Diff of the two buildlogs: -- --- b1/build.log 2024-04-14 17:44:48.918833585 +0000 +++ b2/build.log 2024-04-14 17:57:33.714296467 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Apr 14 05:41:32 -12 2024 -I: pbuilder-time-stamp: 1713116492 +I: Current time: Mon Apr 15 07:45:55 +14 2024 +I: pbuilder-time-stamp: 1713116755 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -26,52 +26,84 @@ dpkg-source: info: unpacking libpdb-redo_3.0.5-2.debian.tar.xz I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/4494/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/18791/tmp/hooks/D01_modify_environment starting +debug: Running on ff64a. +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 Apr 14 17:46 /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/18791/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/18791/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='armhf' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=6 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='78679abfbe94421c87b87fa5c1167942' - 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='4494' - PS1='# ' - PS2='> ' + INVOCATION_ID=e3afaca55c454c22b6984dd8132102a8 + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=18791 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.OWXFxRtM/pbuilderrc_a8QD --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.OWXFxRtM/b1 --logfile b1/build.log libpdb-redo_3.0.5-2.dsc' - SUDO_GID='110' - SUDO_UID='103' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:3142/' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.OWXFxRtM/pbuilderrc_COGs --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.OWXFxRtM/b2 --logfile b2/build.log libpdb-redo_3.0.5-2.dsc' + SUDO_GID=114 + SUDO_UID=109 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:3142/ I: uname -a - Linux virt32z 6.1.0-20-armmp-lpae #1 SMP Debian 6.1.85-1 (2024-04-11) armv7l GNU/Linux + Linux i-capture-the-hostname 6.1.0-20-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Apr 14 07:42 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/4494/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Apr 14 07:45 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/18791/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -231,7 +263,7 @@ Get: 102 http://deb.debian.org/debian unstable/main armhf pkgconf-bin armhf 1.8.1-1+b2 [28.9 kB] Get: 103 http://deb.debian.org/debian unstable/main armhf pkgconf armhf 1.8.1-1+b2 [26.2 kB] Get: 104 http://deb.debian.org/debian unstable/main armhf pkg-config armhf 1.8.1-1+b2 [14.0 kB] -Fetched 62.2 MB in 3s (18.3 MB/s) +Fetched 62.2 MB in 2s (33.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libproc2-0:armhf. (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 ... 19442 files and directories currently installed.) @@ -662,7 +694,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/libpdb-redo-3.0.5/ && 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 > ../libpdb-redo_3.0.5-2_source.changes +I: user script /srv/workspace/pbuilder/18791/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/18791/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/libpdb-redo-3.0.5/ && 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 > ../libpdb-redo_3.0.5-2_source.changes dpkg-buildpackage: info: source package libpdb-redo dpkg-buildpackage: info: source version 3.0.5-2 dpkg-buildpackage: info: source distribution unstable @@ -718,8 +754,8 @@ -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success -- Performing Test COMPILER_HAS_DEPRECATED_ATTR -- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success --- Configuring done (5.6s) --- Generating done (0.0s) +-- Configuring done (43.6s) +-- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: @@ -732,7 +768,7 @@ -- Build files have been written to: /build/reproducible-path/libpdb-redo-3.0.5/obj-arm-linux-gnueabihf make[1]: Leaving directory '/build/reproducible-path/libpdb-redo-3.0.5' dh_auto_build - cd obj-arm-linux-gnueabihf && make -j3 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-arm-linux-gnueabihf && make -j6 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/libpdb-redo-3.0.5/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/build/reproducible-path/libpdb-redo-3.0.5 -B/build/reproducible-path/libpdb-redo-3.0.5/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/libpdb-redo-3.0.5/obj-arm-linux-gnueabihf/CMakeFiles /build/reproducible-path/libpdb-redo-3.0.5/obj-arm-linux-gnueabihf//CMakeFiles/progress.marks @@ -744,12 +780,18 @@ make[3]: Leaving directory '/build/reproducible-path/libpdb-redo-3.0.5/obj-arm-linux-gnueabihf' make -f CMakeFiles/pdb-redo.dir/build.make CMakeFiles/pdb-redo.dir/build make[3]: Entering directory '/build/reproducible-path/libpdb-redo-3.0.5/obj-arm-linux-gnueabihf' -[ 14%] Building CXX object CMakeFiles/pdb-redo.dir/src/BondMap.cpp.o -[ 14%] Building CXX object CMakeFiles/pdb-redo.dir/src/AtomShape.cpp.o -[ 21%] Building CXX object CMakeFiles/pdb-redo.dir/src/ClipperWrapper.cpp.o +[ 7%] Building CXX object CMakeFiles/pdb-redo.dir/src/AtomShape.cpp.o /usr/bin/c++ -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.0.5/include -I/build/reproducible-path/libpdb-redo-3.0.5/obj-arm-linux-gnueabihf -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++17 -fPIC -MD -MT CMakeFiles/pdb-redo.dir/src/AtomShape.cpp.o -MF CMakeFiles/pdb-redo.dir/src/AtomShape.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/AtomShape.cpp.o -c /build/reproducible-path/libpdb-redo-3.0.5/src/AtomShape.cpp +[ 14%] Building CXX object CMakeFiles/pdb-redo.dir/src/BondMap.cpp.o /usr/bin/c++ -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.0.5/include -I/build/reproducible-path/libpdb-redo-3.0.5/obj-arm-linux-gnueabihf -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++17 -fPIC -MD -MT CMakeFiles/pdb-redo.dir/src/BondMap.cpp.o -MF CMakeFiles/pdb-redo.dir/src/BondMap.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/BondMap.cpp.o -c /build/reproducible-path/libpdb-redo-3.0.5/src/BondMap.cpp +[ 21%] Building CXX object CMakeFiles/pdb-redo.dir/src/DistanceMap.cpp.o +/usr/bin/c++ -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.0.5/include -I/build/reproducible-path/libpdb-redo-3.0.5/obj-arm-linux-gnueabihf -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++17 -fPIC -MD -MT CMakeFiles/pdb-redo.dir/src/DistanceMap.cpp.o -MF CMakeFiles/pdb-redo.dir/src/DistanceMap.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/DistanceMap.cpp.o -c /build/reproducible-path/libpdb-redo-3.0.5/src/DistanceMap.cpp +[ 28%] Building CXX object CMakeFiles/pdb-redo.dir/src/ClipperWrapper.cpp.o /usr/bin/c++ -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.0.5/include -I/build/reproducible-path/libpdb-redo-3.0.5/obj-arm-linux-gnueabihf -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++17 -fPIC -MD -MT CMakeFiles/pdb-redo.dir/src/ClipperWrapper.cpp.o -MF CMakeFiles/pdb-redo.dir/src/ClipperWrapper.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/ClipperWrapper.cpp.o -c /build/reproducible-path/libpdb-redo-3.0.5/src/ClipperWrapper.cpp +[ 35%] Building CXX object CMakeFiles/pdb-redo.dir/src/MapMaker.cpp.o +/usr/bin/c++ -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.0.5/include -I/build/reproducible-path/libpdb-redo-3.0.5/obj-arm-linux-gnueabihf -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++17 -fPIC -MD -MT CMakeFiles/pdb-redo.dir/src/MapMaker.cpp.o -MF CMakeFiles/pdb-redo.dir/src/MapMaker.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/MapMaker.cpp.o -c /build/reproducible-path/libpdb-redo-3.0.5/src/MapMaker.cpp +[ 42%] Building CXX object CMakeFiles/pdb-redo.dir/src/Compound.cpp.o +/usr/bin/c++ -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.0.5/include -I/build/reproducible-path/libpdb-redo-3.0.5/obj-arm-linux-gnueabihf -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++17 -fPIC -MD -MT CMakeFiles/pdb-redo.dir/src/Compound.cpp.o -MF CMakeFiles/pdb-redo.dir/src/Compound.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/Compound.cpp.o -c /build/reproducible-path/libpdb-redo-3.0.5/src/Compound.cpp /build/reproducible-path/libpdb-redo-3.0.5/src/AtomShape.cpp: In constructor ‘pdb_redo::AtomShapeImpl::AtomShapeImpl(cif::point, cif::atom_type, int, float, float, float, float, bool)’: /build/reproducible-path/libpdb-redo-3.0.5/src/AtomShape.cpp:477:23: warning: possibly dangling reference to a temporary [-Wdangling-reference] 477 | auto &D = @@ -764,10 +806,6 @@ /build/reproducible-path/libpdb-redo-3.0.5/src/AtomShape.cpp:555:76: note: the temporary was destroyed at the end of the full expression ‘cif::atom_type_traits(symbol).cif::atom_type_traits::elsf()’ 555 | mElectronScattering ? atom_type_traits(symbol).elsf() : atom_type_traits(symbol).wksf(charge); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ -[ 28%] Building CXX object CMakeFiles/pdb-redo.dir/src/Compound.cpp.o -/usr/bin/c++ -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.0.5/include -I/build/reproducible-path/libpdb-redo-3.0.5/obj-arm-linux-gnueabihf -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++17 -fPIC -MD -MT CMakeFiles/pdb-redo.dir/src/Compound.cpp.o -MF CMakeFiles/pdb-redo.dir/src/Compound.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/Compound.cpp.o -c /build/reproducible-path/libpdb-redo-3.0.5/src/Compound.cpp -[ 35%] Building CXX object CMakeFiles/pdb-redo.dir/src/DistanceMap.cpp.o -/usr/bin/c++ -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.0.5/include -I/build/reproducible-path/libpdb-redo-3.0.5/obj-arm-linux-gnueabihf -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++17 -fPIC -MD -MT CMakeFiles/pdb-redo.dir/src/DistanceMap.cpp.o -MF CMakeFiles/pdb-redo.dir/src/DistanceMap.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/DistanceMap.cpp.o -c /build/reproducible-path/libpdb-redo-3.0.5/src/DistanceMap.cpp /build/reproducible-path/libpdb-redo-3.0.5/src/DistanceMap.cpp: In member function ‘std::vector pdb_redo::DistanceMap::near(const cif::mm::atom&, float) const’: /build/reproducible-path/libpdb-redo-3.0.5/src/DistanceMap.cpp:448:15: warning: possibly dangling reference to a temporary [-Wdangling-reference] 448 | auto &atom_site = atom.get_row().get_category(); @@ -775,8 +813,14 @@ /build/reproducible-path/libpdb-redo-3.0.5/src/DistanceMap.cpp:448:54: note: the temporary was destroyed at the end of the full expression ‘(& atom)->cif::mm::atom::get_row().cif::row_handle::get_category()’ 448 | auto &atom_site = atom.get_row().get_category(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ -[ 42%] Building CXX object CMakeFiles/pdb-redo.dir/src/MapMaker.cpp.o -/usr/bin/c++ -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.0.5/include -I/build/reproducible-path/libpdb-redo-3.0.5/obj-arm-linux-gnueabihf -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++17 -fPIC -MD -MT CMakeFiles/pdb-redo.dir/src/MapMaker.cpp.o -MF CMakeFiles/pdb-redo.dir/src/MapMaker.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/MapMaker.cpp.o -c /build/reproducible-path/libpdb-redo-3.0.5/src/MapMaker.cpp +/build/reproducible-path/libpdb-redo-3.0.5/src/MapMaker.cpp: In member function ‘void pdb_redo::MapMaker::fixMTZ() [with FTYPE = float]’: +/build/reproducible-path/libpdb-redo-3.0.5/src/MapMaker.cpp:1118:22: note: parameter passing for argument of type ‘clipper::datatypes::F_phi’ when C++17 is enabled changed to match C++14 in GCC 10.1 + 1118 | auto mFo = mFbData[ih] - mFdData[ih]; + | ^~~ +[ 50%] Building CXX object CMakeFiles/pdb-redo.dir/src/Ramachandran.cpp.o +/usr/bin/c++ -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.0.5/include -I/build/reproducible-path/libpdb-redo-3.0.5/obj-arm-linux-gnueabihf -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++17 -fPIC -MD -MT CMakeFiles/pdb-redo.dir/src/Ramachandran.cpp.o -MF CMakeFiles/pdb-redo.dir/src/Ramachandran.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/Ramachandran.cpp.o -c /build/reproducible-path/libpdb-redo-3.0.5/src/Ramachandran.cpp +[ 57%] Building CXX object CMakeFiles/pdb-redo.dir/src/ResolutionCalculator.cpp.o +/usr/bin/c++ -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.0.5/include -I/build/reproducible-path/libpdb-redo-3.0.5/obj-arm-linux-gnueabihf -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++17 -fPIC -MD -MT CMakeFiles/pdb-redo.dir/src/ResolutionCalculator.cpp.o -MF CMakeFiles/pdb-redo.dir/src/ResolutionCalculator.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/ResolutionCalculator.cpp.o -c /build/reproducible-path/libpdb-redo-3.0.5/src/ResolutionCalculator.cpp In file included from /usr/include/c++/13/vector:72, from /usr/include/cif++/forward_decl.hpp:32, from /usr/include/cif++/category.hpp:29, @@ -793,16 +837,27 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpdb-redo-3.0.5/src/MapMaker.cpp: In member function ‘void pdb_redo::MapMaker::fixMTZ() [with FTYPE = float]’: -/build/reproducible-path/libpdb-redo-3.0.5/src/MapMaker.cpp:1118:22: note: parameter passing for argument of type ‘clipper::datatypes::F_phi’ when C++17 is enabled changed to match C++14 in GCC 10.1 - 1118 | auto mFo = mFbData[ih] - mFdData[ih]; - | ^~~ -[ 50%] Building CXX object CMakeFiles/pdb-redo.dir/src/Ramachandran.cpp.o -/usr/bin/c++ -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.0.5/include -I/build/reproducible-path/libpdb-redo-3.0.5/obj-arm-linux-gnueabihf -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++17 -fPIC -MD -MT CMakeFiles/pdb-redo.dir/src/Ramachandran.cpp.o -MF CMakeFiles/pdb-redo.dir/src/Ramachandran.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/Ramachandran.cpp.o -c /build/reproducible-path/libpdb-redo-3.0.5/src/Ramachandran.cpp -[ 57%] Building CXX object CMakeFiles/pdb-redo.dir/src/ResolutionCalculator.cpp.o -/usr/bin/c++ -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.0.5/include -I/build/reproducible-path/libpdb-redo-3.0.5/obj-arm-linux-gnueabihf -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++17 -fPIC -MD -MT CMakeFiles/pdb-redo.dir/src/ResolutionCalculator.cpp.o -MF CMakeFiles/pdb-redo.dir/src/ResolutionCalculator.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/ResolutionCalculator.cpp.o -c /build/reproducible-path/libpdb-redo-3.0.5/src/ResolutionCalculator.cpp [ 64%] Building CXX object CMakeFiles/pdb-redo.dir/src/SkipList.cpp.o /usr/bin/c++ -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.0.5/include -I/build/reproducible-path/libpdb-redo-3.0.5/obj-arm-linux-gnueabihf -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++17 -fPIC -MD -MT CMakeFiles/pdb-redo.dir/src/SkipList.cpp.o -MF CMakeFiles/pdb-redo.dir/src/SkipList.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/SkipList.cpp.o -c /build/reproducible-path/libpdb-redo-3.0.5/src/SkipList.cpp +[ 71%] Building CXX object CMakeFiles/pdb-redo.dir/src/Statistics.cpp.o +/usr/bin/c++ -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.0.5/include -I/build/reproducible-path/libpdb-redo-3.0.5/obj-arm-linux-gnueabihf -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++17 -fPIC -MD -MT CMakeFiles/pdb-redo.dir/src/Statistics.cpp.o -MF CMakeFiles/pdb-redo.dir/src/Statistics.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/Statistics.cpp.o -c /build/reproducible-path/libpdb-redo-3.0.5/src/Statistics.cpp +In file included from /usr/include/c++/13/bits/stl_algobase.h:64, + from /usr/include/c++/13/string:51, + from /usr/include/c++/13/bits/locale_classes.h:40, + from /usr/include/c++/13/bits/ios_base.h:41, + from /usr/include/c++/13/ios:44, + from /usr/include/c++/13/istream:40, + from /usr/include/c++/13/fstream:40, + from /build/reproducible-path/libpdb-redo-3.0.5/src/Statistics.cpp:27: +/usr/include/c++/13/bits/stl_pair.h: In instantiation of ‘constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = double; _T2 = double; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp>::type = double; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp2>::type = double]’: +/build/reproducible-path/libpdb-redo-3.0.5/src/Statistics.cpp:545:41: required from here +/usr/include/c++/13/bits/stl_pair.h:922:5: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 + 922 | make_pair(_T1&& __x, _T2&& __y) + | ^~~~~~~~~ +[ 78%] Building CXX object CMakeFiles/pdb-redo.dir/src/Symmetry-2.cpp.o +/usr/bin/c++ -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.0.5/include -I/build/reproducible-path/libpdb-redo-3.0.5/obj-arm-linux-gnueabihf -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++17 -fPIC -MD -MT CMakeFiles/pdb-redo.dir/src/Symmetry-2.cpp.o -MF CMakeFiles/pdb-redo.dir/src/Symmetry-2.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/Symmetry-2.cpp.o -c /build/reproducible-path/libpdb-redo-3.0.5/src/Symmetry-2.cpp +[ 85%] Building CXX object CMakeFiles/pdb-redo.dir/src/Minimizer.cpp.o +/usr/bin/c++ -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.0.5/include -I/build/reproducible-path/libpdb-redo-3.0.5/obj-arm-linux-gnueabihf -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++17 -fPIC -MD -MT CMakeFiles/pdb-redo.dir/src/Minimizer.cpp.o -MF CMakeFiles/pdb-redo.dir/src/Minimizer.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/Minimizer.cpp.o -c /build/reproducible-path/libpdb-redo-3.0.5/src/Minimizer.cpp In file included from /usr/include/c++/13/vector:72, from /usr/include/clipper/ccp4/ccp4_utils.h:49, from /usr/include/clipper/clipper-ccp4.h:7, @@ -821,58 +876,6 @@ /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {clipper::Atom}; _Tp = clipper::Atom; _Alloc = std::allocator]’: -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {clipper::Atom}; _Tp = clipper::Atom; _Alloc = std::allocator]’: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 71%] Building CXX object CMakeFiles/pdb-redo.dir/src/Statistics.cpp.o -/usr/bin/c++ -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.0.5/include -I/build/reproducible-path/libpdb-redo-3.0.5/obj-arm-linux-gnueabihf -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++17 -fPIC -MD -MT CMakeFiles/pdb-redo.dir/src/Statistics.cpp.o -MF CMakeFiles/pdb-redo.dir/src/Statistics.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/Statistics.cpp.o -c /build/reproducible-path/libpdb-redo-3.0.5/src/Statistics.cpp -[ 78%] Building CXX object CMakeFiles/pdb-redo.dir/src/Symmetry-2.cpp.o -/usr/bin/c++ -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.0.5/include -I/build/reproducible-path/libpdb-redo-3.0.5/obj-arm-linux-gnueabihf -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++17 -fPIC -MD -MT CMakeFiles/pdb-redo.dir/src/Symmetry-2.cpp.o -MF CMakeFiles/pdb-redo.dir/src/Symmetry-2.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/Symmetry-2.cpp.o -c /build/reproducible-path/libpdb-redo-3.0.5/src/Symmetry-2.cpp -In file included from /usr/include/c++/13/bits/stl_algobase.h:64, - from /usr/include/c++/13/string:51, - from /usr/include/c++/13/bits/locale_classes.h:40, - from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/istream:40, - from /usr/include/c++/13/fstream:40, - from /build/reproducible-path/libpdb-redo-3.0.5/src/Statistics.cpp:27: -/usr/include/c++/13/bits/stl_pair.h: In instantiation of ‘constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = double; _T2 = double; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp>::type = double; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp2>::type = double]’: -/build/reproducible-path/libpdb-redo-3.0.5/src/Statistics.cpp:545:41: required from here -/usr/include/c++/13/bits/stl_pair.h:922:5: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 - 922 | make_pair(_T1&& __x, _T2&& __y) - | ^~~~~~~~~ -In file included from /usr/include/c++/13/vector:72, - from /usr/include/cif++/forward_decl.hpp:32, - from /usr/include/cif++/category.hpp:29, - from /usr/include/cif++/datablock.hpp:29, - from /usr/include/cif++/file.hpp:32, - from /usr/include/cif++.hpp:30, - from /build/reproducible-path/libpdb-redo-3.0.5/src/Symmetry-2.cpp:30: -/usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {clipper::Coord_orth}; _Tp = clipper::Coord_orth; _Alloc = std::allocator]’: -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {clipper::Coord_orth}; _Tp = clipper::Coord_orth; _Alloc = std::allocator]’, - inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = clipper::Coord_orth; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from ‘clipper::Coord_orth pdb_redo::CalculateOffsetForCell(const cif::mm::structure&, const clipper::Spacegroup&, const clipper::Cell&)’ at /build/reproducible-path/libpdb-redo-3.0.5/src/Symmetry-2.cpp:59:22: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {clipper::RTop_orth}; _Tp = clipper::RTop_orth; _Alloc = std::allocator]’: -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {clipper::RTop_orth}; _Tp = clipper::RTop_orth; _Alloc = std::allocator]’: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 85%] Building CXX object CMakeFiles/pdb-redo.dir/src/Minimizer.cpp.o -/usr/bin/c++ -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.0.5/include -I/build/reproducible-path/libpdb-redo-3.0.5/obj-arm-linux-gnueabihf -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++17 -fPIC -MD -MT CMakeFiles/pdb-redo.dir/src/Minimizer.cpp.o -MF CMakeFiles/pdb-redo.dir/src/Minimizer.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/Minimizer.cpp.o -c /build/reproducible-path/libpdb-redo-3.0.5/src/Minimizer.cpp In file included from /usr/include/c++/13/bits/stl_algo.h:61, from /usr/include/c++/13/functional:67, from /usr/include/cif++/condition.hpp:32, @@ -898,6 +901,16 @@ /usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {clipper::Atom}; _Tp = clipper::Atom; _Alloc = std::allocator]’: +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {clipper::Atom}; _Tp = clipper::Atom; _Alloc = std::allocator]’: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 92%] Building CXX object CMakeFiles/pdb-redo.dir/src/Restraints.cpp.o +/usr/bin/c++ -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.0.5/include -I/build/reproducible-path/libpdb-redo-3.0.5/obj-arm-linux-gnueabihf -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++17 -fPIC -MD -MT CMakeFiles/pdb-redo.dir/src/Restraints.cpp.o -MF CMakeFiles/pdb-redo.dir/src/Restraints.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/Restraints.cpp.o -c /build/reproducible-path/libpdb-redo-3.0.5/src/Restraints.cpp In file included from /usr/include/c++/13/vector:72, from /usr/include/cif++/forward_decl.hpp:32, from /usr/include/cif++/category.hpp:29: @@ -920,6 +933,17 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = clipper::Coord_grid; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = pdb_redo::StatsCollector::cmpGPt; _Alloc = std::allocator >]’: /usr/include/c++/13/bits/stl_tree.h:2458:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, pdb_redo::StatsCollector::cmpGPt, std::allocator > >::const_iterator’ changed in GCC 7.1 +In file included from /usr/include/c++/13/vector:72, + from /usr/include/cif++/forward_decl.hpp:32, + from /usr/include/cif++/category.hpp:29, + from /usr/include/cif++/datablock.hpp:29, + from /usr/include/cif++/file.hpp:32, + from /usr/include/cif++.hpp:30, + from /build/reproducible-path/libpdb-redo-3.0.5/src/Symmetry-2.cpp:30: +/usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {clipper::Coord_orth}; _Tp = clipper::Coord_orth; _Alloc = std::allocator]’: +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/regex:56, from /usr/include/cif++/condition.hpp:34: In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = clipper::Coord_grid; _Tp = double; _Compare = pdb_redo::StatsCollector::cmpGPt; _Alloc = std::allocator >]’, @@ -948,6 +972,20 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {clipper::Coord_orth}; _Tp = clipper::Coord_orth; _Alloc = std::allocator]’, + inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = clipper::Coord_orth; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from ‘clipper::Coord_orth pdb_redo::CalculateOffsetForCell(const cif::mm::structure&, const clipper::Spacegroup&, const clipper::Cell&)’ at /build/reproducible-path/libpdb-redo-3.0.5/src/Symmetry-2.cpp:59:22: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {clipper::RTop_orth}; _Tp = clipper::RTop_orth; _Alloc = std::allocator]’: +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {clipper::RTop_orth}; _Tp = clipper::RTop_orth; _Alloc = std::allocator]’: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {cif::mm::atom&, float&}; _Tp = pdb_redo::AtomData; _Alloc = std::allocator]’: /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: @@ -966,8 +1004,6 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 92%] Building CXX object CMakeFiles/pdb-redo.dir/src/Restraints.cpp.o -/usr/bin/c++ -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.0.5/include -I/build/reproducible-path/libpdb-redo-3.0.5/obj-arm-linux-gnueabihf -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.0.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++17 -fPIC -MD -MT CMakeFiles/pdb-redo.dir/src/Restraints.cpp.o -MF CMakeFiles/pdb-redo.dir/src/Restraints.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/Restraints.cpp.o -c /build/reproducible-path/libpdb-redo-3.0.5/src/Restraints.cpp In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = std::pair; _Compare = std::less >; _Alloc = std::allocator, std::pair > >]’, inlined from ‘void pdb_redo::StatsCollector::initialize()’ at /build/reproducible-path/libpdb-redo-3.0.5/src/Statistics.cpp:402:21: /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, std::pair >, std::_Select1st, std::pair > >, std::less >, std::allocator, std::pair > > >::const_iterator’ changed in GCC 7.1 @@ -1140,7 +1176,7 @@ create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install - cd obj-arm-linux-gnueabihf && make -j3 install DESTDIR=/build/reproducible-path/libpdb-redo-3.0.5/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-arm-linux-gnueabihf && make -j6 install DESTDIR=/build/reproducible-path/libpdb-redo-3.0.5/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/libpdb-redo-3.0.5/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/build/reproducible-path/libpdb-redo-3.0.5 -B/build/reproducible-path/libpdb-redo-3.0.5/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -1156,19 +1192,19 @@ -- Installing: /build/reproducible-path/libpdb-redo-3.0.5/debian/tmp/usr/lib/arm-linux-gnueabihf/cmake/pdb-redo/pdb-redoTargets.cmake -- Installing: /build/reproducible-path/libpdb-redo-3.0.5/debian/tmp/usr/lib/arm-linux-gnueabihf/cmake/pdb-redo/pdb-redoTargets-none.cmake -- Installing: /build/reproducible-path/libpdb-redo-3.0.5/debian/tmp/usr/include/pdb-redo +-- Installing: /build/reproducible-path/libpdb-redo-3.0.5/debian/tmp/usr/include/pdb-redo/BondMap.hpp -- Installing: /build/reproducible-path/libpdb-redo-3.0.5/debian/tmp/usr/include/pdb-redo/SkipList.hpp --- Installing: /build/reproducible-path/libpdb-redo-3.0.5/debian/tmp/usr/include/pdb-redo/Restraints.hpp --- Installing: /build/reproducible-path/libpdb-redo-3.0.5/debian/tmp/usr/include/pdb-redo/DistanceMap.hpp --- Installing: /build/reproducible-path/libpdb-redo-3.0.5/debian/tmp/usr/include/pdb-redo/Symmetry-2.hpp --- Installing: /build/reproducible-path/libpdb-redo-3.0.5/debian/tmp/usr/include/pdb-redo/Minimizer.hpp -- Installing: /build/reproducible-path/libpdb-redo-3.0.5/debian/tmp/usr/include/pdb-redo/Ramachandran.hpp +-- Installing: /build/reproducible-path/libpdb-redo-3.0.5/debian/tmp/usr/include/pdb-redo/DistanceMap.hpp -- Installing: /build/reproducible-path/libpdb-redo-3.0.5/debian/tmp/usr/include/pdb-redo/AtomShape.hpp --- Installing: /build/reproducible-path/libpdb-redo-3.0.5/debian/tmp/usr/include/pdb-redo/ResolutionCalculator.hpp --- Installing: /build/reproducible-path/libpdb-redo-3.0.5/debian/tmp/usr/include/pdb-redo/Compound.hpp +-- Installing: /build/reproducible-path/libpdb-redo-3.0.5/debian/tmp/usr/include/pdb-redo/ClipperWrapper.hpp +-- Installing: /build/reproducible-path/libpdb-redo-3.0.5/debian/tmp/usr/include/pdb-redo/Symmetry-2.hpp -- Installing: /build/reproducible-path/libpdb-redo-3.0.5/debian/tmp/usr/include/pdb-redo/Statistics.hpp --- Installing: /build/reproducible-path/libpdb-redo-3.0.5/debian/tmp/usr/include/pdb-redo/BondMap.hpp +-- Installing: /build/reproducible-path/libpdb-redo-3.0.5/debian/tmp/usr/include/pdb-redo/Compound.hpp -- Installing: /build/reproducible-path/libpdb-redo-3.0.5/debian/tmp/usr/include/pdb-redo/MapMaker.hpp --- Installing: /build/reproducible-path/libpdb-redo-3.0.5/debian/tmp/usr/include/pdb-redo/ClipperWrapper.hpp +-- Installing: /build/reproducible-path/libpdb-redo-3.0.5/debian/tmp/usr/include/pdb-redo/Minimizer.hpp +-- Installing: /build/reproducible-path/libpdb-redo-3.0.5/debian/tmp/usr/include/pdb-redo/ResolutionCalculator.hpp +-- Installing: /build/reproducible-path/libpdb-redo-3.0.5/debian/tmp/usr/include/pdb-redo/Restraints.hpp -- Installing: /build/reproducible-path/libpdb-redo-3.0.5/debian/tmp/usr/include/pdb-redo/exports.hpp -- Installing: /build/reproducible-path/libpdb-redo-3.0.5/debian/tmp/usr/lib/arm-linux-gnueabihf/cmake/pdb-redo/pdb-redoConfig.cmake -- Installing: /build/reproducible-path/libpdb-redo-3.0.5/debian/tmp/usr/lib/arm-linux-gnueabihf/cmake/pdb-redo/pdb-redoConfigVersion.cmake @@ -1194,8 +1230,8 @@ dh_md5sums dh_builddeb dpkg-deb: building package 'libpdb-redo-dev' in '../libpdb-redo-dev_3.0.5-2_armhf.deb'. -dpkg-deb: building package 'libpdb-redo3' in '../libpdb-redo3_3.0.5-2_armhf.deb'. dpkg-deb: building package 'libpdb-redo3-dbgsym' in '../libpdb-redo3-dbgsym_3.0.5-2_armhf.deb'. +dpkg-deb: building package 'libpdb-redo3' in '../libpdb-redo3_3.0.5-2_armhf.deb'. dpkg-genbuildinfo --build=binary -O../libpdb-redo_3.0.5-2_armhf.buildinfo dpkg-genchanges --build=binary -O../libpdb-redo_3.0.5-2_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1203,12 +1239,14 @@ 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/18791/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/18791/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/4494 and its subdirectories -I: Current time: Sun Apr 14 05:44:40 -12 2024 -I: pbuilder-time-stamp: 1713116680 +I: removing directory /srv/workspace/pbuilder/18791 and its subdirectories +I: Current time: Mon Apr 15 07:57:24 +14 2024 +I: pbuilder-time-stamp: 1713117444