Diff of the two buildlogs: -- --- b1/build.log 2025-11-08 23:08:42.619730417 +0000 +++ b2/build.log 2025-11-08 23:09:53.335811098 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Nov 8 11:07:27 -12 2025 -I: pbuilder-time-stamp: 1762643247 +I: Current time: Sat Dec 12 19:31:43 +14 2026 +I: pbuilder-time-stamp: 1797053503 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -22,53 +22,85 @@ dpkg-source: info: unpacking libpdb-redo_3.3.0-2.debian.tar.xz I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1641368/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2969497/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Dec 12 05:31 /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/2969497/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2969497/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='forky' - HOME='/root' - HOST_ARCH='arm64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="3" [2]="3" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.3.3(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 nocheck' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='4b3cbf59d1bd4de583a5eb0c3b0bc520' - 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='1641368' - PS1='# ' - PS2='> ' + INVOCATION_ID=103d43cb08db4522a8cb2880f384c0be + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=2969497 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.hyY7r5KV/pbuilderrc_gzyW --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.hyY7r5KV/b1 --logfile b1/build.log libpdb-redo_3.3.0-2.dsc' - SUDO_GID='109' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.hyY7r5KV/pbuilderrc_pTiU --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.hyY7r5KV/b2 --logfile b2/build.log libpdb-redo_3.3.0-2.dsc' + SUDO_GID=109 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink04-arm64 6.12.48+deb13-cloud-arm64 #1 SMP Debian 6.12.48-1 (2025-09-20) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.12.48+deb13-cloud-arm64 #1 SMP Debian 6.12.48-1 (2025-09-20) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1641368/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2969497/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -256,7 +288,7 @@ Get: 130 http://deb.debian.org/debian forky/main arm64 libgslcblas0 arm64 2.8+dfsg-5.1 [91.8 kB] Get: 131 http://deb.debian.org/debian forky/main arm64 libgsl28 arm64 2.8+dfsg-5.1 [921 kB] Get: 132 http://deb.debian.org/debian forky/main arm64 libgsl-dev arm64 2.8+dfsg-5.1 [1177 kB] -Fetched 132 MB in 1s (202 MB/s) +Fetched 132 MB in 1s (246 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19964 files and directories currently installed.) @@ -799,7 +831,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/libpdb-redo-3.3.0/ && 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_3.3.0-2_source.changes +I: user script /srv/workspace/pbuilder/2969497/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/2969497/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/libpdb-redo-3.3.0/ && 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_3.3.0-2_source.changes dpkg-buildpackage: info: source package libpdb-redo dpkg-buildpackage: info: source version 3.3.0-2 dpkg-buildpackage: info: source distribution unstable @@ -816,7 +852,7 @@ debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/libpdb-redo-3.3.0' dh_auto_configure -- -DBUILD_SHARED_LIBS=ON -DPDB_REDO_BUILD_TESTS=ON -DBUILD_MINIMIZER=OFF - cd obj-aarch64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/aarch64-linux-gnu -DBUILD_SHARED_LIBS=ON -DPDB_REDO_BUILD_TESTS=ON -DBUILD_MINIMIZER=OFF .. + cd obj-aarch64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/aarch64-linux-gnu -DBUILD_TESTING:BOOL=OFF -DBUILD_SHARED_LIBS=ON -DPDB_REDO_BUILD_TESTS=ON -DBUILD_MINIMIZER=OFF .. -- The CXX compiler identification is GNU 15.2.0 -- The C compiler identification is GNU 15.2.0 -- Detecting CXX compiler ABI info @@ -855,7 +891,7 @@ -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success -- Performing Test COMPILER_HAS_DEPRECATED_ATTR -- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success --- Configuring done (2.5s) +-- Configuring done (2.7s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: @@ -881,30 +917,30 @@ make[3]: Leaving directory '/build/reproducible-path/libpdb-redo-3.3.0/obj-aarch64-linux-gnu' make -f CMakeFiles/pdb-redo.dir/build.make CMakeFiles/pdb-redo.dir/build make[3]: Entering directory '/build/reproducible-path/libpdb-redo-3.3.0/obj-aarch64-linux-gnu' -[ 5%] Building CXX object CMakeFiles/pdb-redo.dir/src/AtomShape.cpp.o -[ 17%] Building CXX object CMakeFiles/pdb-redo.dir/src/Compound.cpp.o -[ 17%] Building CXX object CMakeFiles/pdb-redo.dir/src/ClipperWrapper.cpp.o -/usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.3.0/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.3.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -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-3.3.0/src/Compound.cpp -[ 29%] Building CXX object CMakeFiles/pdb-redo.dir/src/SkipList.cpp.o -[ 29%] Building CXX object CMakeFiles/pdb-redo.dir/src/MapMaker.cpp.o +[ 23%] Building CXX object CMakeFiles/pdb-redo.dir/src/MapMaker.cpp.o +[ 23%] Building CXX object CMakeFiles/pdb-redo.dir/src/DistanceMap.cpp.o +[ 23%] Building CXX object CMakeFiles/pdb-redo.dir/src/ClipperWrapper.cpp.o +[ 30%] Building CXX object CMakeFiles/pdb-redo.dir/src/AtomShape.cpp.o +[ 38%] Building CXX object CMakeFiles/pdb-redo.dir/src/Ramachandran.cpp.o /usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.3.0/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.3.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -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-3.3.0/src/AtomShape.cpp /usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.3.0/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.3.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -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-3.3.0/src/ClipperWrapper.cpp -[ 35%] Building CXX object CMakeFiles/pdb-redo.dir/src/Ramachandran.cpp.o +/usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.3.0/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.3.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -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-3.3.0/src/DistanceMap.cpp /usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.3.0/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.3.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -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-3.3.0/src/MapMaker.cpp +[ 46%] Building CXX object CMakeFiles/pdb-redo.dir/src/BondMap.cpp.o /usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.3.0/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.3.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -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-3.3.0/src/Ramachandran.cpp -[ 41%] Building CXX object CMakeFiles/pdb-redo.dir/src/TLS.cpp.o -[ 47%] Building CXX object CMakeFiles/pdb-redo.dir/src/Version.cpp.o -/usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.3.0/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.3.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -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-3.3.0/src/SkipList.cpp 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -MD -MT CMakeFiles/pdb-redo.dir/src/Version.cpp.o -MF CMakeFiles/pdb-redo.dir/src/Version.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/Version.cpp.o -c /build/reproducible-path/libpdb-redo-3.3.0/src/Version.cpp -[ 58%] Building CXX object CMakeFiles/pdb-redo.dir/src/ResolutionCalculator.cpp.o -[ 58%] Building CXX object CMakeFiles/pdb-redo.dir/src/Statistics.cpp.o -[ 64%] Building CXX object CMakeFiles/pdb-redo.dir/src/BondMap.cpp.o -/usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.3.0/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.3.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra 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/build/reproducible-path/libpdb-redo-3.3.0/src/BondMap.cpp +[ 53%] Building CXX object CMakeFiles/pdb-redo.dir/src/ResolutionCalculator.cpp.o +/usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.3.0/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.3.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -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-3.3.0/src/ResolutionCalculator.cpp +[ 61%] Building CXX object CMakeFiles/pdb-redo.dir/src/Statistics.cpp.o /usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.3.0/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.3.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -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-3.3.0/src/Statistics.cpp -[ 70%] Building CXX object CMakeFiles/pdb-redo.dir/src/DistanceMap.cpp.o -/usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.3.0/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.3.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -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-3.3.0/src/DistanceMap.cpp +[ 69%] Building CXX object CMakeFiles/pdb-redo.dir/src/TLS.cpp.o +/usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.3.0/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.3.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -MD -MT CMakeFiles/pdb-redo.dir/src/TLS.cpp.o -MF CMakeFiles/pdb-redo.dir/src/TLS.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/TLS.cpp.o -c /build/reproducible-path/libpdb-redo-3.3.0/src/TLS.cpp +[ 76%] Building CXX object CMakeFiles/pdb-redo.dir/src/Compound.cpp.o +[ 84%] Building CXX object CMakeFiles/pdb-redo.dir/src/SkipList.cpp.o +[ 92%] Building CXX object CMakeFiles/pdb-redo.dir/src/Version.cpp.o +/usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.3.0/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.3.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -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-3.3.0/src/Compound.cpp +/usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.3.0/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.3.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -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-3.3.0/src/SkipList.cpp +/usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.3.0/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.3.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -MD -MT CMakeFiles/pdb-redo.dir/src/Version.cpp.o -MF CMakeFiles/pdb-redo.dir/src/Version.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/Version.cpp.o -c /build/reproducible-path/libpdb-redo-3.3.0/src/Version.cpp In file included from /usr/include/c++/15/bits/stl_algobase.h:64, from /usr/include/c++/15/string:53, from /usr/include/c++/15/bits/locale_classes.h:42, @@ -924,7 +960,7 @@ /build/reproducible-path/libpdb-redo-3.3.0/src/MapMaker.cpp:1135:22: 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 1135 | auto mFo = mFbData[ih] - mFdData[ih]; | ^~~ -[ 76%] Linking CXX shared library libpdb-redo.so +[100%] Linking CXX shared library libpdb-redo.so /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb-redo.dir/link.txt --verbose=1 /usr/lib/aarch64-linux-gnu/libcifpp.so.7.0.9: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libclipper-ccp4.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -939,247 +975,11 @@ /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.3.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -Wl,--dependency-file=CMakeFiles/pdb-redo.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libpdb-redo.so.3.3 -o libpdb-redo.so.3.3.0 "CMakeFiles/pdb-redo.dir/src/AtomShape.cpp.o" "CMakeFiles/pdb-redo.dir/src/BondMap.cpp.o" "CMakeFiles/pdb-redo.dir/src/ClipperWrapper.cpp.o" "CMakeFiles/pdb-redo.dir/src/Compound.cpp.o" "CMakeFiles/pdb-redo.dir/src/DistanceMap.cpp.o" "CMakeFiles/pdb-redo.dir/src/MapMaker.cpp.o" "CMakeFiles/pdb-redo.dir/src/Ramachandran.cpp.o" "CMakeFiles/pdb-redo.dir/src/ResolutionCalculator.cpp.o" "CMakeFiles/pdb-redo.dir/src/SkipList.cpp.o" "CMakeFiles/pdb-redo.dir/src/Statistics.cpp.o" "CMakeFiles/pdb-redo.dir/src/TLS.cpp.o" "CMakeFiles/pdb-redo.dir/src/Version.cpp.o" /usr/lib/aarch64-linux-gnu/libcifpp.so.7.0.9 /usr/lib/aarch64-linux-gnu/libgsl.so /usr/lib/aarch64-linux-gnu/libclipper-ccp4.so /usr/lib/aarch64-linux-gnu/libclipper-contrib.so /usr/lib/aarch64-linux-gnu/libclipper-core.so /usr/lib/aarch64-linux-gnu/libccp4c.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libgslcblas.so /usr/bin/cmake -E cmake_symlink_library libpdb-redo.so.3.3.0 libpdb-redo.so.3.3 libpdb-redo.so make[3]: Leaving directory '/build/reproducible-path/libpdb-redo-3.3.0/obj-aarch64-linux-gnu' -[ 76%] Built target pdb-redo -make -f test/CMakeFiles/pdb-redo-unit-test.dir/build.make test/CMakeFiles/pdb-redo-unit-test.dir/depend -make -f test/CMakeFiles/restr2ccd-test.dir/build.make test/CMakeFiles/restr2ccd-test.dir/depend -make[3]: Entering directory '/build/reproducible-path/libpdb-redo-3.3.0/obj-aarch64-linux-gnu' -cd /build/reproducible-path/libpdb-redo-3.3.0/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libpdb-redo-3.3.0 /build/reproducible-path/libpdb-redo-3.3.0/test /build/reproducible-path/libpdb-redo-3.3.0/obj-aarch64-linux-gnu /build/reproducible-path/libpdb-redo-3.3.0/obj-aarch64-linux-gnu/test /build/reproducible-path/libpdb-redo-3.3.0/obj-aarch64-linux-gnu/test/CMakeFiles/pdb-redo-unit-test.dir/DependInfo.cmake "--color=" -make[3]: Entering directory '/build/reproducible-path/libpdb-redo-3.3.0/obj-aarch64-linux-gnu' -cd /build/reproducible-path/libpdb-redo-3.3.0/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libpdb-redo-3.3.0 /build/reproducible-path/libpdb-redo-3.3.0/test /build/reproducible-path/libpdb-redo-3.3.0/obj-aarch64-linux-gnu /build/reproducible-path/libpdb-redo-3.3.0/obj-aarch64-linux-gnu/test /build/reproducible-path/libpdb-redo-3.3.0/obj-aarch64-linux-gnu/test/CMakeFiles/restr2ccd-test.dir/DependInfo.cmake "--color=" -make[3]: Leaving directory '/build/reproducible-path/libpdb-redo-3.3.0/obj-aarch64-linux-gnu' -make -f test/CMakeFiles/restr2ccd-test.dir/build.make test/CMakeFiles/restr2ccd-test.dir/build -make[3]: Leaving directory '/build/reproducible-path/libpdb-redo-3.3.0/obj-aarch64-linux-gnu' -make -f test/CMakeFiles/pdb-redo-unit-test.dir/build.make test/CMakeFiles/pdb-redo-unit-test.dir/build -make[3]: Entering directory '/build/reproducible-path/libpdb-redo-3.3.0/obj-aarch64-linux-gnu' -make[3]: Entering directory '/build/reproducible-path/libpdb-redo-3.3.0/obj-aarch64-linux-gnu' -[ 88%] Building CXX object test/CMakeFiles/pdb-redo-unit-test.dir/pdb-redo-unit-test.cpp.o -[ 88%] Building CXX object test/CMakeFiles/restr2ccd-test.dir/restr2ccd-test.cpp.o -cd /build/reproducible-path/libpdb-redo-3.3.0/obj-aarch64-linux-gnu/test && /usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -I/build/reproducible-path/libpdb-redo-3.3.0/include -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.3.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -MD -MT test/CMakeFiles/restr2ccd-test.dir/restr2ccd-test.cpp.o -MF CMakeFiles/restr2ccd-test.dir/restr2ccd-test.cpp.o.d -o CMakeFiles/restr2ccd-test.dir/restr2ccd-test.cpp.o -c /build/reproducible-path/libpdb-redo-3.3.0/test/restr2ccd-test.cpp -cd /build/reproducible-path/libpdb-redo-3.3.0/obj-aarch64-linux-gnu/test && /usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -I/build/reproducible-path/libpdb-redo-3.3.0/include -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.3.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -MD -MT test/CMakeFiles/pdb-redo-unit-test.dir/pdb-redo-unit-test.cpp.o -MF CMakeFiles/pdb-redo-unit-test.dir/pdb-redo-unit-test.cpp.o.d -o CMakeFiles/pdb-redo-unit-test.dir/pdb-redo-unit-test.cpp.o -c /build/reproducible-path/libpdb-redo-3.3.0/test/pdb-redo-unit-test.cpp -[ 94%] Linking CXX executable restr2ccd-test -cd /build/reproducible-path/libpdb-redo-3.3.0/obj-aarch64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/restr2ccd-test.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.3.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/restr2ccd-test.dir/link.d "CMakeFiles/restr2ccd-test.dir/restr2ccd-test.cpp.o" -o restr2ccd-test -Wl,-rpath,/build/reproducible-path/libpdb-redo-3.3.0/obj-aarch64-linux-gnu ../libpdb-redo.so.3.3.0 /usr/lib/libCatch2.a /usr/lib/aarch64-linux-gnu/libcifpp.so.7.0.9 /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libgsl.so /usr/lib/aarch64-linux-gnu/libgslcblas.so /usr/lib/aarch64-linux-gnu/libclipper-ccp4.so /usr/lib/aarch64-linux-gnu/libclipper-contrib.so /usr/lib/aarch64-linux-gnu/libclipper-core.so /usr/lib/aarch64-linux-gnu/libccp4c.so -make[3]: Leaving directory '/build/reproducible-path/libpdb-redo-3.3.0/obj-aarch64-linux-gnu' -[ 94%] Built target restr2ccd-test -[100%] Linking CXX executable pdb-redo-unit-test -cd /build/reproducible-path/libpdb-redo-3.3.0/obj-aarch64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb-redo-unit-test.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.3.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pdb-redo-unit-test.dir/link.d "CMakeFiles/pdb-redo-unit-test.dir/pdb-redo-unit-test.cpp.o" -o pdb-redo-unit-test -Wl,-rpath,/build/reproducible-path/libpdb-redo-3.3.0/obj-aarch64-linux-gnu ../libpdb-redo.so.3.3.0 /usr/lib/libCatch2.a /usr/lib/aarch64-linux-gnu/libcifpp.so.7.0.9 /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libgsl.so /usr/lib/aarch64-linux-gnu/libgslcblas.so /usr/lib/aarch64-linux-gnu/libclipper-ccp4.so /usr/lib/aarch64-linux-gnu/libclipper-contrib.so /usr/lib/aarch64-linux-gnu/libclipper-core.so /usr/lib/aarch64-linux-gnu/libccp4c.so -make[3]: Leaving directory '/build/reproducible-path/libpdb-redo-3.3.0/obj-aarch64-linux-gnu' -[100%] Built target pdb-redo-unit-test +[100%] Built target pdb-redo make[2]: Leaving directory '/build/reproducible-path/libpdb-redo-3.3.0/obj-aarch64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/libpdb-redo-3.3.0/obj-aarch64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/libpdb-redo-3.3.0/obj-aarch64-linux-gnu' - dh_auto_test - cd obj-aarch64-linux-gnu && make -j12 test ARGS\+=--verbose ARGS\+=-j12 -make[1]: Entering directory '/build/reproducible-path/libpdb-redo-3.3.0/obj-aarch64-linux-gnu' -Running tests... -/usr/bin/ctest --force-new-ctest-process --verbose -j12 -UpdateCTestConfiguration from :/build/reproducible-path/libpdb-redo-3.3.0/obj-aarch64-linux-gnu/DartConfiguration.tcl -Parse Config file:/build/reproducible-path/libpdb-redo-3.3.0/obj-aarch64-linux-gnu/DartConfiguration.tcl -UpdateCTestConfiguration from :/build/reproducible-path/libpdb-redo-3.3.0/obj-aarch64-linux-gnu/DartConfiguration.tcl -Parse Config file:/build/reproducible-path/libpdb-redo-3.3.0/obj-aarch64-linux-gnu/DartConfiguration.tcl -Test project /build/reproducible-path/libpdb-redo-3.3.0/obj-aarch64-linux-gnu -Constructing a list of tests -Done constructing a list of tests -Updating test list for fixtures -Added 0 tests to meet fixture requirements -Checking test dependency graph... -Checking test dependency graph end -Connected to MAKE jobserver -test 1 - Start 1: pdb-redo-unit-test - -1: Test command: /build/reproducible-path/libpdb-redo-3.3.0/obj-aarch64-linux-gnu/test/pdb-redo-unit-test "--data-dir" "/build/reproducible-path/libpdb-redo-3.3.0/test" -1: Working Directory: /build/reproducible-path/libpdb-redo-3.3.0/obj-aarch64-linux-gnu/test -1: Test timeout computed to be: 1500 -test 2 - Start 2: restr2ccd-test - -2: Test command: /build/reproducible-path/libpdb-redo-3.3.0/obj-aarch64-linux-gnu/test/restr2ccd-test "--data-dir" "/build/reproducible-path/libpdb-redo-3.3.0/test" -2: Working Directory: /build/reproducible-path/libpdb-redo-3.3.0/obj-aarch64-linux-gnu/test -2: Test timeout computed to be: 1500 -2: CCD components.cif resource was not found -2: Randomness seeded to: 2777166917 -2: Could not load the mon_lib_list.cif file from CCP4, please make sure you have installed CCP4 and sourced the environment. -2: -2: Configuration error: -2: -2: The attempt to retrieve compound information for "Z57-a" failed. -2: -2: This information is searched for in a CCD file called components.cif or -2: components.cif.gz which should be located in one of the following directories: -2: -2: "/var/cache/libcifpp" -2: "/usr/share/libcifpp" -2: -2: (Note that you can add a directory to the search paths by setting the -2: LIBCIFPP_DATA_DIR environmental variable) -2: -2: On Linux an optional cron script might have been installed that automatically updates -2: components.cif and mmCIF dictionary files. This script only works when the file -2: libcifpp.conf contains an uncommented line with the text: -2: -2: update=true -2: -2: If you do not have a working cron script, you can manually update the files -2: in /var/cache/libcifpp using the following commands: -2: -2: curl -o /var/cache/libcifpp/components.cif https://files.wwpdb.org/pub/pdb/data/monomers/components.cif -2: curl -o /var/cache/libcifpp/mmcif_pdbx.dic https://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic -2: curl -o /var/cache/libcifpp/mmcif_ma.dic https://github.com/ihmwg/ModelCIF/raw/master/dist/mmcif_ma.dic -2: -2: The current order of compound factory objects is: -2: -2: CCD components file: "/build/reproducible-path/libpdb-redo-3.3.0/test/minimal-components.cif" -2: =============================================================================== -2: All tests passed (12 assertions in 1 test case) -2: -1/2 Test #2: restr2ccd-test ................... Passed 0.03 sec -1: Randomness seeded to: 1610248571 -1: Reading map from "/build/reproducible-path/libpdb-redo-3.3.0/test/../examples/1cbs_map.mtz" -1: with labels: FB: FWT,PHWT -1: with labels: FD: DELFWT,PHDELWT -1: with labels: FA: FAN,PHAN -1: with labels: FO: FP,SIGFP -1: with labels: FC: FC_ALL,PHIC_ALL -1: Read Xmaps with sampling rate: 1.5 -1: stored resolution: 1.79991 -1: calculated reshi = 1.80009 reslo = 7.99918 -1: spacegroup: P 21 21 21 -1: cell: Cell ( 45.65, 47.56, 77.61, 90, 90, 90) -1: grid: Nuvw = ( 80, 80, 132) -1: R-factor : 0.180853 -1: Free R-factor : 0.184876 -1: Loading component LYS... done -1: Loading component ILE... done -1: Loading component ARG... done -1: Loading component GLU... done -1: Loading component LEU... done -1: Loading component VAL... done -1: Loading component MET... done -1: Loading component ALA... done -1: Loading component GLN... done -1: Loading component ASP... done -1: Loading component THR... done -1: Loading component TYR... done -1: Loading component CYS... done -1: Loading component REA... done -1: Loading component HOH... done -1: -1: Intercept & gradient before LS: -0.0761355 (0.000425541) 0.113376 (0.000666367) -1: -1: Rescale SD(delta-rho) using Q-Q plot for asym A: -1: ====================================================== -1: Input & updated SD(delta-rho): 0.123854 ; 0.137896 -1: -1: -1: Intercept & gradient before LS: 0.112013 (0.00322152) -0.0975523 (0.00506053) -1: -1: Rescale SD(delta-rho) using Q-Q plot for asym B: -1: ====================================================== -1: Input & updated SD(delta-rho): 0.123854 ; 0.111772 -1: -1: -1: Intercept & gradient before LS: -0.038699 (0.00144741) -0.0997851 (0.00226694) -1: -1: Rescale SD(delta-rho) using Q-Q plot for asym C: -1: ====================================================== -1: Input & updated SD(delta-rho): 0.123854 ; 0.111495 -1: -1: Calculating radii with B Factor 24.9788 -1: Radius for atom with type N is 1.03582 -1: Radius for atom with type C is 1.04896 -1: Radius for atom with type O is 1.02401 -1: Radius for atom with type S is 1.01993 -1: skipping water in bond map calculation -1: The asym ID's of ndb_poly_seq_scheme and pdbx_poly_seq_scheme are not equal, dropping ndb_poly_seq_scheme -1: Reading map from "/build/reproducible-path/libpdb-redo-3.3.0/test/../examples/1cbs_map.mtz" -1: with labels: FB: FWT,PHWT -1: with labels: FD: DELFWT,PHDELWT -1: with labels: FA: FAN,PHAN -1: with labels: FO: FP,SIGFP -1: with labels: FC: FC_ALL,PHIC_ALL -1: Read Xmaps with sampling rate: 0.75 -1: stored resolution: 1.79991 -1: calculated reshi = 1.80009 reslo = 7.99918 -1: spacegroup: P 21 21 21 -1: cell: Cell ( 45.65, 47.56, 77.61, 90, 90, 90) -1: grid: Nuvw = ( 40, 40, 72) -1: R-factor : 0.180853 -1: Free R-factor : 0.184876 -1: Loading component U_K... -1: Configuration error: -1: -1: The attempt to retrieve compound information for "U_K" failed. -1: -1: This information is searched for in a CCD file called components.cif or -1: components.cif.gz which should be located in one of the following directories: -1: -1: "/var/cache/libcifpp" -1: "/usr/share/libcifpp" -1: -1: (Note that you can add a directory to the search paths by setting the -1: LIBCIFPP_DATA_DIR environmental variable) -1: -1: On Linux an optional cron script might have been installed that automatically updates -1: components.cif and mmCIF dictionary files. This script only works when the file -1: libcifpp.conf contains an uncommented line with the text: -1: -1: update=true -1: -1: If you do not have a working cron script, you can manually update the files -1: in /var/cache/libcifpp using the following commands: -1: -1: curl -o /var/cache/libcifpp/components.cif https://files.wwpdb.org/pub/pdb/data/monomers/components.cif -1: curl -o /var/cache/libcifpp/mmcif_pdbx.dic https://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic -1: curl -o /var/cache/libcifpp/mmcif_ma.dic https://github.com/ihmwg/ModelCIF/raw/master/dist/mmcif_ma.dic -1: -1: The current order of compound factory objects is: -1: -1: CCD components file: "/build/reproducible-path/libpdb-redo-3.3.0/test/minimal-components.cif" -1: done -1: -1: Intercept & gradient before LS: -0.0615663 (0.000573911) 0.0873704 (0.000898727) -1: -1: Rescale SD(delta-rho) using Q-Q plot for asym A: -1: ====================================================== -1: Input & updated SD(delta-rho): 0.11509 ; 0.125146 -1: -1: -1: Intercept & gradient before LS: 0.0679982 (0.0146148) -0.0420235 (0.0228119) -1: -1: Rescale SD(delta-rho) using Q-Q plot for asym B: -1: ====================================================== -1: Input & updated SD(delta-rho): 0.11509 ; 0.110254 -1: -1: -1: Intercept & gradient before LS: -0.00860157 (0.000800545) -0.185508 (0.00125356) -1: -1: Rescale SD(delta-rho) using Q-Q plot for asym C: -1: ====================================================== -1: Input & updated SD(delta-rho): 0.11509 ; 0.09374 -1: -1: Calculating radii with B Factor 24.9788 -1: Radius for atom with type N is 1.03582 -1: Radius for atom with type C is 1.04896 -1: Radius for atom with type O is 1.02401 -1: Radius for atom with type S is 1.01993 -1: skipping water in bond map calculation -1: Missing compound bond info for U_K -1: Missing information for compound 'U_K' -1: Missing bond information for compound U_K -1: The asym ID's of ndb_poly_seq_scheme and pdbx_poly_seq_scheme are not equal, dropping ndb_poly_seq_scheme -1: skipping water in bond map calculation -1: skipping water in bond map calculation -1: =============================================================================== -1: All tests passed (738136 assertions in 7 test cases) -1: -2/2 Test #1: pdb-redo-unit-test ............... Passed 2.33 sec - -100% tests passed, 0 tests failed out of 2 - -Total Test time (real) = 2.33 sec -make[1]: Leaving directory '/build/reproducible-path/libpdb-redo-3.3.0/obj-aarch64-linux-gnu' +dh: command-omitted: The call to "dh_auto_test" was omitted due to "DEB_BUILD_OPTIONS=nocheck" create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install @@ -1240,9 +1040,9 @@ dh_gencontrol dh_md5sums dh_builddeb +dpkg-deb: building package 'libpdb-redo3.3-dbgsym' in '../libpdb-redo3.3-dbgsym_3.3.0-2_arm64.deb'. dpkg-deb: building package 'libpdb-redo-dev' in '../libpdb-redo-dev_3.3.0-2_arm64.deb'. dpkg-deb: building package 'libpdb-redo3.3' in '../libpdb-redo3.3_3.3.0-2_arm64.deb'. -dpkg-deb: building package 'libpdb-redo3.3-dbgsym' in '../libpdb-redo3.3-dbgsym_3.3.0-2_arm64.deb'. dpkg-genbuildinfo --build=binary -O../libpdb-redo_3.3.0-2_arm64.buildinfo dpkg-genchanges --build=binary -O../libpdb-redo_3.3.0-2_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1250,12 +1050,14 @@ 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/2969497/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2969497/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/1641368 and its subdirectories -I: Current time: Sat Nov 8 11:08:41 -12 2025 -I: pbuilder-time-stamp: 1762643321 +I: removing directory /srv/workspace/pbuilder/2969497 and its subdirectories +I: Current time: Sat Dec 12 19:32:51 +14 2026 +I: pbuilder-time-stamp: 1797053571