x86_64-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/spotfinder_dxtbx_ext.cpython-311-x86_64-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/iotbx_detectors_bruker_ext.cpython-311-x86_64-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_cablam_align_utils_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyErr_Occurred: 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/smtbx_refinement_constraints_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyObject_Call: it's probably a plugin +dpkg-shlibdeps: warning: 30 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/boost_rational_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol _Py_NoneStruct: it's probably a plugin +dpkg-shlibdeps: warning: 12 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_cubicle_neighbors_ext.cpython-311-x86_64-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/dxtbx_ext.cpython-311-x86_64-linux-gnu.so contains an unresolvable reference to symbol PyBytes_FromStringAndSize: it's probably a plugin +dpkg-shlibdeps: warning: 4 other similar warnings have been skipped (use -v to see them all) dh_installdeb -O--buildsystem=pybuild install -m0755 -d debian/libcctbx0/DEBIAN install -p -m0644 debian/.debhelper/generated/libcctbx0/triggers debian/libcctbx0/DEBIAN/triggers @@ -40732,6 +40769,10 @@ mv debian/libcctbx-dev.substvars.new debian/libcctbx-dev.substvars mv debian/python3-cctbx.substvars.new debian/python3-cctbx.substvars dh_gencontrol -O--buildsystem=pybuild + install -m0755 -d debian/libcctbx-dev/DEBIAN + echo misc:Depends= >> debian/libcctbx-dev.substvars + echo misc:Pre-Depends= >> debian/libcctbx-dev.substvars + dpkg-gencontrol -plibcctbx-dev -ldebian/changelog -Tdebian/libcctbx-dev.substvars -Pdebian/libcctbx-dev install -m0755 -d debian/python3-cctbx/DEBIAN echo misc:Depends= >> debian/python3-cctbx.substvars echo misc:Pre-Depends= >> debian/python3-cctbx.substvars @@ -40742,44 +40783,40 @@ echo misc:Pre-Depends= >> debian/libcctbx0.substvars install -m0755 -d debian/.debhelper/libcctbx0/dbgsym-root/DEBIAN dpkg-gencontrol -plibcctbx0 -ldebian/changelog -Tdebian/libcctbx0.substvars -Pdebian/.debhelper/libcctbx0/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -UBuilt-Using -DAuto-Built-Package=debug-symbols -UProtected -DPackage=libcctbx0-dbgsym "-DDepends=libcctbx0 (= \${binary:Version})" "-DDescription=debug symbols for libcctbx0" "-DBuild-Ids=0a2f275febbc6951e6020e3141cdef5fcb6ec196 13c13e4215dab022c78ea194fde76f5218c2bfb3 1b901ea9849a37a5b2c5590204a6140f000afa4b 277ab65c7fe1c2f5be9c08819d7f8df0fc82ad3c 2acc55783bf1a7b57854330de851a6500e52fe7d 5e9fb1988db97c930a20601f44e281da3811ec21 6514d95ea89054f3114ee0ea74a455d099c5974b 78d0f1cddef4727da37689ebaa72d1d0adc2ba1e 8706be60fc7d8b6bbf549315588e614113a3faf7 8884e1c6f27bd4f2122bb958099ca54baf00bd10 9124948b8943cd61f0c7735eda0aec2d9b713051 98baa098940028adeb4fc84ba0c1f5c3cad26cb8 9a388c5bfe68a69674ea465c91d72ad36dec6e88 9e97a2697cdd8a0b0b059456d0f0f6c14ca21fa1 ac9b71290ef6b611ad3a006931c3dca91bf5143f b83e5da383ada23e9dd10de29ea2693284671d18 c9787b229213c169b5cba39568a0b7ca3cdc99bd db382071e6a2037dcee62f96f5e3eddc28905bed f6fe37f3a3f966f64d035e43789c5959965d8bab" -DSection=debug -UMulti-Arch -UReplaces -UBreaks - install -m0755 -d debian/libcctbx-dev/DEBIAN - echo misc:Depends= >> debian/libcctbx-dev.substvars - echo misc:Pre-Depends= >> debian/libcctbx-dev.substvars - dpkg-gencontrol -plibcctbx-dev -ldebian/changelog -Tdebian/libcctbx-dev.substvars -Pdebian/libcctbx-dev dpkg-gencontrol: warning: package libcctbx0: substitution variable ${python3:Depends} unused, but is defined 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/.debhelper/python3-cctbx/dbgsym-root/DEBIAN/control dpkg-gencontrol -ppython3-cctbx -ldebian/changelog -Tdebian/python3-cctbx.substvars -Pdebian/python3-cctbx -dpkg-gencontrol: warning: package libcctbx-dev: substitution variable ${python3:Depends} unused, but is defined chmod 0644 -- debian/libcctbx-dev/DEBIAN/control dpkg-gencontrol: warning: package libcctbx0: substitution variable ${python3:Depends} unused, but is defined 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 - cd debian/libcctbx-dev >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums - install -m0755 -d debian/libcctbx0/DEBIAN install -m0755 -d debian/python3-cctbx/DEBIAN + install -m0755 -d debian/libcctbx0/DEBIAN + install -m0755 -d debian/libcctbx-dev/DEBIAN cd debian/libcctbx0 >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums + cd debian/libcctbx-dev >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/python3-cctbx >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums - chmod 0644 -- debian/libcctbx-dev/DEBIAN/md5sums chmod 0644 -- debian/libcctbx0/DEBIAN/md5sums install -m0755 -d debian/.debhelper/libcctbx0/dbgsym-root/DEBIAN cd debian/.debhelper/libcctbx0/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums + chmod 0644 -- debian/libcctbx-dev/DEBIAN/md5sums chmod 0644 -- debian/.debhelper/libcctbx0/dbgsym-root/DEBIAN/md5sums chmod 0644 -- debian/python3-cctbx/DEBIAN/md5sums install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/DEBIAN cd debian/.debhelper/python3-cctbx/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/DEBIAN/md5sums dh_builddeb -O--buildsystem=pybuild - dpkg-deb --root-owner-group --build debian/.debhelper/libcctbx0/dbgsym-root .. 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/.debhelper/python3-cctbx/dbgsym-root .. dpkg-deb --root-owner-group --build debian/python3-cctbx .. -dpkg-deb: building package 'libcctbx0-dbgsym' in '../libcctbx0-dbgsym_2022.9+ds2+~3.11.2+ds1-6_amd64.deb'. + dpkg-deb --root-owner-group --build debian/.debhelper/python3-cctbx/dbgsym-root .. dpkg-deb: building package 'libcctbx0' in '../libcctbx0_2022.9+ds2+~3.11.2+ds1-6_amd64.deb'. +dpkg-deb: building package 'libcctbx0-dbgsym' in '../libcctbx0-dbgsym_2022.9+ds2+~3.11.2+ds1-6_amd64.deb'. dpkg-deb: building package 'libcctbx-dev' in '../libcctbx-dev_2022.9+ds2+~3.11.2+ds1-6_amd64.deb'. dpkg-deb: building package 'python3-cctbx-dbgsym' in '../python3-cctbx-dbgsym_2022.9+ds2+~3.11.2+ds1-6_amd64.deb'. dpkg-deb: building package 'python3-cctbx' in '../python3-cctbx_2022.9+ds2+~3.11.2+ds1-6_amd64.deb'. @@ -40790,12 +40827,14 @@ 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/21364/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/21364/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/2033141 and its subdirectories -I: Current time: Sat Jan 6 01:27:31 -12 2024 -I: pbuilder-time-stamp: 1704547651 +I: removing directory /srv/workspace/pbuilder/21364 and its subdirectories +I: Current time: Sat Feb 8 10:12:09 +14 2025 +I: pbuilder-time-stamp: 1738959129