Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/g/gemmi/gemmi_0.5.1+ds-1_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/gemmi-0.5.1+ds-1dq0b2tos/gemmi_0.5.1+ds-1_amd64.buildinfo Get source package info: gemmi=0.5.1+ds-1 Source URL: http://snapshot.notset.fr/mr/package/gemmi/0.5.1+ds-1/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.71-2 automake=1:1.16.5-1.1 autopoint=0.21-4 autotools-dev=20180224.1+nmu1 base-files=12 base-passwd=3.5.52 bash=5.1-5 binutils=2.37-10 binutils-common=2.37-10 binutils-x86-64-linux-gnu=2.37-10 bsdextrautils=2.37.2-4 bsdutils=1:2.37.2-4 build-essential=12.9 bzip2=1.0.8-5 cmake=3.22.1-1+b1 cmake-data=3.22.1-1 coreutils=8.32-4.1 cpp=4:11.2.0-2 cpp-11=11.2.0-12 dash=0.5.11+git20210903+057cd650a4ed-3 debconf=1.5.79 debhelper=13.5.2 debianutils=5.5-1 dh-autoreconf=20 dh-elpa-helper=2.0.9 dh-python=5.20211213 dh-strip-nondeterminism=1.12.1-1 diffutils=1:3.7-5 dpkg=1.21.1 dpkg-dev=1.21.1 dwz=0.14-1 emacsen-common=3.0.4 file=1:5.41-2 findutils=4.8.0-1 g++=4:11.2.0-2 g++-11=11.2.0-12 gcc=4:11.2.0-2 gcc-11=11.2.0-12 gcc-11-base=11.2.0-12 gettext=0.21-4 gettext-base=0.21-4 grep=3.7-1 groff-base=1.22.4-7 gzip=1.10-4 help2man=1.48.5 hostname=3.23 init-system-helpers=1.61 intltool-debian=0.35.0+20060710.5 libacl1=2.3.1-1 libarchive-zip-perl=1.68-1 libarchive13=3.4.3-2+b1 libasan6=11.2.0-12 libatomic1=11.2.0-12 libattr1=1:2.5.1-1 libaudit-common=1:3.0.6-1 libaudit1=1:3.0.6-1+b1 libbinutils=2.37-10 libblkid1=2.37.2-4 libbrotli1=1.0.9-2+b3 libbz2-1.0=1.0.8-5 libc-bin=2.33-1 libc-dev-bin=2.33-1 libc6=2.33-1 libc6-dev=2.33-1 libcap-ng0=0.7.9-2.2+b1 libcap2=1:2.44-1 libcc1-0=11.2.0-12 libcom-err2=1.46.4-1 libcrypt-dev=1:4.4.26-1 libcrypt1=1:4.4.26-1 libctf-nobfd0=2.37-10 libctf0=2.37-10 libcurl4=7.79.1-2 libdb5.3=5.3.28+dfsg1-0.8 libdebconfclient0=0.261 libdebhelper-perl=13.5.2 libdpkg-perl=1.21.1 libelf1=0.186-1 libexpat1=2.4.1-3 libexpat1-dev=2.4.1-3 libffi8=3.4.2-3 libfile-stripnondeterminism-perl=1.12.1-1 libgcc-11-dev=11.2.0-12 libgcc-s1=11.2.0-12 libgcrypt20=1.9.4-4 libgdbm-compat4=1.22-1 libgdbm6=1.22-1 libgmp10=2:6.2.1+dfsg-3 libgnutls30=3.7.2-2 libgomp1=11.2.0-12 libgpg-error0=1.42-3 libgssapi-krb5-2=1.18.3-7 libhogweed6=3.7.3-1 libicu67=67.1-7 libidn2-0=2.3.2-2 libisl23=0.24-2 libitm1=11.2.0-12 libjs-jquery=3.5.1+dfsg+~3.5.5-8 libjs-sphinxdoc=4.3.1-2 libjs-underscore=1.9.1~dfsg-4 libjsoncpp25=1.9.5-2 libk5crypto3=1.18.3-7 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-7 libkrb5support0=1.18.3-7 libldap-2.4-2=2.4.59+dfsg-1 liblocale-gettext-perl=1.07-4+b1 liblsan0=11.2.0-12 liblz4-1=1.9.3-2 liblzma5=5.2.5-2 libmagic-mgc=1:5.41-2 libmagic1=1:5.41-2 libmount1=2.37.2-4 libmpc3=1.2.1-1 libmpdec3=2.5.1-2 libmpfr6=4.1.0-3 libncurses6=6.3-1 libncursesw6=6.3-1 libnettle8=3.7.3-1 libnghttp2-14=1.43.0-1 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libp11-kit0=0.24.0-6 libpam-modules=1.4.0-11 libpam-modules-bin=1.4.0-11 libpam-runtime=1.4.0-11 libpam0g=1.4.0-11 libpcre2-8-0=10.39-3 libpcre3=2:8.39-13 libperl5.32=5.32.1-6 libpipeline1=1.5.4-1 libprocps8=2:3.3.17-5 libpsl5=0.21.0-1.2 libpython3-dev=3.9.8-1 libpython3-stdlib=3.9.8-1 libpython3.9=3.9.9-1 libpython3.9-dev=3.9.9-1 libpython3.9-minimal=3.9.9-1 libpython3.9-stdlib=3.9.9-1 libquadmath0=11.2.0-12 libreadline8=8.1-2 librhash0=1.4.2-1 librtmp1=2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2=2.1.27+dfsg2-2 libsasl2-modules-db=2.1.27+dfsg2-2 libseccomp2=2.5.3-2 libselinux1=3.3-1+b1 libsigsegv2=2.13-1 libsmartcols1=2.37.2-4 libsqlite3-0=3.36.0-2 libssh2-1=1.10.0-2 libssl1.1=1.1.1l-1 libstb-dev=0.0~git20200713.b42009b+ds-1 libstb0=0.0~git20200713.b42009b+ds-1 libstdc++-11-dev=11.2.0-12 libstdc++6=11.2.0-12 libsub-override-perl=0.09-2 libsystemd0=249.7-1 libtasn1-6=4.18.0-4 libtinfo6=6.3-1 libtirpc-common=1.3.2-2 libtirpc-dev=1.3.2-2 libtirpc3=1.3.2-2 libtool=2.4.6-15 libtsan0=11.2.0-12 libubsan1=11.2.0-12 libuchardet0=0.0.7-1 libudev1=249.7-1 libunistring2=0.9.10-6 libuuid1=2.37.2-4 libuv1=1.42.0-1 libxml2=2.9.12+dfsg-5+b1 libzstd1=1.4.8+dfsg-3 linux-libc-dev=5.15.5-1 login=1:4.8.1-2 lsb-base=11.1.0 m4=1.4.18-5 make=4.3-4.1 man-db=2.9.4-2 mawk=1.3.4.20200120-2 media-types=4.0.0 ncurses-base=6.3-1 ncurses-bin=6.3-1 patch=2.7.6-7 perl=5.32.1-6 perl-base=5.32.1-6 perl-modules-5.32=5.32.1-6 po-debconf=1.0.21+nmu1 procps=2:3.3.17-5 pybind11-dev=2.7.1-2 python3=3.9.8-1 python3-attr=20.3.0-1 python3-dev=3.9.8-1 python3-distutils=3.9.9-3 python3-importlib-metadata=4.6.4-1 python3-iniconfig=1.1.1-1 python3-lib2to3=3.9.9-3 python3-minimal=3.9.8-1 python3-more-itertools=8.10.0-2 python3-packaging=21.3-1 python3-pkg-resources=59.4.0-1 python3-pluggy=0.13.0-7.1 python3-py=1.10.0-1 python3-pybind11=2.7.1-2 python3-pyparsing=2.4.7-1 python3-pytest=6.2.5-1 python3-toml=0.10.2-1 python3-zipp=1.0.0-3 python3.9=3.9.9-1 python3.9-dev=3.9.9-1 python3.9-minimal=3.9.9-1 readline-common=8.1-2 rpcsvc-proto=1.4.2-4 sed=4.8-1 sensible-utils=0.0.17 sysvinit-utils=3.00-1 tao-pegtl-dev=2.8.3-3 tar=1.34+dfsg-1 tzdata=2021e-1 util-linux=2.37.2-4 xz-utils=5.2.5-2 zlib1g=1:1.2.11.dfsg-2 zlib1g-dev=1:1.2.11.dfsg-2 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20211217T030032Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20211217T030032Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20211214T153755Z/ unstable main' >> /etc/apt/sources.list && apt-get update" --customize-hook=chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash --customize-hook=chroot "$1" env sh -c "apt-get source --only-source -d gemmi=0.5.1+ds-1 && mkdir -p /build/gemmi-xn1Oeh && dpkg-source --no-check -x /*.dsc /build/gemmi-xn1Oeh/gemmi-0.5.1+ds && chown -R builduser:builduser /build/gemmi-xn1Oeh" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/gemmi-xn1Oeh/gemmi-0.5.1+ds && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1639466316" dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/gemmi-xn1Oeh /tmp/gemmi-0.5.1+ds-1dq0b2tos bookworm /dev/null deb http://snapshot.notset.fr/archive/debian/20211214T153755Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: tar I: using /tmp/mmdebstrap.PzfuZt1Tlc as tempdir I: running apt-get update... I: downloading packages with apt... I: extracting archives... I: installing essential packages... I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "apt-get --yes install fakeroot util-linux"' exec /tmp/mmdebstrap.PzfuZt1Tlc Reading package lists... Building dependency tree... util-linux is already the newest version (2.37.2-4). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 134 kB of archives. After this operation, 397 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20211214T153755Z unstable/main amd64 libfakeroot amd64 1.26-1 [47.3 kB] Get:2 http://snapshot.notset.fr/archive/debian/20211214T153755Z unstable/main amd64 fakeroot amd64 1.26-1 [87.1 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (1091 kB/s) Selecting previously unselected package libfakeroot:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4679 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.26-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.26-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.26-1_amd64.deb ... Unpacking fakeroot (1.26-1) ... Setting up libfakeroot:amd64 (1.26-1) ... Setting up fakeroot (1.26-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.33-1) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20211217T030032Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20211217T030032Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20211214T153755Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.PzfuZt1Tlc Get:1 http://snapshot.notset.fr/archive/debian/20211217T030032Z bookworm InRelease [129 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20211214T153755Z unstable InRelease Ign:3 http://snapshot.notset.fr/archive/debian/20211217T030032Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20211217T030032Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20211217T030032Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20211217T030032Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20211217T030032Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20211217T030032Z bookworm/main amd64 Packages Get:3 http://snapshot.notset.fr/archive/debian/20211217T030032Z bookworm/main Sources [11.8 MB] Get:4 http://snapshot.notset.fr/archive/debian/20211217T030032Z bookworm/main amd64 Packages [11.2 MB] Fetched 23.1 MB in 19s (1188 kB/s) Reading package lists... I: installing remaining packages inside the chroot... I: running --customize-hook in shell: sh -c 'chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash' exec /tmp/mmdebstrap.PzfuZt1Tlc I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d gemmi=0.5.1+ds-1 && mkdir -p /build/gemmi-xn1Oeh && dpkg-source --no-check -x /*.dsc /build/gemmi-xn1Oeh/gemmi-0.5.1+ds && chown -R builduser:builduser /build/gemmi-xn1Oeh"' exec /tmp/mmdebstrap.PzfuZt1Tlc Reading package lists... NOTICE: 'gemmi' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/debichem-team/gemmi.git Please use: git clone https://salsa.debian.org/debichem-team/gemmi.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 1190 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20211217T030032Z bookworm/main gemmi 0.5.1+ds-1 (dsc) [2226 B] Get:2 http://snapshot.notset.fr/archive/debian/20211217T030032Z bookworm/main gemmi 0.5.1+ds-1 (tar) [1183 kB] Get:3 http://snapshot.notset.fr/archive/debian/20211217T030032Z bookworm/main gemmi 0.5.1+ds-1 (diff) [4996 B] Fetched 1190 kB in 1s (1253 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'gemmi_0.5.1+ds-1.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting gemmi in /build/gemmi-xn1Oeh/gemmi-0.5.1+ds dpkg-source: info: unpacking gemmi_0.5.1+ds.orig.tar.xz dpkg-source: info: unpacking gemmi_0.5.1+ds-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use-system-tao-pegtl.patch dpkg-source: info: applying change_error_type_in_test.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/gemmi-xn1Oeh/gemmi-0.5.1+ds && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1639466316" dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.PzfuZt1Tlc dpkg-buildpackage: info: source package gemmi dpkg-buildpackage: info: source version 0.5.1+ds-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andrius Merkys dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --buildsystem=cmake --with python3 dh_auto_clean -O--buildsystem=cmake dh_autoreconf_clean -O--buildsystem=cmake dh_clean -O--buildsystem=cmake debian/rules binary-arch dh binary-arch --buildsystem=cmake --with python3 dh_update_autotools_config -a -O--buildsystem=cmake dh_autoreconf -a -O--buildsystem=cmake debian/rules override_dh_auto_configure make[1]: Entering directory '/build/gemmi-xn1Oeh/gemmi-0.5.1+ds' dh_auto_configure -- -DUSE_PYTHON=1 -DINSTALL_EGG_INFO=OFF cd obj-x86_64-linux-gnu && 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 -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DUSE_PYTHON=1 -DINSTALL_EGG_INFO=OFF .. -- The C compiler identification is GNU 11.2.0 -- The CXX compiler identification is GNU 11.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Skipping Fortran bindings. Add -D USE_FORTRAN=1 to build them. -- Compiling with C++ standard: 17 -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11") -- Benchmarks not configured. -- The python module will be built. -- Found PythonInterp: /usr/bin/python3.9 (found version "3.9.9") -- Found PythonLibs: /usr/lib/x86_64-linux-gnu/libpython3.9.so -- Performing Test HAS_FLTO -- Performing Test HAS_FLTO - Success -- Found pybind11: /usr/include (found version "2.7.1" ) -- Found pybind11 2.7.1: /usr/include;/usr/include/python3.9 -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR -- Build files have been written to: /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/gemmi-xn1Oeh/gemmi-0.5.1+ds' dh_auto_build -a -O--buildsystem=cmake cd obj-x86_64-linux-gnu && make -j4 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/gemmi-xn1Oeh/gemmi-0.5.1+ds -B/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu/CMakeFiles /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' make -f CMakeFiles/input.dir/build.make CMakeFiles/input.dir/depend make -f CMakeFiles/options.dir/build.make CMakeFiles/options.dir/depend make -f CMakeFiles/output.dir/build.make CMakeFiles/output.dir/depend make[3]: Entering directory '/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' cd /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gemmi-xn1Oeh/gemmi-0.5.1+ds /build/gemmi-xn1Oeh/gemmi-0.5.1+ds /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu/CMakeFiles/input.dir/DependInfo.cmake --color= make -f CMakeFiles/mapcoef.dir/build.make CMakeFiles/mapcoef.dir/depend make[3]: Entering directory '/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' cd /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gemmi-xn1Oeh/gemmi-0.5.1+ds /build/gemmi-xn1Oeh/gemmi-0.5.1+ds /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu/CMakeFiles/output.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' cd /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gemmi-xn1Oeh/gemmi-0.5.1+ds /build/gemmi-xn1Oeh/gemmi-0.5.1+ds /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu/CMakeFiles/options.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' cd /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gemmi-xn1Oeh/gemmi-0.5.1+ds /build/gemmi-xn1Oeh/gemmi-0.5.1+ds /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu/CMakeFiles/mapcoef.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' make -f CMakeFiles/options.dir/build.make CMakeFiles/options.dir/build make[3]: Entering directory '/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' make -f CMakeFiles/input.dir/build.make CMakeFiles/input.dir/build make[3]: Entering directory '/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' make -f CMakeFiles/output.dir/build.make CMakeFiles/output.dir/build make[3]: Leaving directory '/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' make -f CMakeFiles/mapcoef.dir/build.make CMakeFiles/mapcoef.dir/build make[3]: Entering directory '/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' [ 2%] Building CXX object CMakeFiles/options.dir/src/options.cpp.o /usr/bin/c++ -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/include -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-xn1Oeh/gemmi-0.5.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/options.dir/src/options.cpp.o -MF CMakeFiles/options.dir/src/options.cpp.o.d -o CMakeFiles/options.dir/src/options.cpp.o -c /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/src/options.cpp [ 7%] Building CXX object CMakeFiles/mapcoef.dir/src/mapcoef.cpp.o [ 7%] Building CXX object CMakeFiles/output.dir/src/output.cpp.o [ 7%] Building CXX object CMakeFiles/input.dir/src/input.cpp.o /usr/bin/c++ -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/include -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-xn1Oeh/gemmi-0.5.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/input.dir/src/input.cpp.o -MF CMakeFiles/input.dir/src/input.cpp.o.d -o CMakeFiles/input.dir/src/input.cpp.o -c /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/src/input.cpp /usr/bin/c++ -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/include -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-xn1Oeh/gemmi-0.5.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/output.dir/src/output.cpp.o -MF CMakeFiles/output.dir/src/output.cpp.o.d -o CMakeFiles/output.dir/src/output.cpp.o -c /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/src/output.cpp /usr/bin/c++ -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/include -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-xn1Oeh/gemmi-0.5.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/mapcoef.dir/src/mapcoef.cpp.o -MF CMakeFiles/mapcoef.dir/src/mapcoef.cpp.o.d -o CMakeFiles/mapcoef.dir/src/mapcoef.cpp.o -c /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/src/mapcoef.cpp In file included from /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/src/output.cpp:6: /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/include/gemmi/sprintf.hpp:26:4: warning: #warning "Using system stb_sprintf.h, not the bundled one. It may not work." [-Wcpp] 26 | # warning "Using system stb_sprintf.h, not the bundled one. It may not work." | ^~~~~~~ make[3]: Leaving directory '/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' [ 7%] Built target options make -f CMakeFiles/py.dir/build.make CMakeFiles/py.dir/depend make[3]: Entering directory '/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' cd /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gemmi-xn1Oeh/gemmi-0.5.1+ds /build/gemmi-xn1Oeh/gemmi-0.5.1+ds /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu/CMakeFiles/py.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' make -f CMakeFiles/py.dir/build.make CMakeFiles/py.dir/build make[3]: Entering directory '/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' [ 7%] Building CXX object CMakeFiles/py.dir/python/mol.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/include -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/third_party -isystem /usr/include/python3.9 -g -O2 -ffile-prefix-map=/build/gemmi-xn1Oeh/gemmi-0.5.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -std=c++17 -MD -MT CMakeFiles/py.dir/python/mol.cpp.o -MF CMakeFiles/py.dir/python/mol.cpp.o.d -o CMakeFiles/py.dir/python/mol.cpp.o -c /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/python/mol.cpp make[3]: Leaving directory '/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' [ 7%] Built target output [ 9%] Building CXX object CMakeFiles/py.dir/python/gemmi.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/include -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/third_party -isystem /usr/include/python3.9 -g -O2 -ffile-prefix-map=/build/gemmi-xn1Oeh/gemmi-0.5.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -std=c++17 -MD -MT CMakeFiles/py.dir/python/gemmi.cpp.o -MF CMakeFiles/py.dir/python/gemmi.cpp.o.d -o CMakeFiles/py.dir/python/gemmi.cpp.o -c /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/python/gemmi.cpp make[3]: Leaving directory '/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' [ 9%] Built target mapcoef [ 12%] Building CXX object CMakeFiles/py.dir/python/align.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/include -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/third_party -isystem /usr/include/python3.9 -g -O2 -ffile-prefix-map=/build/gemmi-xn1Oeh/gemmi-0.5.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -std=c++17 -MD -MT CMakeFiles/py.dir/python/align.cpp.o -MF CMakeFiles/py.dir/python/align.cpp.o.d -o CMakeFiles/py.dir/python/align.cpp.o -c /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/python/align.cpp In file included from /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/include/gemmi/select.hpp:16, from /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/python/align.cpp:5: /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/include/gemmi/sprintf.hpp:26:4: warning: #warning "Using system stb_sprintf.h, not the bundled one. It may not work." [-Wcpp] 26 | # warning "Using system stb_sprintf.h, not the bundled one. 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-D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -std=c++17 -MD -MT CMakeFiles/py.dir/python/chemcomp.cpp.o -MF CMakeFiles/py.dir/python/chemcomp.cpp.o.d -o CMakeFiles/py.dir/python/chemcomp.cpp.o -c /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/python/chemcomp.cpp make[3]: Leaving directory '/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' [ 14%] Built target input make -f CMakeFiles/program.dir/build.make CMakeFiles/program.dir/depend make[3]: Entering directory '/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' cd /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gemmi-xn1Oeh/gemmi-0.5.1+ds /build/gemmi-xn1Oeh/gemmi-0.5.1+ds /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu/CMakeFiles/program.dir/DependInfo.cmake --color= make[3]: Leaving directory 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/usr/bin/c++ -Dpy_EXPORTS -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/include -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/third_party -isystem /usr/include/python3.9 -g -O2 -ffile-prefix-map=/build/gemmi-xn1Oeh/gemmi-0.5.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -std=c++17 -MD -MT CMakeFiles/py.dir/python/custom.cpp.o -MF CMakeFiles/py.dir/python/custom.cpp.o.d -o CMakeFiles/py.dir/python/custom.cpp.o -c /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/python/custom.cpp [ 24%] Building CXX object CMakeFiles/py.dir/python/elem.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/include -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/third_party -isystem /usr/include/python3.9 -g -O2 -ffile-prefix-map=/build/gemmi-xn1Oeh/gemmi-0.5.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -std=c++17 -MD -MT CMakeFiles/py.dir/python/elem.cpp.o -MF CMakeFiles/py.dir/python/elem.cpp.o.d -o CMakeFiles/py.dir/python/elem.cpp.o -c /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/python/elem.cpp [ 26%] Building CXX object CMakeFiles/py.dir/python/grid.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/include -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/third_party -isystem /usr/include/python3.9 -g -O2 -ffile-prefix-map=/build/gemmi-xn1Oeh/gemmi-0.5.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -std=c++17 -MD -MT CMakeFiles/py.dir/python/grid.cpp.o -MF CMakeFiles/py.dir/python/grid.cpp.o.d -o CMakeFiles/py.dir/python/grid.cpp.o -c /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/python/grid.cpp [ 26%] Building CXX object CMakeFiles/program.dir/src/cif2mtz.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/include -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/third_party -g -O2 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CMakeFiles/program.dir/src/cif2json.cpp.o.d -o CMakeFiles/program.dir/src/cif2json.cpp.o -c /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/src/cif2json.cpp [ 34%] Building CXX object CMakeFiles/py.dir/python/monlib.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/include -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/third_party -isystem /usr/include/python3.9 -g -O2 -ffile-prefix-map=/build/gemmi-xn1Oeh/gemmi-0.5.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -std=c++17 -MD -MT CMakeFiles/py.dir/python/monlib.cpp.o -MF CMakeFiles/py.dir/python/monlib.cpp.o.d -o CMakeFiles/py.dir/python/monlib.cpp.o -c /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/python/monlib.cpp [ 36%] Building CXX object CMakeFiles/program.dir/src/contact.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/include -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-xn1Oeh/gemmi-0.5.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/contact.cpp.o -MF CMakeFiles/program.dir/src/contact.cpp.o.d -o CMakeFiles/program.dir/src/contact.cpp.o -c /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/src/contact.cpp [ 39%] Building CXX object CMakeFiles/py.dir/python/mtz.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/include -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/third_party -isystem /usr/include/python3.9 -g -O2 -ffile-prefix-map=/build/gemmi-xn1Oeh/gemmi-0.5.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -std=c++17 -Wno-psabi -MD -MT CMakeFiles/py.dir/python/mtz.cpp.o -MF CMakeFiles/py.dir/python/mtz.cpp.o.d -o CMakeFiles/py.dir/python/mtz.cpp.o -c /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/python/mtz.cpp [ 41%] Building CXX object CMakeFiles/program.dir/src/contents.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/include -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-xn1Oeh/gemmi-0.5.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/contents.cpp.o -MF CMakeFiles/program.dir/src/contents.cpp.o.d -o CMakeFiles/program.dir/src/contents.cpp.o -c /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/src/contents.cpp [ 43%] Building CXX object CMakeFiles/py.dir/python/read.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/include -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/third_party -isystem /usr/include/python3.9 -g -O2 -ffile-prefix-map=/build/gemmi-xn1Oeh/gemmi-0.5.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -std=c++17 -MD -MT CMakeFiles/py.dir/python/read.cpp.o -MF CMakeFiles/py.dir/python/read.cpp.o.d -o CMakeFiles/py.dir/python/read.cpp.o -c /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/python/read.cpp In file included from /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/include/gemmi/smcif.hpp:12, from /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/python/read.cpp:7: /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/include/gemmi/sprintf.hpp:26:4: warning: #warning "Using system stb_sprintf.h, not the bundled one. 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It may not work." [-Wcpp] 26 | # warning "Using system stb_sprintf.h, not the bundled one. It may not work." | ^~~~~~~ [ 46%] Building CXX object CMakeFiles/py.dir/python/scaling.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/include -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/third_party -isystem /usr/include/python3.9 -g -O2 -ffile-prefix-map=/build/gemmi-xn1Oeh/gemmi-0.5.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -std=c++17 -MD -MT CMakeFiles/py.dir/python/scaling.cpp.o -MF CMakeFiles/py.dir/python/scaling.cpp.o.d -o CMakeFiles/py.dir/python/scaling.cpp.o -c /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/python/scaling.cpp [ 48%] Building CXX object CMakeFiles/py.dir/python/sf.cpp.o [ 51%] Building CXX object CMakeFiles/py.dir/python/search.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/include -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/third_party -isystem /usr/include/python3.9 -g -O2 -ffile-prefix-map=/build/gemmi-xn1Oeh/gemmi-0.5.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -std=c++17 -MD -MT CMakeFiles/py.dir/python/sf.cpp.o -MF CMakeFiles/py.dir/python/sf.cpp.o.d -o CMakeFiles/py.dir/python/sf.cpp.o -c /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/python/sf.cpp /usr/bin/c++ -Dpy_EXPORTS -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/include -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/third_party -isystem /usr/include/python3.9 -g -O2 -ffile-prefix-map=/build/gemmi-xn1Oeh/gemmi-0.5.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -std=c++17 -MD -MT CMakeFiles/py.dir/python/search.cpp.o -MF CMakeFiles/py.dir/python/search.cpp.o.d -o CMakeFiles/py.dir/python/search.cpp.o -c /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/python/search.cpp [ 51%] Building CXX object CMakeFiles/py.dir/python/sym.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/include -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/third_party -isystem /usr/include/python3.9 -g -O2 -ffile-prefix-map=/build/gemmi-xn1Oeh/gemmi-0.5.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -std=c++17 -MD -MT CMakeFiles/py.dir/python/sym.cpp.o -MF CMakeFiles/py.dir/python/sym.cpp.o.d -o CMakeFiles/py.dir/python/sym.cpp.o -c /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/python/sym.cpp [ 53%] Building CXX object CMakeFiles/py.dir/python/topo.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/include -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/third_party -isystem /usr/include/python3.9 -g -O2 -ffile-prefix-map=/build/gemmi-xn1Oeh/gemmi-0.5.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -std=c++17 -MD -MT CMakeFiles/py.dir/python/topo.cpp.o -MF 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-I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/include -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/third_party -isystem /usr/include/python3.9 -g -O2 -ffile-prefix-map=/build/gemmi-xn1Oeh/gemmi-0.5.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -std=c++17 -MD -MT CMakeFiles/py.dir/python/write.cpp.o -MF CMakeFiles/py.dir/python/write.cpp.o.d -o CMakeFiles/py.dir/python/write.cpp.o -c /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/python/write.cpp In file included from /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/python/write.cpp:4: /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/include/gemmi/sprintf.hpp:26:4: warning: #warning "Using system stb_sprintf.h, not the bundled one. 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It may not work." | ^~~~~~~ [ 60%] Building CXX object CMakeFiles/program.dir/src/h.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/include -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-xn1Oeh/gemmi-0.5.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/h.cpp.o -MF CMakeFiles/program.dir/src/h.cpp.o.d -o CMakeFiles/program.dir/src/h.cpp.o -c /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/src/h.cpp [ 63%] Building CXX object CMakeFiles/program.dir/src/json2cif.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/include -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-xn1Oeh/gemmi-0.5.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/json2cif.cpp.o -MF CMakeFiles/program.dir/src/json2cif.cpp.o.d -o CMakeFiles/program.dir/src/json2cif.cpp.o -c /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/src/json2cif.cpp [ 65%] Building CXX object CMakeFiles/program.dir/src/main.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/include -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-xn1Oeh/gemmi-0.5.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/main.cpp.o -MF CMakeFiles/program.dir/src/main.cpp.o.d -o CMakeFiles/program.dir/src/main.cpp.o -c /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/src/main.cpp [ 68%] Building CXX object CMakeFiles/program.dir/src/map.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/include -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-xn1Oeh/gemmi-0.5.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security 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-ffile-prefix-map=/build/gemmi-xn1Oeh/gemmi-0.5.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/mask.cpp.o -MF CMakeFiles/program.dir/src/mask.cpp.o.d -o CMakeFiles/program.dir/src/mask.cpp.o -c /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/src/mask.cpp [ 73%] Linking CXX shared module gemmi.cpython-39-x86_64-linux-gnu.so /usr/bin/cmake -E cmake_link_script CMakeFiles/py.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/gemmi-xn1Oeh/gemmi-0.5.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -flto -Wl,-z,relro -shared -o gemmi.cpython-39-x86_64-linux-gnu.so CMakeFiles/py.dir/python/mol.cpp.o CMakeFiles/py.dir/python/gemmi.cpp.o CMakeFiles/py.dir/python/align.cpp.o CMakeFiles/py.dir/python/ccp4.cpp.o CMakeFiles/py.dir/python/chemcomp.cpp.o CMakeFiles/py.dir/python/cif.cpp.o CMakeFiles/py.dir/python/custom.cpp.o CMakeFiles/py.dir/python/elem.cpp.o CMakeFiles/py.dir/python/grid.cpp.o CMakeFiles/py.dir/python/hkl.cpp.o CMakeFiles/py.dir/python/meta.cpp.o CMakeFiles/py.dir/python/monlib.cpp.o CMakeFiles/py.dir/python/mtz.cpp.o CMakeFiles/py.dir/python/read.cpp.o CMakeFiles/py.dir/python/recgrid.cpp.o CMakeFiles/py.dir/python/scaling.cpp.o CMakeFiles/py.dir/python/search.cpp.o CMakeFiles/py.dir/python/sf.cpp.o CMakeFiles/py.dir/python/sym.cpp.o CMakeFiles/py.dir/python/topo.cpp.o CMakeFiles/py.dir/python/unitcell.cpp.o CMakeFiles/py.dir/python/write.cpp.o /usr/lib/x86_64-linux-gnu/libz.so [ 75%] Building CXX object CMakeFiles/program.dir/src/merge.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/include -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-xn1Oeh/gemmi-0.5.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/merge.cpp.o -MF CMakeFiles/program.dir/src/merge.cpp.o.d -o CMakeFiles/program.dir/src/merge.cpp.o -c /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/src/merge.cpp In file included from /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/include/gemmi/mtz2cif.hpp:24, from /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/src/merge.cpp:14: /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/include/gemmi/sprintf.hpp:26:4: warning: #warning "Using system stb_sprintf.h, not the bundled one. It may not work." [-Wcpp] 26 | # warning "Using system stb_sprintf.h, not the bundled one. 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It may not work." [-Wcpp] 26 | # warning "Using system stb_sprintf.h, not the bundled one. It may not work." | ^~~~~~~ [ 82%] Building CXX object CMakeFiles/program.dir/src/reindex.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/include -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-xn1Oeh/gemmi-0.5.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/reindex.cpp.o -MF CMakeFiles/program.dir/src/reindex.cpp.o.d -o CMakeFiles/program.dir/src/reindex.cpp.o -c /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/src/reindex.cpp [ 82%] Building CXX object CMakeFiles/program.dir/src/residues.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/include -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-xn1Oeh/gemmi-0.5.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/residues.cpp.o -MF CMakeFiles/program.dir/src/residues.cpp.o.d -o CMakeFiles/program.dir/src/residues.cpp.o -c /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/src/residues.cpp In file included from /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/include/gemmi/select.hpp:16, from /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/src/residues.cpp:5: /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/include/gemmi/sprintf.hpp:26:4: warning: #warning "Using system stb_sprintf.h, not the bundled one. It may not work." [-Wcpp] 26 | # warning "Using system stb_sprintf.h, not the bundled one. It may not work." | ^~~~~~~ [ 85%] Building CXX object CMakeFiles/program.dir/src/rmsz.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/include -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-xn1Oeh/gemmi-0.5.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/rmsz.cpp.o -MF CMakeFiles/program.dir/src/rmsz.cpp.o.d -o CMakeFiles/program.dir/src/rmsz.cpp.o -c /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/src/rmsz.cpp [ 87%] Building CXX object CMakeFiles/program.dir/src/sf2map.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/include -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-xn1Oeh/gemmi-0.5.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/sf2map.cpp.o -MF CMakeFiles/program.dir/src/sf2map.cpp.o.d -o CMakeFiles/program.dir/src/sf2map.cpp.o -c /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/src/sf2map.cpp In file included from /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/include/gemmi/select.hpp:16, from /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/src/sf2map.cpp:8: /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/include/gemmi/sprintf.hpp:26:4: warning: #warning "Using system stb_sprintf.h, not the bundled one. 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[-Wcpp] 26 | # warning "Using system stb_sprintf.h, not the bundled one. 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CMakeFiles/program.dir/src/residues.cpp.o CMakeFiles/program.dir/src/rmsz.cpp.o CMakeFiles/program.dir/src/sf2map.cpp.o CMakeFiles/program.dir/src/sfcalc.cpp.o CMakeFiles/program.dir/src/sg.cpp.o CMakeFiles/program.dir/src/tags.cpp.o CMakeFiles/program.dir/src/validate.cpp.o CMakeFiles/program.dir/src/validate_mon.cpp.o CMakeFiles/program.dir/src/wcn.cpp.o CMakeFiles/mapcoef.dir/src/mapcoef.cpp.o CMakeFiles/input.dir/src/input.cpp.o CMakeFiles/output.dir/src/output.cpp.o CMakeFiles/options.dir/src/options.cpp.o -o gemmi /usr/lib/x86_64-linux-gnu/libz.so make[3]: Leaving directory '/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' [100%] Built target program /usr/include/c++/11/bits/stl_heap.h: In function ‘__adjust_heap.constprop’: /usr/include/c++/11/bits/stl_heap.h:223:5: note: the ABI of passing structure with ‘complex float’ member has changed in GCC 4.4 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^ /usr/bin/strip 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CMakeFiles/doc_maybegz.dir/docs/code/maybegz.cpp.o.d -o CMakeFiles/doc_maybegz.dir/docs/code/maybegz.cpp.o -c /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/docs/code/maybegz.cpp [ 24%] Linking CXX executable hello /usr/bin/cmake -E cmake_link_script CMakeFiles/hello.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gemmi-xn1Oeh/gemmi-0.5.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/hello.dir/examples/hello.cpp.o -o hello make[5]: Leaving directory '/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' [ 26%] Linking CXX executable doc_example2 /usr/bin/cmake -E cmake_link_script CMakeFiles/doc_example2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gemmi-xn1Oeh/gemmi-0.5.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/doc_example2.dir/docs/code/cif_cc.cpp.o -o doc_example2 [ 26%] Built target hello make[5]: Leaving directory '/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' make -f CMakeFiles/doc_newmtz.dir/build.make CMakeFiles/doc_newmtz.dir/depend make[5]: Entering directory '/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' cd /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gemmi-xn1Oeh/gemmi-0.5.1+ds /build/gemmi-xn1Oeh/gemmi-0.5.1+ds /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu/CMakeFiles/doc_newmtz.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' make -f CMakeFiles/doc_newmtz.dir/build.make CMakeFiles/doc_newmtz.dir/build make[5]: Entering directory '/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' [ 26%] Building CXX object CMakeFiles/doc_newmtz.dir/docs/code/newmtz.cpp.o /usr/bin/c++ -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/include -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-xn1Oeh/gemmi-0.5.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/doc_newmtz.dir/docs/code/newmtz.cpp.o -MF CMakeFiles/doc_newmtz.dir/docs/code/newmtz.cpp.o.d -o CMakeFiles/doc_newmtz.dir/docs/code/newmtz.cpp.o -c /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/docs/code/newmtz.cpp In file included from /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/include/gemmi/mtz.hpp:1135, from /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/docs/code/newmtz.cpp:2: /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/include/gemmi/sprintf.hpp:26:4: warning: #warning "Using system stb_sprintf.h, not the bundled one. It may not work." [-Wcpp] 26 | # warning "Using system stb_sprintf.h, not the bundled one. It may not work." | ^~~~~~~ [ 26%] Built target doc_example2 make -f CMakeFiles/test_disulf.dir/build.make CMakeFiles/test_disulf.dir/depend make[5]: Entering directory '/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' cd /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gemmi-xn1Oeh/gemmi-0.5.1+ds /build/gemmi-xn1Oeh/gemmi-0.5.1+ds /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu/CMakeFiles/test_disulf.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' make -f CMakeFiles/test_disulf.dir/build.make CMakeFiles/test_disulf.dir/build make[5]: Entering directory '/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' [ 29%] Building CXX object CMakeFiles/test_disulf.dir/tests/disulf.cpp.o /usr/bin/c++ -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/include -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-xn1Oeh/gemmi-0.5.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/test_disulf.dir/tests/disulf.cpp.o -MF CMakeFiles/test_disulf.dir/tests/disulf.cpp.o.d -o CMakeFiles/test_disulf.dir/tests/disulf.cpp.o -c /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/tests/disulf.cpp [ 31%] Building CXX object CMakeFiles/cpptest.dir/tests/cif.cpp.o /usr/bin/c++ -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/include -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-xn1Oeh/gemmi-0.5.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/cpptest.dir/tests/cif.cpp.o -MF CMakeFiles/cpptest.dir/tests/cif.cpp.o.d -o CMakeFiles/cpptest.dir/tests/cif.cpp.o -c /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/tests/cif.cpp In file included from /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/include/gemmi/mtz.hpp:1135, from /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/include/gemmi/merge.hpp:15, from /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/tests/cif.cpp:93: /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/include/gemmi/sprintf.hpp:26:4: warning: #warning "Using system stb_sprintf.h, not the bundled one. It may not work." [-Wcpp] 26 | # warning "Using system stb_sprintf.h, not the bundled one. It may not work." | ^~~~~~~ [ 34%] Linking CXX executable doc_newmtz /usr/bin/cmake -E cmake_link_script CMakeFiles/doc_newmtz.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gemmi-xn1Oeh/gemmi-0.5.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/doc_newmtz.dir/docs/code/newmtz.cpp.o -o doc_newmtz make[5]: Leaving directory '/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' [ 34%] Built target doc_newmtz make -f CMakeFiles/check_conn.dir/build.make CMakeFiles/check_conn.dir/depend make[5]: Entering directory '/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' cd /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gemmi-xn1Oeh/gemmi-0.5.1+ds /build/gemmi-xn1Oeh/gemmi-0.5.1+ds /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu/CMakeFiles/check_conn.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' make -f CMakeFiles/check_conn.dir/build.make CMakeFiles/check_conn.dir/build make[5]: Entering directory '/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' [ 36%] Building CXX object CMakeFiles/check_conn.dir/examples/check_conn.cpp.o /usr/bin/c++ -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/include -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-xn1Oeh/gemmi-0.5.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/check_conn.dir/examples/check_conn.cpp.o -MF CMakeFiles/check_conn.dir/examples/check_conn.cpp.o.d -o CMakeFiles/check_conn.dir/examples/check_conn.cpp.o -c /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/examples/check_conn.cpp [ 39%] Linking CXX executable cpptest /usr/bin/cmake -E cmake_link_script CMakeFiles/cpptest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gemmi-xn1Oeh/gemmi-0.5.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/cpptest.dir/tests/main.cpp.o CMakeFiles/cpptest.dir/tests/cif.cpp.o -o cpptest make[5]: Leaving directory '/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' [ 39%] Built target cpptest make -f CMakeFiles/program.dir/build.make CMakeFiles/program.dir/depend make[5]: Entering directory '/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' cd /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gemmi-xn1Oeh/gemmi-0.5.1+ds /build/gemmi-xn1Oeh/gemmi-0.5.1+ds /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu/CMakeFiles/program.dir/DependInfo.cmake --color= Dependencies file "CMakeFiles/program.dir/src/align.cpp.o.d" is newer than depends file "/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu/CMakeFiles/program.dir/compiler_depend.internal". Dependencies file "CMakeFiles/program.dir/src/blobs.cpp.o.d" is newer than depends file "/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu/CMakeFiles/program.dir/compiler_depend.internal". Dependencies file "CMakeFiles/program.dir/src/cif2json.cpp.o.d" is newer than depends file "/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu/CMakeFiles/program.dir/compiler_depend.internal". Dependencies file "CMakeFiles/program.dir/src/cif2mtz.cpp.o.d" is newer than depends file "/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu/CMakeFiles/program.dir/compiler_depend.internal". Dependencies file "CMakeFiles/program.dir/src/contact.cpp.o.d" is newer than depends file "/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu/CMakeFiles/program.dir/compiler_depend.internal". Dependencies file "CMakeFiles/program.dir/src/contents.cpp.o.d" is newer than depends file "/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu/CMakeFiles/program.dir/compiler_depend.internal". Dependencies file "CMakeFiles/program.dir/src/convert.cpp.o.d" is newer than depends file "/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu/CMakeFiles/program.dir/compiler_depend.internal". Dependencies file "CMakeFiles/program.dir/src/fprime.cpp.o.d" is newer than depends file "/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu/CMakeFiles/program.dir/compiler_depend.internal". Dependencies file "CMakeFiles/program.dir/src/grep.cpp.o.d" is newer than depends file "/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu/CMakeFiles/program.dir/compiler_depend.internal". Dependencies file "CMakeFiles/program.dir/src/h.cpp.o.d" is newer than depends file "/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu/CMakeFiles/program.dir/compiler_depend.internal". Dependencies file "CMakeFiles/program.dir/src/json2cif.cpp.o.d" is newer than depends file "/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu/CMakeFiles/program.dir/compiler_depend.internal". 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Dependencies file "CMakeFiles/program.dir/src/mondiff.cpp.o.d" is newer than depends file "/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu/CMakeFiles/program.dir/compiler_depend.internal". Dependencies file "CMakeFiles/program.dir/src/mtz.cpp.o.d" is newer than depends file "/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu/CMakeFiles/program.dir/compiler_depend.internal". Dependencies file "CMakeFiles/program.dir/src/mtz2cif.cpp.o.d" is newer than depends file "/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu/CMakeFiles/program.dir/compiler_depend.internal". Dependencies file "CMakeFiles/program.dir/src/reindex.cpp.o.d" is newer than depends file "/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu/CMakeFiles/program.dir/compiler_depend.internal". Dependencies file "CMakeFiles/program.dir/src/residues.cpp.o.d" is newer than depends file "/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu/CMakeFiles/program.dir/compiler_depend.internal". Dependencies file "CMakeFiles/program.dir/src/rmsz.cpp.o.d" is newer than depends file "/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu/CMakeFiles/program.dir/compiler_depend.internal". Dependencies file "CMakeFiles/program.dir/src/sf2map.cpp.o.d" is newer than depends file "/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu/CMakeFiles/program.dir/compiler_depend.internal". Dependencies file "CMakeFiles/program.dir/src/sfcalc.cpp.o.d" is newer than depends file "/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu/CMakeFiles/program.dir/compiler_depend.internal". Dependencies file "CMakeFiles/program.dir/src/sg.cpp.o.d" is newer than depends file "/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu/CMakeFiles/program.dir/compiler_depend.internal". Dependencies file "CMakeFiles/program.dir/src/tags.cpp.o.d" is newer than depends file "/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu/CMakeFiles/program.dir/compiler_depend.internal". 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Consolidate compiler generated dependencies of target program make[5]: Leaving directory '/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' make -f CMakeFiles/program.dir/build.make CMakeFiles/program.dir/build make[5]: Entering directory '/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'CMakeFiles/program.dir/build'. make[5]: Leaving directory '/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' [ 92%] Built target program [ 95%] Building CXX object CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o /usr/bin/c++ -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/include -I/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-xn1Oeh/gemmi-0.5.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o -MF CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o.d -o CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o -c /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/docs/code/mutate.cpp make -f CMakeFiles/print-version.dir/build.make CMakeFiles/print-version.dir/depend make[5]: Entering directory '/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' cd /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gemmi-xn1Oeh/gemmi-0.5.1+ds /build/gemmi-xn1Oeh/gemmi-0.5.1+ds /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu/CMakeFiles/print-version.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' make -f CMakeFiles/print-version.dir/build.make CMakeFiles/print-version.dir/build make[5]: Entering directory '/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' [ 95%] gemmi --version cd /build/gemmi-xn1Oeh/gemmi-0.5.1+ds && /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu/gemmi --version gemmi 0.5.1 make[5]: Leaving directory '/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' [ 95%] Built target print-version [ 97%] Linking CXX executable doc_maybegz /usr/bin/cmake -E cmake_link_script CMakeFiles/doc_maybegz.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gemmi-xn1Oeh/gemmi-0.5.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/doc_maybegz.dir/docs/code/maybegz.cpp.o CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o -o doc_maybegz /usr/lib/x86_64-linux-gnu/libz.so make[5]: Leaving directory '/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' [ 97%] Built target doc_maybegz [ 97%] Linking CXX executable check_conn /usr/bin/cmake -E cmake_link_script CMakeFiles/check_conn.dir/link.txt --verbose=1 [100%] Linking CXX executable test_disulf /usr/bin/cmake -E cmake_link_script CMakeFiles/test_disulf.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gemmi-xn1Oeh/gemmi-0.5.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/test_disulf.dir/tests/disulf.cpp.o -o test_disulf /usr/lib/x86_64-linux-gnu/libz.so /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gemmi-xn1Oeh/gemmi-0.5.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/check_conn.dir/examples/check_conn.cpp.o -o check_conn /usr/lib/x86_64-linux-gnu/libz.so make[5]: Leaving directory '/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' [100%] Built target check_conn make[5]: Leaving directory '/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' [100%] Built target test_disulf make -f CMakeFiles/check.dir/build.make CMakeFiles/check.dir/depend make[5]: Entering directory '/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' cd /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gemmi-xn1Oeh/gemmi-0.5.1+ds /build/gemmi-xn1Oeh/gemmi-0.5.1+ds /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu/CMakeFiles/check.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' make -f CMakeFiles/check.dir/build.make CMakeFiles/check.dir/build make[5]: Entering directory '/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' /usr/bin/ctest -C None Test project /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu Start 1: cpptest 1/1 Test #1: cpptest .......................... Passed 0.01 sec 100% tests passed, 0 tests failed out of 1 Total Test time (real) = 0.02 sec make[5]: Leaving directory '/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' [100%] Built target check make[4]: Leaving directory '/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu/CMakeFiles 0 make[3]: Leaving directory '/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' make[2]: Leaving directory '/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' PYTHONPATH=$(find . -name 'obj-*') pytest-3 ============================= test session starts ============================== platform linux -- Python 3.9.9, pytest-6.2.5, py-1.10.0, pluggy-0.13.0 rootdir: /build/gemmi-xn1Oeh/gemmi-0.5.1+ds collected 148 items tests/test_cif.py ................. [ 11%] tests/test_cif_json.py .... [ 14%] tests/test_elem.py .... [ 16%] tests/test_examples.py ........... 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[100%] ======================= 137 passed, 11 skipped in 2.45s ======================== make[1]: Leaving directory '/build/gemmi-xn1Oeh/gemmi-0.5.1+ds' create-stamp debian/debhelper-build-stamp dh_testroot -a -O--buildsystem=cmake dh_prep -a -O--buildsystem=cmake dh_auto_install -a -O--buildsystem=cmake cd obj-x86_64-linux-gnu && make -j4 install DESTDIR=/build/gemmi-xn1Oeh/gemmi-0.5.1\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/gemmi-xn1Oeh/gemmi-0.5.1+ds -B/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' Install the project... 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/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi.cpython-39-x86_64-linux-gnu.so -- Installing: /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi-examples -- Installing: /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi-examples/__init__.py -- Installing: /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi-examples/__main__.py -- Installing: /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi-examples/aafreq.py -- Installing: /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi-examples/ccd_gi.py -- Installing: /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi-examples/ccd_subgraph.py -- Installing: /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi-examples/cif_i_sigi.py -- Installing: /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi-examples/col_order.py -- Installing: /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi-examples/from_json.py -- Installing: /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi-examples/hello.py -- Installing: /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi-examples/long_geom.py -- Installing: /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi-examples/map2mtz.py -- Installing: /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi-examples/maskcheck.py -- Installing: /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi-examples/maskdiff.py -- Installing: /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi-examples/matthews.py -- Installing: /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi-examples/merge_mtz_mmcif.py -- Installing: /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi-examples/monomers.py -- Installing: /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi-examples/mtrix_iso.py -- Installing: /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi-examples/mtz_i_sigi.py -- Installing: /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi-examples/multiproc.py -- Installing: /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi-examples/patterson_slice.py -- Installing: /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi-examples/rama_gather.py -- Installing: /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi-examples/rama_plot.py -- Installing: /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi-examples/simple_search.py -- Installing: /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi-examples/sub_ccd.py -- Installing: /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi-examples/weight.py -- Installing: /build/gemmi-xn1Oeh/gemmi-0.5.1+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi-examples/__pycache__ make[1]: Leaving directory '/build/gemmi-xn1Oeh/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' dh_install -a -O--buildsystem=cmake dh_installdocs -a -O--buildsystem=cmake dh_installchangelogs -a -O--buildsystem=cmake debian/rules override_dh_installman make[1]: Entering directory '/build/gemmi-xn1Oeh/gemmi-0.5.1+ds' help2man 'tail -n +9 docs/gemmi-help.txt' \ --version-string 0.5.1+ds --name 'CLI for GEMMI library' \ --no-info --help-option '' > debian/gemmi.1 sed -i 's/.TH GEMMI-HELP.TXT/.TH gemmi/' debian/gemmi.1 sed -i 's/gemmi-help.txt/gemmi/' debian/gemmi.1 dh_installman make[1]: Leaving directory '/build/gemmi-xn1Oeh/gemmi-0.5.1+ds' dh_python3 -a -O--buildsystem=cmake dh_installsystemduser -a -O--buildsystem=cmake dh_perl -a -O--buildsystem=cmake dh_link -a -O--buildsystem=cmake dh_strip_nondeterminism -a -O--buildsystem=cmake dh_compress -a -O--buildsystem=cmake dh_fixperms -a -O--buildsystem=cmake dh_missing -a -O--buildsystem=cmake dh_dwz -a -O--buildsystem=cmake dwz: debian/python3-gemmi/usr/lib/python3/dist-packages/gemmi.cpython-39-x86_64-linux-gnu.so: .debug_info section not present dh_strip -a -O--buildsystem=cmake dh_makeshlibs -a -O--buildsystem=cmake dh_shlibdeps -a -O--buildsystem=cmake dh_installdeb -a -O--buildsystem=cmake dh_gencontrol -a -O--buildsystem=cmake dpkg-gencontrol: warning: package python3-gemmi: substitution variable ${python3:Versions} unused, but is defined dh_md5sums -a -O--buildsystem=cmake dh_builddeb -a -O--buildsystem=cmake dpkg-deb: building package 'gemmi-dev' in '../gemmi-dev_0.5.1+ds-1_amd64.deb'. dpkg-deb: building package 'gemmi-dbgsym' in '../gemmi-dbgsym_0.5.1+ds-1_amd64.deb'. dpkg-deb: building package 'gemmi' in '../gemmi_0.5.1+ds-1_amd64.deb'. dpkg-deb: building package 'python3-gemmi' in '../python3-gemmi_0.5.1+ds-1_amd64.deb'. dpkg-genbuildinfo --build=any -O../gemmi_0.5.1+ds-1_amd64.buildinfo dpkg-genchanges --build=any -O../gemmi_0.5.1+ds-1_amd64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/gemmi-xn1Oeh /tmp/gemmi-0.5.1+ds-1dq0b2tos I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.PzfuZt1Tlc... I: success in 2969.6956 seconds md5: gemmi-dbgsym_0.5.1+ds-1_amd64.deb: OK md5: gemmi-dev_0.5.1+ds-1_amd64.deb: OK md5: gemmi_0.5.1+ds-1_amd64.deb: OK md5: python3-gemmi_0.5.1+ds-1_amd64.deb: OK sha1: gemmi-dbgsym_0.5.1+ds-1_amd64.deb: OK sha1: gemmi-dev_0.5.1+ds-1_amd64.deb: OK sha1: gemmi_0.5.1+ds-1_amd64.deb: OK sha1: python3-gemmi_0.5.1+ds-1_amd64.deb: OK sha256: gemmi-dbgsym_0.5.1+ds-1_amd64.deb: OK sha256: gemmi-dev_0.5.1+ds-1_amd64.deb: OK sha256: gemmi_0.5.1+ds-1_amd64.deb: OK sha256: python3-gemmi_0.5.1+ds-1_amd64.deb: OK Checksums: OK