* Package: sci-libs/chemkit-0.1-r2 * Repository: gentoo * Maintainer: sci-chemistry@gentoo.org * USE: abi_x86_64 amd64 elibc_glibc kernel_linux python python_targets_python2_7 userland_GNU * FEATURES: network-sandbox preserve-libs sandbox userpriv usersandbox >>> Unpacking source... >>> Unpacking chemkit-0.1.tar.gz to /var/tmp/portage/sci-libs/chemkit-0.1-r2/work >>> Source unpacked in /var/tmp/portage/sci-libs/chemkit-0.1-r2/work >>> Preparing source in /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit ... removed 'src/3rdparty/inchi/util.h' removed 'src/3rdparty/inchi/util.c' removed 'src/3rdparty/inchi/strutil.h' removed 'src/3rdparty/inchi/strutil.c' removed 'src/3rdparty/inchi/sha2.h' removed 'src/3rdparty/inchi/sha2.c' removed 'src/3rdparty/inchi/runichi.c' removed 'src/3rdparty/inchi/mode.h' removed 'src/3rdparty/inchi/lreadmol.h' removed 'src/3rdparty/inchi/inpdef.h' removed 'src/3rdparty/inchi/incomdef.h' removed 'src/3rdparty/inchi/inchicmp.h' removed 'src/3rdparty/inchi/inchi_dll_main.h' removed 'src/3rdparty/inchi/inchi_dll_main.c' removed 'src/3rdparty/inchi/inchi_dll_a2.c' removed 'src/3rdparty/inchi/inchi_dll_a.h' removed 'src/3rdparty/inchi/inchi_dll_a.c' removed 'src/3rdparty/inchi/inchi_dll.c' removed 'src/3rdparty/inchi/inchi_api.h' removed 'src/3rdparty/inchi/ikey_dll.c' removed 'src/3rdparty/inchi/ikey_base26.h' removed 'src/3rdparty/inchi/ikey_base26.c' removed 'src/3rdparty/inchi/ichitime.h' removed 'src/3rdparty/inchi/ichitaut.h' removed 'src/3rdparty/inchi/ichitaut.c' removed 'src/3rdparty/inchi/ichister.h' removed 'src/3rdparty/inchi/ichister.c' removed 'src/3rdparty/inchi/ichisort.c' removed 'src/3rdparty/inchi/ichisize.h' removed 'src/3rdparty/inchi/ichirvrs.h' removed 'src/3rdparty/inchi/ichirvr7.c' removed 'src/3rdparty/inchi/ichirvr6.c' removed 'src/3rdparty/inchi/ichirvr5.c' removed 'src/3rdparty/inchi/ichirvr4.c' removed 'src/3rdparty/inchi/ichirvr3.c' removed 'src/3rdparty/inchi/ichirvr2.c' removed 'src/3rdparty/inchi/ichirvr1.c' removed 'src/3rdparty/inchi/ichiring.h' removed 'src/3rdparty/inchi/ichiring.c' removed 'src/3rdparty/inchi/ichiread.c' removed 'src/3rdparty/inchi/ichiqueu.c' removed 'src/3rdparty/inchi/ichiprt3.c' removed 'src/3rdparty/inchi/ichiprt2.c' removed 'src/3rdparty/inchi/ichiprt1.c' removed 'src/3rdparty/inchi/ichiparm.h' removed 'src/3rdparty/inchi/ichiparm.c' removed 'src/3rdparty/inchi/ichinorm.h' removed 'src/3rdparty/inchi/ichinorm.c' removed 'src/3rdparty/inchi/ichimap4.c' removed 'src/3rdparty/inchi/ichimap2.c' removed 'src/3rdparty/inchi/ichimap1.c' removed 'src/3rdparty/inchi/ichimake.h' removed 'src/3rdparty/inchi/ichimake.c' removed 'src/3rdparty/inchi/ichimak2.c' removed 'src/3rdparty/inchi/ichimain.h' removed 'src/3rdparty/inchi/ichilnct.c' removed 'src/3rdparty/inchi/ichiisot.c' removed 'src/3rdparty/inchi/ichierr.h' removed 'src/3rdparty/inchi/ichidrp.h' removed 'src/3rdparty/inchi/ichicomp.h' removed 'src/3rdparty/inchi/ichicomn.h' removed 'src/3rdparty/inchi/ichicant.h' removed 'src/3rdparty/inchi/ichicans.c' removed 'src/3rdparty/inchi/ichicano.h' removed 'src/3rdparty/inchi/ichicano.c' removed 'src/3rdparty/inchi/ichican2.c' removed 'src/3rdparty/inchi/ichi_io.h' removed 'src/3rdparty/inchi/ichi_io.c' removed 'src/3rdparty/inchi/ichi_bns.h' removed 'src/3rdparty/inchi/ichi_bns.c' removed 'src/3rdparty/inchi/ichi.h' removed 'src/3rdparty/inchi/extr_ct.h' removed 'src/3rdparty/inchi/aux2atom.h' removed directory 'src/3rdparty/inchi' removed 'src/3rdparty/khronos/GL/glext.h' removed directory 'src/3rdparty/khronos/GL' removed directory 'src/3rdparty/khronos' removed 'src/3rdparty/lemon/lemon/unionfind.h' removed 'src/3rdparty/lemon/lemon/tolerance.h' removed 'src/3rdparty/lemon/lemon/time_measure.h' removed 'src/3rdparty/lemon/lemon/suurballe.h' removed 'src/3rdparty/lemon/lemon/static_graph.h' removed 'src/3rdparty/lemon/lemon/soplex.h' removed 'src/3rdparty/lemon/lemon/soplex.cc' removed 'src/3rdparty/lemon/lemon/smart_graph.h' removed 'src/3rdparty/lemon/lemon/random.h' removed 'src/3rdparty/lemon/lemon/random.cc' removed 'src/3rdparty/lemon/lemon/radix_sort.h' removed 'src/3rdparty/lemon/lemon/radix_heap.h' removed 'src/3rdparty/lemon/lemon/quad_heap.h' removed 'src/3rdparty/lemon/lemon/preflow.h' removed 'src/3rdparty/lemon/lemon/planarity.h' removed 'src/3rdparty/lemon/lemon/path.h' removed 'src/3rdparty/lemon/lemon/pairing_heap.h' removed 'src/3rdparty/lemon/lemon/network_simplex.h' removed 'src/3rdparty/lemon/lemon/nauty_reader.h' removed 'src/3rdparty/lemon/lemon/min_cost_arborescence.h' removed 'src/3rdparty/lemon/lemon/math.h' removed 'src/3rdparty/lemon/lemon/matching.h' removed 'src/3rdparty/lemon/lemon/maps.h' removed 'src/3rdparty/lemon/lemon/lp_skeleton.h' removed 'src/3rdparty/lemon/lemon/lp_skeleton.cc' removed 'src/3rdparty/lemon/lemon/lp_base.h' removed 'src/3rdparty/lemon/lemon/lp_base.cc' removed 'src/3rdparty/lemon/lemon/lp.h' removed 'src/3rdparty/lemon/lemon/list_graph.h' removed 'src/3rdparty/lemon/lemon/lgf_writer.h' removed 'src/3rdparty/lemon/lemon/lgf_reader.h' removed 'src/3rdparty/lemon/lemon/lemon.pc.in' removed 'src/3rdparty/lemon/lemon/kruskal.h' removed 'src/3rdparty/lemon/lemon/karp_mmc.h' removed 'src/3rdparty/lemon/lemon/hypercube_graph.h' removed 'src/3rdparty/lemon/lemon/howard_mmc.h' removed 'src/3rdparty/lemon/lemon/hartmann_orlin_mmc.h' removed 'src/3rdparty/lemon/lemon/hao_orlin.h' removed 'src/3rdparty/lemon/lemon/grid_graph.h' removed 'src/3rdparty/lemon/lemon/graph_to_eps.h' removed 'src/3rdparty/lemon/lemon/gomory_hu.h' removed 'src/3rdparty/lemon/lemon/glpk.h' removed 'src/3rdparty/lemon/lemon/glpk.cc' removed 'src/3rdparty/lemon/lemon/full_graph.h' removed 'src/3rdparty/lemon/lemon/fractional_matching.h' removed 'src/3rdparty/lemon/lemon/fib_heap.h' removed 'src/3rdparty/lemon/lemon/euler.h' removed 'src/3rdparty/lemon/lemon/error.h' removed 'src/3rdparty/lemon/lemon/elevator.h' removed 'src/3rdparty/lemon/lemon/edge_set.h' removed 'src/3rdparty/lemon/lemon/dimacs.h' removed 'src/3rdparty/lemon/lemon/dim2.h' removed 'src/3rdparty/lemon/lemon/dijkstra.h' removed 'src/3rdparty/lemon/lemon/dheap.h' removed 'src/3rdparty/lemon/lemon/dfs.h' removed 'src/3rdparty/lemon/lemon/cycle_canceling.h' removed 'src/3rdparty/lemon/lemon/cplex.h' removed 'src/3rdparty/lemon/lemon/cplex.cc' removed 'src/3rdparty/lemon/lemon/counter.h' removed 'src/3rdparty/lemon/lemon/cost_scaling.h' removed 'src/3rdparty/lemon/lemon/core.h' removed 'src/3rdparty/lemon/lemon/connectivity.h' removed 'src/3rdparty/lemon/lemon/config.h.in' removed 'src/3rdparty/lemon/lemon/config.h.cmake' removed 'src/3rdparty/lemon/lemon/config.h' removed 'src/3rdparty/lemon/lemon/concepts/path.h' removed 'src/3rdparty/lemon/lemon/concepts/maps.h' removed 'src/3rdparty/lemon/lemon/concepts/heap.h' removed 'src/3rdparty/lemon/lemon/concepts/graph_components.h' removed 'src/3rdparty/lemon/lemon/concepts/graph.h' removed 'src/3rdparty/lemon/lemon/concepts/digraph.h' removed directory 'src/3rdparty/lemon/lemon/concepts' removed 'src/3rdparty/lemon/lemon/concept_check.h' removed 'src/3rdparty/lemon/lemon/color.h' removed 'src/3rdparty/lemon/lemon/color.cc' removed 'src/3rdparty/lemon/lemon/clp.h' removed 'src/3rdparty/lemon/lemon/clp.cc' removed 'src/3rdparty/lemon/lemon/circulation.h' removed 'src/3rdparty/lemon/lemon/cbc.h' removed 'src/3rdparty/lemon/lemon/cbc.cc' removed 'src/3rdparty/lemon/lemon/capacity_scaling.h' removed 'src/3rdparty/lemon/lemon/bucket_heap.h' removed 'src/3rdparty/lemon/lemon/bits/windows.h' removed 'src/3rdparty/lemon/lemon/bits/windows.cc' removed 'src/3rdparty/lemon/lemon/bits/vector_map.h' removed 'src/3rdparty/lemon/lemon/bits/variant.h' removed 'src/3rdparty/lemon/lemon/bits/traits.h' removed 'src/3rdparty/lemon/lemon/bits/solver_bits.h' removed 'src/3rdparty/lemon/lemon/bits/path_dump.h' removed 'src/3rdparty/lemon/lemon/bits/map_extender.h' removed 'src/3rdparty/lemon/lemon/bits/graph_extender.h' removed 'src/3rdparty/lemon/lemon/bits/graph_adaptor_extender.h' removed 'src/3rdparty/lemon/lemon/bits/enable_if.h' removed 'src/3rdparty/lemon/lemon/bits/edge_set_extender.h' removed 'src/3rdparty/lemon/lemon/bits/default_map.h' removed 'src/3rdparty/lemon/lemon/bits/bezier.h' removed 'src/3rdparty/lemon/lemon/bits/array_map.h' removed 'src/3rdparty/lemon/lemon/bits/alteration_notifier.h' removed directory 'src/3rdparty/lemon/lemon/bits' removed 'src/3rdparty/lemon/lemon/binomial_heap.h' removed 'src/3rdparty/lemon/lemon/bin_heap.h' removed 'src/3rdparty/lemon/lemon/bfs.h' removed 'src/3rdparty/lemon/lemon/bellman_ford.h' removed 'src/3rdparty/lemon/lemon/base.cc' removed 'src/3rdparty/lemon/lemon/assert.h' removed 'src/3rdparty/lemon/lemon/arg_parser.h' removed 'src/3rdparty/lemon/lemon/arg_parser.cc' removed 'src/3rdparty/lemon/lemon/adaptors.h' removed 'src/3rdparty/lemon/lemon/CMakeLists.txt' removed directory 'src/3rdparty/lemon/lemon' removed 'src/3rdparty/lemon/README' removed 'src/3rdparty/lemon/LICENSE' removed 'src/3rdparty/lemon/AUTHORS' removed directory 'src/3rdparty/lemon' removed 'src/3rdparty/rapidxml/rapidxml.hpp' removed 'src/3rdparty/rapidxml/license.txt' removed directory 'src/3rdparty/rapidxml' * Applying chemkit-0.1-multilib.patch ... [ ok ] * Applying chemkit-0.1-unbundle.patch ... [ ok ] * Hardcoded definition(s) removed in CMakeLists.txt: * set(CMAKE_BUILD_TYPE Release CACHE STRING "Choose the type of build." FORCE >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit ... >>> Working in BUILD_DIR: "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build" cmake -C /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/gentoo_common_config.cmake -G Unix Makefiles -DCMAKE_INSTALL_PREFIX=/usr -DCHEMKIT_BUILD_EXAMPLES=no -DCHEMKIT_BUILD_DEMOS=no -DCHEMKIT_BUILD_BINDINGS_PYTHON=yes -DCHEMKIT_BUILD_APPS=OFF -DCHEMKIT_BUILD_PLUGIN_BABEL=OFF -DCHEMKIT_BUILD_QT_DESIGNER_PLUGINS=OFF -DCHEMKIT_WITH_GRAPHICS=OFF -DCHEMKIT_WITH_GUI=OFF -DCHEMKIT_WITH_WEB=OFF -DCHEMKIT_BUILD_TESTS=no -DUSE_SYSTEM_INCHI=ON -DUSE_SYSTEM_JSONCPP=OFF -DUSE_SYSTEM_RAPIDXML=ON -DUSE_SYSTEM_XDRF=OFF -DCMAKE_BUILD_TYPE=Gentoo -DCMAKE_TOOLCHAIN_FILE=/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/gentoo_toolchain.cmake /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit loading initial cache file /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/gentoo_common_config.cmake -- The C compiler identification is GNU 9.1.0 -- The CXX compiler identification is GNU 9.1.0 -- Check for working C compiler: /usr/bin/x86_64-pc-linux-gnu-gcc -- Check for working C compiler: /usr/bin/x86_64-pc-linux-gnu-gcc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/x86_64-pc-linux-gnu-g++ -- Check for working CXX compiler: /usr/bin/x86_64-pc-linux-gnu-g++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Eigen3: /usr/include/eigen3 (Required is at least version "2.91.0") -- Found Boost: /usr/include (found version "1.70.0") -- Looking for pthread.h -- Looking for pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Found Boost: /usr/include (found version "1.70.0") found components: system filesystem thread chrono date_time atomic CMake Warning (dev) at src/CMakeLists.txt:14 (get_target_property): Policy CMP0026 is not set: Disallow use of the LOCATION target property. Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy command to set the policy and suppress this warning. The LOCATION property should not be read from target "chemkit". Use the target name directly with add_custom_command, or use the generator expression $, as appropriate. Call Stack (most recent call first): src/chemkit/CMakeLists.txt:129 (add_chemkit_library) This warning is for project developers. Use -Wno-dev to suppress it. -- Found Boost: /usr/include (found version "1.70.0") found components: iostreams regex CMake Warning (dev) at src/CMakeLists.txt:14 (get_target_property): Policy CMP0026 is not set: Disallow use of the LOCATION target property. Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy command to set the policy and suppress this warning. The LOCATION property should not be read from target "chemkit-io". Use the target name directly with add_custom_command, or use the generator expression $, as appropriate. Call Stack (most recent call first): src/io/CMakeLists.txt:35 (add_chemkit_library) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at src/CMakeLists.txt:14 (get_target_property): Policy CMP0026 is not set: Disallow use of the LOCATION target property. Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy command to set the policy and suppress this warning. The LOCATION property should not be read from target "chemkit-md". Use the target name directly with add_custom_command, or use the generator expression $, as appropriate. Call Stack (most recent call first): src/md/CMakeLists.txt:40 (add_chemkit_library) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at src/CMakeLists.txt:14 (get_target_property): Policy CMP0026 is not set: Disallow use of the LOCATION target property. Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy command to set the policy and suppress this warning. The LOCATION property should not be read from target "chemkit-md-io". Use the target name directly with add_custom_command, or use the generator expression $, as appropriate. Call Stack (most recent call first): src/md-io/CMakeLists.txt:27 (add_chemkit_library) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at src/plugins/CMakeLists.txt:12 (get_target_property): Policy CMP0026 is not set: Disallow use of the LOCATION target property. Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy command to set the policy and suppress this warning. The LOCATION property should not be read from target "amber". Use the target name directly with add_custom_command, or use the generator expression $, as appropriate. Call Stack (most recent call first): src/plugins/amber/CMakeLists.txt:18 (add_chemkit_plugin) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at src/plugins/CMakeLists.txt:12 (get_target_property): Policy CMP0026 is not set: Disallow use of the LOCATION target property. Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy command to set the policy and suppress this warning. The LOCATION property should not be read from target "apol". Use the target name directly with add_custom_command, or use the generator expression $, as appropriate. Call Stack (most recent call first): src/plugins/apol/CMakeLists.txt:9 (add_chemkit_plugin) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at src/plugins/CMakeLists.txt:12 (get_target_property): Policy CMP0026 is not set: Disallow use of the LOCATION target property. Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy command to set the policy and suppress this warning. The LOCATION property should not be read from target "chemjson". Use the target name directly with add_custom_command, or use the generator expression $, as appropriate. Call Stack (most recent call first): src/plugins/chemjson/CMakeLists.txt:19 (add_chemkit_plugin) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at src/plugins/CMakeLists.txt:12 (get_target_property): Policy CMP0026 is not set: Disallow use of the LOCATION target property. Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy command to set the policy and suppress this warning. The LOCATION property should not be read from target "cml". Use the target name directly with add_custom_command, or use the generator expression $, as appropriate. Call Stack (most recent call first): src/plugins/cml/CMakeLists.txt:13 (add_chemkit_plugin) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at src/plugins/CMakeLists.txt:12 (get_target_property): Policy CMP0026 is not set: Disallow use of the LOCATION target property. Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy command to set the policy and suppress this warning. The LOCATION property should not be read from target "countdescriptors". Use the target name directly with add_custom_command, or use the generator expression $, as appropriate. Call Stack (most recent call first): src/plugins/countdescriptors/CMakeLists.txt:9 (add_chemkit_plugin) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at src/plugins/CMakeLists.txt:12 (get_target_property): Policy CMP0026 is not set: Disallow use of the LOCATION target property. Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy command to set the policy and suppress this warning. The LOCATION property should not be read from target "elementtypers". Use the target name directly with add_custom_command, or use the generator expression $, as appropriate. Call Stack (most recent call first): src/plugins/elementtypers/CMakeLists.txt:11 (add_chemkit_plugin) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at src/plugins/CMakeLists.txt:12 (get_target_property): Policy CMP0026 is not set: Disallow use of the LOCATION target property. Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy command to set the policy and suppress this warning. The LOCATION property should not be read from target "fhz". Use the target name directly with add_custom_command, or use the generator expression $, as appropriate. Call Stack (most recent call first): src/plugins/fhz/CMakeLists.txt:13 (add_chemkit_plugin) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at src/plugins/CMakeLists.txt:12 (get_target_property): Policy CMP0026 is not set: Disallow use of the LOCATION target property. Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy command to set the policy and suppress this warning. The LOCATION property should not be read from target "formula". Use the target name directly with add_custom_command, or use the generator expression $, as appropriate. Call Stack (most recent call first): src/plugins/formula/CMakeLists.txt:11 (add_chemkit_plugin) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at src/plugins/CMakeLists.txt:12 (get_target_property): Policy CMP0026 is not set: Disallow use of the LOCATION target property. Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy command to set the policy and suppress this warning. The LOCATION property should not be read from target "fp2". Use the target name directly with add_custom_command, or use the generator expression $, as appropriate. Call Stack (most recent call first): src/plugins/fp2/CMakeLists.txt:9 (add_chemkit_plugin) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at src/plugins/CMakeLists.txt:12 (get_target_property): Policy CMP0026 is not set: Disallow use of the LOCATION target property. Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy command to set the policy and suppress this warning. The LOCATION property should not be read from target "fps". Use the target name directly with add_custom_command, or use the generator expression $, as appropriate. Call Stack (most recent call first): src/plugins/fps/CMakeLists.txt:13 (add_chemkit_plugin) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at src/plugins/CMakeLists.txt:12 (get_target_property): Policy CMP0026 is not set: Disallow use of the LOCATION target property. Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy command to set the policy and suppress this warning. The LOCATION property should not be read from target "gasteiger". Use the target name directly with add_custom_command, or use the generator expression $, as appropriate. Call Stack (most recent call first): src/plugins/gasteiger/CMakeLists.txt:9 (add_chemkit_plugin) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at src/plugins/CMakeLists.txt:12 (get_target_property): Policy CMP0026 is not set: Disallow use of the LOCATION target property. Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy command to set the policy and suppress this warning. The LOCATION property should not be read from target "gaussian". Use the target name directly with add_custom_command, or use the generator expression $, as appropriate. Call Stack (most recent call first): src/plugins/gaussian/CMakeLists.txt:13 (add_chemkit_plugin) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at src/plugins/CMakeLists.txt:12 (get_target_property): Policy CMP0026 is not set: Disallow use of the LOCATION target property. Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy command to set the policy and suppress this warning. The LOCATION property should not be read from target "graphdescriptors". Use the target name directly with add_custom_command, or use the generator expression $, as appropriate. Call Stack (most recent call first): src/plugins/graphdescriptors/CMakeLists.txt:9 (add_chemkit_plugin) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at src/plugins/CMakeLists.txt:12 (get_target_property): Policy CMP0026 is not set: Disallow use of the LOCATION target property. Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy command to set the policy and suppress this warning. The LOCATION property should not be read from target "gromacs". Use the target name directly with add_custom_command, or use the generator expression $, as appropriate. Call Stack (most recent call first): src/plugins/gromacs/CMakeLists.txt:14 (add_chemkit_plugin) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at src/plugins/CMakeLists.txt:12 (get_target_property): Policy CMP0026 is not set: Disallow use of the LOCATION target property. Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy command to set the policy and suppress this warning. The LOCATION property should not be read from target "hydrogenbonds". Use the target name directly with add_custom_command, or use the generator expression $, as appropriate. Call Stack (most recent call first): src/plugins/hydrogenbonds/CMakeLists.txt:10 (add_chemkit_plugin) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at src/plugins/CMakeLists.txt:12 (get_target_property): Policy CMP0026 is not set: Disallow use of the LOCATION target property. Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy command to set the policy and suppress this warning. The LOCATION property should not be read from target "inchi". Use the target name directly with add_custom_command, or use the generator expression $, as appropriate. Call Stack (most recent call first): src/plugins/inchi/CMakeLists.txt:14 (add_chemkit_plugin) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at src/plugins/CMakeLists.txt:12 (get_target_property): Policy CMP0026 is not set: Disallow use of the LOCATION target property. Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy command to set the policy and suppress this warning. The LOCATION property should not be read from target "mannhold". Use the target name directly with add_custom_command, or use the generator expression $, as appropriate. Call Stack (most recent call first): src/plugins/mannhold/CMakeLists.txt:9 (add_chemkit_plugin) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at src/plugins/CMakeLists.txt:12 (get_target_property): Policy CMP0026 is not set: Disallow use of the LOCATION target property. Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy command to set the policy and suppress this warning. The LOCATION property should not be read from target "massdescriptors". Use the target name directly with add_custom_command, or use the generator expression $, as appropriate. Call Stack (most recent call first): src/plugins/massdescriptors/CMakeLists.txt:9 (add_chemkit_plugin) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at src/plugins/CMakeLists.txt:12 (get_target_property): Policy CMP0026 is not set: Disallow use of the LOCATION target property. Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy command to set the policy and suppress this warning. The LOCATION property should not be read from target "mcdl". Use the target name directly with add_custom_command, or use the generator expression $, as appropriate. Call Stack (most recent call first): src/plugins/mcdl/CMakeLists.txt:10 (add_chemkit_plugin) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at src/plugins/CMakeLists.txt:12 (get_target_property): Policy CMP0026 is not set: Disallow use of the LOCATION target property. Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy command to set the policy and suppress this warning. The LOCATION property should not be read from target "mdl". Use the target name directly with add_custom_command, or use the generator expression $, as appropriate. Call Stack (most recent call first): src/plugins/mdl/CMakeLists.txt:13 (add_chemkit_plugin) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at src/plugins/CMakeLists.txt:12 (get_target_property): Policy CMP0026 is not set: Disallow use of the LOCATION target property. Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy command to set the policy and suppress this warning. The LOCATION property should not be read from target "mmff". Use the target name directly with add_custom_command, or use the generator expression $, as appropriate. Call Stack (most recent call first): src/plugins/mmff/CMakeLists.txt:15 (add_chemkit_plugin) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at src/plugins/CMakeLists.txt:12 (get_target_property): Policy CMP0026 is not set: Disallow use of the LOCATION target property. Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy command to set the policy and suppress this warning. The LOCATION property should not be read from target "mopac". Use the target name directly with add_custom_command, or use the generator expression $, as appropriate. Call Stack (most recent call first): src/plugins/mopac/CMakeLists.txt:14 (add_chemkit_plugin) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at src/plugins/CMakeLists.txt:12 (get_target_property): Policy CMP0026 is not set: Disallow use of the LOCATION target property. Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy command to set the policy and suppress this warning. The LOCATION property should not be read from target "moriguchi". Use the target name directly with add_custom_command, or use the generator expression $, as appropriate. Call Stack (most recent call first): src/plugins/moriguchi/CMakeLists.txt:9 (add_chemkit_plugin) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at src/plugins/CMakeLists.txt:12 (get_target_property): Policy CMP0026 is not set: Disallow use of the LOCATION target property. Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy command to set the policy and suppress this warning. The LOCATION property should not be read from target "opls". Use the target name directly with add_custom_command, or use the generator expression $, as appropriate. Call Stack (most recent call first): src/plugins/opls/CMakeLists.txt:12 (add_chemkit_plugin) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at src/plugins/CMakeLists.txt:12 (get_target_property): Policy CMP0026 is not set: Disallow use of the LOCATION target property. Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy command to set the policy and suppress this warning. The LOCATION property should not be read from target "pdb". Use the target name directly with add_custom_command, or use the generator expression $, as appropriate. Call Stack (most recent call first): src/plugins/pdb/CMakeLists.txt:14 (add_chemkit_plugin) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at src/plugins/CMakeLists.txt:12 (get_target_property): Policy CMP0026 is not set: Disallow use of the LOCATION target property. Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy command to set the policy and suppress this warning. The LOCATION property should not be read from target "pqr". Use the target name directly with add_custom_command, or use the generator expression $, as appropriate. Call Stack (most recent call first): src/plugins/pqr/CMakeLists.txt:13 (add_chemkit_plugin) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at src/plugins/CMakeLists.txt:12 (get_target_property): Policy CMP0026 is not set: Disallow use of the LOCATION target property. Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy command to set the policy and suppress this warning. The LOCATION property should not be read from target "pubchem". Use the target name directly with add_custom_command, or use the generator expression $, as appropriate. Call Stack (most recent call first): src/plugins/pubchem/CMakeLists.txt:9 (add_chemkit_plugin) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at src/plugins/CMakeLists.txt:12 (get_target_property): Policy CMP0026 is not set: Disallow use of the LOCATION target property. Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy command to set the policy and suppress this warning. The LOCATION property should not be read from target "randicindex". Use the target name directly with add_custom_command, or use the generator expression $, as appropriate. Call Stack (most recent call first): src/plugins/randicindex/CMakeLists.txt:9 (add_chemkit_plugin) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at src/plugins/CMakeLists.txt:12 (get_target_property): Policy CMP0026 is not set: Disallow use of the LOCATION target property. Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy command to set the policy and suppress this warning. The LOCATION property should not be read from target "rof5". Use the target name directly with add_custom_command, or use the generator expression $, as appropriate. Call Stack (most recent call first): src/plugins/rof5/CMakeLists.txt:10 (add_chemkit_plugin) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at src/plugins/CMakeLists.txt:12 (get_target_property): Policy CMP0026 is not set: Disallow use of the LOCATION target property. Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy command to set the policy and suppress this warning. The LOCATION property should not be read from target "rotatablebonds". Use the target name directly with add_custom_command, or use the generator expression $, as appropriate. Call Stack (most recent call first): src/plugins/rotatablebonds/CMakeLists.txt:9 (add_chemkit_plugin) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at src/plugins/CMakeLists.txt:12 (get_target_property): Policy CMP0026 is not set: Disallow use of the LOCATION target property. Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy command to set the policy and suppress this warning. The LOCATION property should not be read from target "smiles". Use the target name directly with add_custom_command, or use the generator expression $, as appropriate. Call Stack (most recent call first): src/plugins/smiles/CMakeLists.txt:14 (add_chemkit_plugin) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at src/plugins/CMakeLists.txt:12 (get_target_property): Policy CMP0026 is not set: Disallow use of the LOCATION target property. Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy command to set the policy and suppress this warning. The LOCATION property should not be read from target "surfacedescriptors". Use the target name directly with add_custom_command, or use the generator expression $, as appropriate. Call Stack (most recent call first): src/plugins/surfacedescriptors/CMakeLists.txt:9 (add_chemkit_plugin) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at src/plugins/CMakeLists.txt:12 (get_target_property): Policy CMP0026 is not set: Disallow use of the LOCATION target property. Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy command to set the policy and suppress this warning. The LOCATION property should not be read from target "sybyl". Use the target name directly with add_custom_command, or use the generator expression $, as appropriate. Call Stack (most recent call first): src/plugins/sybyl/CMakeLists.txt:13 (add_chemkit_plugin) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at src/plugins/CMakeLists.txt:12 (get_target_property): Policy CMP0026 is not set: Disallow use of the LOCATION target property. Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy command to set the policy and suppress this warning. The LOCATION property should not be read from target "tpsa". Use the target name directly with add_custom_command, or use the generator expression $, as appropriate. Call Stack (most recent call first): src/plugins/tpsa/CMakeLists.txt:9 (add_chemkit_plugin) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at src/plugins/CMakeLists.txt:12 (get_target_property): Policy CMP0026 is not set: Disallow use of the LOCATION target property. Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy command to set the policy and suppress this warning. The LOCATION property should not be read from target "txyz". Use the target name directly with add_custom_command, or use the generator expression $, as appropriate. Call Stack (most recent call first): src/plugins/txyz/CMakeLists.txt:13 (add_chemkit_plugin) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at src/plugins/CMakeLists.txt:12 (get_target_property): Policy CMP0026 is not set: Disallow use of the LOCATION target property. Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy command to set the policy and suppress this warning. The LOCATION property should not be read from target "uff". Use the target name directly with add_custom_command, or use the generator expression $, as appropriate. Call Stack (most recent call first): src/plugins/uff/CMakeLists.txt:17 (add_chemkit_plugin) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at src/plugins/CMakeLists.txt:12 (get_target_property): Policy CMP0026 is not set: Disallow use of the LOCATION target property. Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy command to set the policy and suppress this warning. The LOCATION property should not be read from target "vabc". Use the target name directly with add_custom_command, or use the generator expression $, as appropriate. Call Stack (most recent call first): src/plugins/vabc/CMakeLists.txt:9 (add_chemkit_plugin) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at src/plugins/CMakeLists.txt:12 (get_target_property): Policy CMP0026 is not set: Disallow use of the LOCATION target property. Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy command to set the policy and suppress this warning. The LOCATION property should not be read from target "wienerindex". Use the target name directly with add_custom_command, or use the generator expression $, as appropriate. Call Stack (most recent call first): src/plugins/wienerindex/CMakeLists.txt:9 (add_chemkit_plugin) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at src/plugins/CMakeLists.txt:12 (get_target_property): Policy CMP0026 is not set: Disallow use of the LOCATION target property. Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy command to set the policy and suppress this warning. The LOCATION property should not be read from target "xyz". Use the target name directly with add_custom_command, or use the generator expression $, as appropriate. Call Stack (most recent call first): src/plugins/xyz/CMakeLists.txt:13 (add_chemkit_plugin) This warning is for project developers. Use -Wno-dev to suppress it. -- Found PythonLibs: /usr/lib64/libpython2.7.so (found version "2.7.16") -- Found PythonInterp: /var/tmp/portage/sci-libs/chemkit-0.1-r2/temp/python2.7/bin/python (found version "2.7.16") -- <<< Gentoo configuration >>> Build type Gentoo Install path /usr Compiler flags: C -O2 -pipe -march=native C++ -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML Linker flags: Executable -Wl,-O1 -Wl,--as-needed Module -Wl,-O1 -Wl,--as-needed Shared -Wl,-O1 -Wl,--as-needed -- Configuring done -- Generating done -- Build files have been written to: /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit ... >>> Working in BUILD_DIR: "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build" make -j1 VERBOSE=1 /usr/bin/cmake -S/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit -B/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/CMakeFiles /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[1]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' make -f src/chemkit/CMakeFiles/chemkit.dir/build.make src/chemkit/CMakeFiles/chemkit.dir/depend make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit/CMakeFiles/chemkit.dir/DependInfo.cmake Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit/CMakeFiles/chemkit.dir/DependInfo.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit/CMakeFiles/chemkit.dir/depend.internal". Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit/CMakeFiles/chemkit.dir/depend.internal". Scanning dependencies of target chemkit make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' make -f src/chemkit/CMakeFiles/chemkit.dir/build.make src/chemkit/CMakeFiles/chemkit.dir/build make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 0%] Building CXX object src/chemkit/CMakeFiles/chemkit.dir/alphashape.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit && /usr/bin/x86_64-pc-linux-gnu-g++ -DCHEMKIT_LIBRARY -Dchemkit_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/chemkit.dir/alphashape.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/alphashape.cpp [ 1%] Building CXX object src/chemkit/CMakeFiles/chemkit.dir/aminoacid.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit && /usr/bin/x86_64-pc-linux-gnu-g++ -DCHEMKIT_LIBRARY -Dchemkit_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/chemkit.dir/aminoacid.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/aminoacid.cpp [ 1%] Building CXX object src/chemkit/CMakeFiles/chemkit.dir/aromaticitymodel.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit && /usr/bin/x86_64-pc-linux-gnu-g++ -DCHEMKIT_LIBRARY -Dchemkit_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/chemkit.dir/aromaticitymodel.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/aromaticitymodel.cpp [ 2%] Building CXX object src/chemkit/CMakeFiles/chemkit.dir/atom.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit && /usr/bin/x86_64-pc-linux-gnu-g++ -DCHEMKIT_LIBRARY -Dchemkit_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/chemkit.dir/atom.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/atom.cpp [ 2%] Building CXX object src/chemkit/CMakeFiles/chemkit.dir/atomtyper.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit && /usr/bin/x86_64-pc-linux-gnu-g++ -DCHEMKIT_LIBRARY -Dchemkit_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/chemkit.dir/atomtyper.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/atomtyper.cpp [ 3%] Building CXX object src/chemkit/CMakeFiles/chemkit.dir/bond.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit && /usr/bin/x86_64-pc-linux-gnu-g++ -DCHEMKIT_LIBRARY -Dchemkit_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/chemkit.dir/bond.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/bond.cpp [ 3%] Building CXX object src/chemkit/CMakeFiles/chemkit.dir/bondpredictor.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit && /usr/bin/x86_64-pc-linux-gnu-g++ -DCHEMKIT_LIBRARY -Dchemkit_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/chemkit.dir/bondpredictor.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/bondpredictor.cpp [ 4%] Building CXX object src/chemkit/CMakeFiles/chemkit.dir/cartesiancoordinates.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit && /usr/bin/x86_64-pc-linux-gnu-g++ -DCHEMKIT_LIBRARY -Dchemkit_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/chemkit.dir/cartesiancoordinates.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/cartesiancoordinates.cpp In file included from /usr/include/eigen3/Eigen/Core:439, from /usr/include/eigen3/Eigen/Dense:1, from /usr/include/eigen3/Eigen/Eigen:1, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/matrix.h:41, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/cartesiancoordinates.h:45, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/cartesiancoordinates.cpp:36: /usr/include/eigen3/Eigen/src/Core/Product.h: In instantiation of ‘Eigen::Product::Product(const Lhs&, const Rhs&) [with _Lhs = Eigen::Transpose >; _Rhs = Eigen::Matrix; int Option = 0; Eigen::Product::Lhs = Eigen::Transpose >; Eigen::Product::Rhs = Eigen::Matrix]’: /usr/include/eigen3/Eigen/src/Core/GeneralProduct.h:415:10: required from ‘const Eigen::Product Eigen::MatrixBase::operator*(const Eigen::MatrixBase&) const [with OtherDerived = Eigen::Matrix; Derived = Eigen::Transpose >]’ /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/cartesiancoordinates.cpp:433:59: required from here /usr/include/eigen3/Eigen/src/Core/Product.h:93:86: warning: implicitly-declared ‘constexpr Eigen::Transpose >::Transpose(const Eigen::Transpose >&)’ is deprecated [-Wdeprecated-copy] 93 | oduct(const Lhs& lhs, const Rhs& rhs) : m_lhs(lhs), m_rhs(rhs) | ^ In file included from /usr/include/eigen3/Eigen/Core:445, from /usr/include/eigen3/Eigen/Dense:1, from /usr/include/eigen3/Eigen/Eigen:1, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/matrix.h:41, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/cartesiancoordinates.h:45, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/cartesiancoordinates.cpp:36: /usr/include/eigen3/Eigen/src/Core/Assign.h:55:30: note: because ‘Eigen::Transpose >’ has user-provided ‘Derived& Eigen::MatrixBase::operator=(const Eigen::MatrixBase&) [with Derived = Eigen::Transpose >]’ 55 | EIGEN_STRONG_INLINE Derived& MatrixBase::operator=(const MatrixBase& other) | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/eigen3/Eigen/Core:461, from /usr/include/eigen3/Eigen/Dense:1, from /usr/include/eigen3/Eigen/Eigen:1, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/matrix.h:41, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/cartesiancoordinates.h:45, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/cartesiancoordinates.cpp:36: /usr/include/eigen3/Eigen/src/Core/CwiseBinaryOp.h: In instantiation of ‘Eigen::CwiseBinaryOp::CwiseBinaryOp(const Lhs&, const Rhs&, const BinaryOp&) [with BinaryOp = Eigen::internal::scalar_sum_op; LhsType = const Eigen::ArrayWrapper, const Eigen::Matrix, const Eigen::Matrix > >; RhsType = const Eigen::CwiseNullaryOp, const Eigen::Array >; Eigen::CwiseBinaryOp::Lhs = Eigen::ArrayWrapper, const Eigen::Matrix, const Eigen::Matrix > >; Eigen::CwiseBinaryOp::Rhs = Eigen::CwiseNullaryOp, const Eigen::Array >]’: /usr/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseBinaryOps.h:215:1: required from ‘typename Eigen::internal::enable_if::Scalar, typename Eigen::internal::promote_scalar_arg::Scalar, T, Eigen::internal::has_ReturnType::Scalar, T, Eigen::internal::scalar_sum_op::Scalar, T> > >::value>::type>, const Derived, const typename Eigen::internal::plain_constant_type::Scalar, T, Eigen::internal::has_ReturnType::Scalar, T, Eigen::internal::scalar_sum_op::Scalar, T> > >::value>::type>::type> >::type Eigen::ArrayBase::operator+(const T&) const [with T = double; Derived = Eigen::ArrayWrapper, const Eigen::Matrix, const Eigen::Matrix > >; typename Eigen::internal::enable_if::Scalar, typename Eigen::internal::promote_scalar_arg::Scalar, T, Eigen::internal::has_ReturnType::Scalar, T, Eigen::internal::scalar_sum_op::Scalar, T> > >::value>::type>, const Derived, const typename Eigen::internal::plain_constant_type::Scalar, T, Eigen::internal::has_ReturnType::Scalar, T, Eigen::internal::scalar_sum_op::Scalar, T> > >::value>::type>::type> >::type = const Eigen::CwiseBinaryOp, const Eigen::ArrayWrapper, const Eigen::Matrix, const Eigen::Matrix > >, const Eigen::CwiseNullaryOp, const Eigen::Array > >]’ /usr/include/eigen3/Eigen/src/Geometry/AngleAxis.h:240:61: required from ‘Eigen::AngleAxis::Matrix3 Eigen::AngleAxis::toRotationMatrix() const [with _Scalar = double; Eigen::AngleAxis::Matrix3 = Eigen::Matrix]’ /usr/include/eigen3/Eigen/src/Geometry/RotationBase.h:45:110: required from ‘Eigen::RotationBase::RotationMatrixType Eigen::RotationBase::toRotationMatrix() const [with Derived = Eigen::AngleAxis; int _Dim = 3; Eigen::RotationBase::RotationMatrixType = Eigen::Matrix; typename Eigen::internal::traits::Scalar = double]’ /usr/include/eigen3/Eigen/src/Geometry/RotationBase.h:191:29: required from ‘Eigen::Matrix Eigen::internal::toRotationMatrix(const Eigen::RotationBase&) [with Scalar = double; int Dim = 3; OtherDerived = Eigen::AngleAxis]’ /usr/include/eigen3/Eigen/src/Geometry/Transform.h:1030:52: required from ‘Eigen::Transform& Eigen::Transform::operator=(const Eigen::RotationBase&) [with Derived = Eigen::AngleAxis; _Scalar = double; int _Dim = 3; int _Mode = 3; int _Options = 0]’ /usr/include/eigen3/Eigen/src/Geometry/Transform.h:282:11: required from ‘Eigen::Transform::Transform(const Eigen::RotationBase&) [with Derived = Eigen::AngleAxis; _Scalar = double; int _Dim = 3; int _Mode = 3; int _Options = 0]’ /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/cartesiancoordinates.cpp:295:85: required from here /usr/include/eigen3/Eigen/src/Core/CwiseBinaryOp.h:105:49: warning: implicitly-declared ‘Eigen::ArrayWrapper, const Eigen::Matrix, const Eigen::Matrix > >::ArrayWrapper(const Eigen::ArrayWrapper, const Eigen::Matrix, const Eigen::Matrix > >&)’ is deprecated [-Wdeprecated-copy] 105 | : m_lhs(aLhs), m_rhs(aRhs), m_functor(func) | ^ In file included from /usr/include/eigen3/Eigen/Core:448, from /usr/include/eigen3/Eigen/Dense:1, from /usr/include/eigen3/Eigen/Eigen:1, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/matrix.h:41, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/cartesiancoordinates.h:45, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/cartesiancoordinates.cpp:36: /usr/include/eigen3/Eigen/src/Core/ArrayBase.h:107:14: note: because ‘Eigen::ArrayWrapper, const Eigen::Matrix, const Eigen::Matrix > >’ has user-provided ‘Derived& Eigen::ArrayBase::operator=(const Eigen::ArrayBase&) [with Derived = Eigen::ArrayWrapper, const Eigen::Matrix, const Eigen::Matrix > >]’ 107 | Derived& operator=(const ArrayBase& other) | ^~~~~~~~ In file included from /usr/include/eigen3/Eigen/Core:439, from /usr/include/eigen3/Eigen/Dense:1, from /usr/include/eigen3/Eigen/Eigen:1, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/matrix.h:41, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/cartesiancoordinates.h:45, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/cartesiancoordinates.cpp:36: /usr/include/eigen3/Eigen/src/Core/Product.h: In instantiation of ‘Eigen::Product::Product(const Lhs&, const Rhs&) [with _Lhs = Eigen::Transpose >; _Rhs = Eigen::Matrix; int Option = 1; Eigen::Product::Lhs = Eigen::Transpose >; Eigen::Product::Rhs = Eigen::Matrix]’: /usr/include/eigen3/Eigen/src/Core/GeneralProduct.h:450:10: required from ‘const Eigen::Product Eigen::MatrixBase::lazyProduct(const Eigen::MatrixBase&) const [with OtherDerived = Eigen::Matrix; Derived = Eigen::Transpose >]’ /usr/include/eigen3/Eigen/src/Core/ProductEvaluators.h:397:29: required from ‘static void Eigen::internal::generic_product_impl::evalTo(Dst&, const Lhs&, const Rhs&) [with Dst = Eigen::Matrix; Lhs = Eigen::Transpose >; Rhs = Eigen::Matrix]’ /usr/include/eigen3/Eigen/src/Core/products/GeneralMatrixMatrix.h:431:26: required from ‘static void Eigen::internal::generic_product_impl::evalTo(Dst&, const Lhs&, const Rhs&) [with Dst = Eigen::Matrix; Lhs = Eigen::Transpose >; Rhs = Eigen::Matrix]’ /usr/include/eigen3/Eigen/src/Core/ProductEvaluators.h:148:43: required from ‘static void Eigen::internal::Assignment, Eigen::internal::assign_op, Eigen::internal::Dense2Dense, typename Eigen::internal::enable_if<((Options == Eigen::DefaultProduct) || (Options == Eigen::AliasFreeProduct))>::type>::run(DstXprType&, const SrcXprType&, const Eigen::internal::assign_op&) [with DstXprType = Eigen::Matrix; Lhs = Eigen::Transpose >; Rhs = Eigen::Matrix; int Options = 0; Scalar = double; Eigen::internal::Assignment, Eigen::internal::assign_op, Eigen::internal::Dense2Dense, typename Eigen::internal::enable_if<((Options == Eigen::DefaultProduct) || (Options == Eigen::AliasFreeProduct))>::type>::SrcXprType = Eigen::Product >, Eigen::Matrix, 0>]’ /usr/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:49: required from ‘void Eigen::internal::call_assignment_no_alias(Dst&, const Src&, const Func&) [with Dst = Eigen::Matrix; Src = Eigen::Product >, Eigen::Matrix, 0>; Func = Eigen::internal::assign_op]’ /usr/include/eigen3/Eigen/src/Core/PlainObjectBase.h:732:41: required from ‘Derived& Eigen::PlainObjectBase::_set_noalias(const Eigen::DenseBase&) [with OtherDerived = Eigen::Product >, Eigen::Matrix, 0>; Derived = Eigen::Matrix]’ /usr/include/eigen3/Eigen/src/Core/PlainObjectBase.h:537:7: required from ‘Eigen::PlainObjectBase::PlainObjectBase(const Eigen::DenseBase&) [with OtherDerived = Eigen::Product >, Eigen::Matrix, 0>; Derived = Eigen::Matrix]’ /usr/include/eigen3/Eigen/src/Core/Matrix.h:377:29: required from ‘Eigen::Matrix<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>::Matrix(const Eigen::EigenBase&) [with OtherDerived = Eigen::Product >, Eigen::Matrix, 0>; _Scalar = double; int _Rows = 3; int _Cols = 3; int _Options = 0; int _MaxRows = 3; int _MaxCols = 3]’ /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/cartesiancoordinates.cpp:433:59: required from here /usr/include/eigen3/Eigen/src/Core/Product.h:93:86: warning: implicitly-declared ‘constexpr Eigen::Transpose >::Transpose(const Eigen::Transpose >&)’ is deprecated [-Wdeprecated-copy] 93 | oduct(const Lhs& lhs, const Rhs& rhs) : m_lhs(lhs), m_rhs(rhs) | ^ In file included from /usr/include/eigen3/Eigen/Core:445, from /usr/include/eigen3/Eigen/Dense:1, from /usr/include/eigen3/Eigen/Eigen:1, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/matrix.h:41, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/cartesiancoordinates.h:45, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/cartesiancoordinates.cpp:36: /usr/include/eigen3/Eigen/src/Core/Assign.h:55:30: note: because ‘Eigen::Transpose >’ has user-provided ‘Derived& Eigen::MatrixBase::operator=(const Eigen::MatrixBase&) [with Derived = Eigen::Transpose >]’ 55 | EIGEN_STRONG_INLINE Derived& MatrixBase::operator=(const MatrixBase& other) | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/eigen3/Eigen/Core:493, from /usr/include/eigen3/Eigen/Dense:1, from /usr/include/eigen3/Eigen/Eigen:1, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/matrix.h:41, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/cartesiancoordinates.h:45, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/cartesiancoordinates.cpp:36: /usr/include/eigen3/Eigen/src/Core/ProductEvaluators.h: In instantiation of ‘Eigen::internal::product_evaluator, ProductTag, Eigen::DenseShape, Eigen::DenseShape>::product_evaluator(const XprType&) [with Lhs = Eigen::Transpose >; Rhs = Eigen::Matrix; int ProductTag = 8; typename Eigen::internal::traits::Rhs>::Scalar = double; typename Eigen::internal::traits::Lhs>::Scalar = double; Eigen::internal::product_evaluator, ProductTag, Eigen::DenseShape, Eigen::DenseShape>::XprType = Eigen::Product >, Eigen::Matrix, 1>]’: /usr/include/eigen3/Eigen/src/Core/ProductEvaluators.h:35:90: required from ‘Eigen::internal::evaluator >::evaluator(const XprType&) [with Lhs = Eigen::Transpose >; Rhs = Eigen::Matrix; int Options = 1; Eigen::internal::evaluator >::XprType = Eigen::Product >, Eigen::Matrix, 1>]’ /usr/include/eigen3/Eigen/src/Core/AssignEvaluator.h:730:20: required from ‘void Eigen::internal::call_dense_assignment_loop(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen::Matrix; SrcXprType = Eigen::Product >, Eigen::Matrix, 1>; Functor = Eigen::internal::assign_op]’ /usr/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:31: required from ‘static void Eigen::internal::Assignment::run(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen::Matrix; SrcXprType = Eigen::Product >, Eigen::Matrix, 1>; Functor = Eigen::internal::assign_op; Weak = void]’ /usr/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:49: required from ‘void Eigen::internal::call_assignment_no_alias(Dst&, const Src&, const Func&) [with Dst = Eigen::Matrix; Src = Eigen::Product >, Eigen::Matrix, 1>; Func = Eigen::internal::assign_op]’ /usr/include/eigen3/Eigen/src/Core/ProductEvaluators.h:397:29: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /usr/include/eigen3/Eigen/src/Core/ProductEvaluators.h:148:43: required from ‘static void Eigen::internal::Assignment, Eigen::internal::assign_op, Eigen::internal::Dense2Dense, typename Eigen::internal::enable_if<((Options == Eigen::DefaultProduct) || (Options == Eigen::AliasFreeProduct))>::type>::run(DstXprType&, const SrcXprType&, const Eigen::internal::assign_op&) [with DstXprType = Eigen::Matrix; Lhs = Eigen::Transpose >; Rhs = Eigen::Matrix; int Options = 0; Scalar = double; Eigen::internal::Assignment, Eigen::internal::assign_op, Eigen::internal::Dense2Dense, typename Eigen::internal::enable_if<((Options == Eigen::DefaultProduct) || (Options == Eigen::AliasFreeProduct))>::type>::SrcXprType = Eigen::Product >, Eigen::Matrix, 0>]’ /usr/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:49: required from ‘void Eigen::internal::call_assignment_no_alias(Dst&, const Src&, const Func&) [with Dst = Eigen::Matrix; Src = Eigen::Product >, Eigen::Matrix, 0>; Func = Eigen::internal::assign_op]’ /usr/include/eigen3/Eigen/src/Core/PlainObjectBase.h:732:41: required from ‘Derived& Eigen::PlainObjectBase::_set_noalias(const Eigen::DenseBase&) [with OtherDerived = Eigen::Product >, Eigen::Matrix, 0>; Derived = Eigen::Matrix]’ /usr/include/eigen3/Eigen/src/Core/PlainObjectBase.h:537:7: required from ‘Eigen::PlainObjectBase::PlainObjectBase(const Eigen::DenseBase&) [with OtherDerived = Eigen::Product >, Eigen::Matrix, 0>; Derived = Eigen::Matrix]’ /usr/include/eigen3/Eigen/src/Core/Matrix.h:377:29: required from ‘Eigen::Matrix<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>::Matrix(const Eigen::EigenBase&) [with OtherDerived = Eigen::Product >, Eigen::Matrix, 0>; _Scalar = double; int _Rows = 3; int _Cols = 3; int _Options = 0; int _MaxRows = 3; int _MaxCols = 3]’ /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/cartesiancoordinates.cpp:433:59: required from here /usr/include/eigen3/Eigen/src/Core/ProductEvaluators.h:451:34: warning: implicitly-declared ‘constexpr Eigen::Transpose >::Transpose(const Eigen::Transpose >&)’ is deprecated [-Wdeprecated-copy] 451 | m_innerDim(xpr.lhs().cols()) | ^ In file included from /usr/include/eigen3/Eigen/Core:445, from /usr/include/eigen3/Eigen/Dense:1, from /usr/include/eigen3/Eigen/Eigen:1, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/matrix.h:41, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/cartesiancoordinates.h:45, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/cartesiancoordinates.cpp:36: /usr/include/eigen3/Eigen/src/Core/Assign.h:55:30: note: because ‘Eigen::Transpose >’ has user-provided ‘Derived& Eigen::MatrixBase::operator=(const Eigen::MatrixBase&) [with Derived = Eigen::Transpose >]’ 55 | EIGEN_STRONG_INLINE Derived& MatrixBase::operator=(const MatrixBase& other) | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/eigen3/Eigen/Core:474, from /usr/include/eigen3/Eigen/Dense:1, from /usr/include/eigen3/Eigen/Eigen:1, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/matrix.h:41, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/cartesiancoordinates.h:45, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/cartesiancoordinates.cpp:36: /usr/include/eigen3/Eigen/src/Core/Transpose.h: In instantiation of ‘Eigen::Transpose::Transpose(MatrixType&) [with MatrixType = const Eigen::Block >, 1, -1, true>]’: /usr/include/eigen3/Eigen/src/Core/Transpose.h:186:10: required from ‘Eigen::DenseBase::ConstTransposeReturnType Eigen::DenseBase::transpose() const [with Derived = Eigen::Block >, 1, -1, true>; Eigen::DenseBase::ConstTransposeReturnType = const Eigen::Transpose >, 1, -1, true> >]’ /usr/include/eigen3/Eigen/src/Core/ProductEvaluators.h:552:40: required from ‘const CoeffReturnType Eigen::internal::product_evaluator, ProductTag, Eigen::DenseShape, Eigen::DenseShape>::coeff(Eigen::Index, Eigen::Index) const [with Lhs = Eigen::Transpose >; Rhs = Eigen::Matrix; int ProductTag = 8; typename Eigen::internal::traits::Rhs>::Scalar = double; typename Eigen::internal::traits::Lhs>::Scalar = double; Eigen::internal::product_evaluator, ProductTag, Eigen::DenseShape, Eigen::DenseShape>::CoeffReturnType = double; Eigen::Index = long int]’ /usr/include/eigen3/Eigen/src/Core/AssignEvaluator.h:631:5: required from ‘void Eigen::internal::generic_dense_assignment_kernel::assignCoeff(Eigen::Index, Eigen::Index) [with DstEvaluatorTypeT = Eigen::internal::evaluator >; SrcEvaluatorTypeT = Eigen::internal::evaluator >, Eigen::Matrix, 1> >; Functor = Eigen::internal::assign_op; int Version = 0; Eigen::Index = long int]’ /usr/include/eigen3/Eigen/src/Core/AssignEvaluator.h:645:5: required from ‘void Eigen::internal::generic_dense_assignment_kernel::assignCoeffByOuterInner(Eigen::Index, Eigen::Index) [with DstEvaluatorTypeT = Eigen::internal::evaluator >; SrcEvaluatorTypeT = Eigen::internal::evaluator >, Eigen::Matrix, 1> >; Functor = Eigen::internal::assign_op; int Version = 0; Eigen::Index = long int]’ /usr/include/eigen3/Eigen/src/Core/AssignEvaluator.h:326:9: required from ‘static void Eigen::internal::dense_assignment_loop::run(Kernel&) [with Kernel = Eigen::internal::generic_dense_assignment_kernel >, Eigen::internal::evaluator >, Eigen::Matrix, 1> >, Eigen::internal::assign_op, 0>]’ /usr/include/eigen3/Eigen/src/Core/AssignEvaluator.h:741:37: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /usr/include/eigen3/Eigen/src/Core/ProductEvaluators.h:148:43: required from ‘static void Eigen::internal::Assignment, Eigen::internal::assign_op, Eigen::internal::Dense2Dense, typename Eigen::internal::enable_if<((Options == Eigen::DefaultProduct) || (Options == Eigen::AliasFreeProduct))>::type>::run(DstXprType&, const SrcXprType&, const Eigen::internal::assign_op&) [with DstXprType = Eigen::Matrix; Lhs = Eigen::Transpose >; Rhs = Eigen::Matrix; int Options = 0; Scalar = double; Eigen::internal::Assignment, Eigen::internal::assign_op, Eigen::internal::Dense2Dense, typename Eigen::internal::enable_if<((Options == Eigen::DefaultProduct) || (Options == Eigen::AliasFreeProduct))>::type>::SrcXprType = Eigen::Product >, Eigen::Matrix, 0>]’ /usr/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:49: required from ‘void Eigen::internal::call_assignment_no_alias(Dst&, const Src&, const Func&) [with Dst = Eigen::Matrix; Src = Eigen::Product >, Eigen::Matrix, 0>; Func = Eigen::internal::assign_op]’ /usr/include/eigen3/Eigen/src/Core/PlainObjectBase.h:732:41: required from ‘Derived& Eigen::PlainObjectBase::_set_noalias(const Eigen::DenseBase&) [with OtherDerived = Eigen::Product >, Eigen::Matrix, 0>; Derived = Eigen::Matrix]’ /usr/include/eigen3/Eigen/src/Core/PlainObjectBase.h:537:7: required from ‘Eigen::PlainObjectBase::PlainObjectBase(const Eigen::DenseBase&) [with OtherDerived = Eigen::Product >, Eigen::Matrix, 0>; Derived = Eigen::Matrix]’ /usr/include/eigen3/Eigen/src/Core/Matrix.h:377:29: required from ‘Eigen::Matrix<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>::Matrix(const Eigen::EigenBase&) [with OtherDerived = Eigen::Product >, Eigen::Matrix, 0>; _Scalar = double; int _Rows = 3; int _Cols = 3; int _Options = 0; int _MaxRows = 3; int _MaxCols = 3]’ /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/cartesiancoordinates.cpp:433:59: required from here /usr/include/eigen3/Eigen/src/Core/Transpose.h:64:68: warning: implicitly-declared ‘Eigen::Block >, 1, -1, true>::Block(const Eigen::Block >, 1, -1, true>&)’ is deprecated [-Wdeprecated-copy] 64 | explicit inline Transpose(MatrixType& matrix) : m_matrix(matrix) {} | ^ In file included from /usr/include/eigen3/Eigen/Core:88, from /usr/include/eigen3/Eigen/Dense:1, from /usr/include/eigen3/Eigen/Eigen:1, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/matrix.h:41, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/cartesiancoordinates.h:45, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/cartesiancoordinates.cpp:36: /usr/include/eigen3/Eigen/src/Core/util/Macros.h:830:52: note: because ‘Eigen::Block >, 1, -1, true>’ has user-provided ‘Eigen::BlockImpl& Eigen::BlockImpl::operator=(const Eigen::BlockImpl&) [with XprType = const Eigen::Transpose >; int BlockRows = 1; int BlockCols = -1; bool InnerPanel = true]’ 830 | EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Derived& operator=(const Derived& other) \ | ^~~~~~~~ /usr/include/eigen3/Eigen/src/Core/util/Macros.h:842:53: note: in expansion of macro ‘EIGEN_INHERIT_ASSIGNMENT_EQUAL_OPERATOR’ 842 | #define EIGEN_INHERIT_ASSIGNMENT_OPERATORS(Derived) EIGEN_INHERIT_ASSIGNMENT_EQUAL_OPERATOR(Derived) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/eigen3/Eigen/src/Core/Block.h:161:5: note: in expansion of macro ‘EIGEN_INHERIT_ASSIGNMENT_OPERATORS’ 161 | EIGEN_INHERIT_ASSIGNMENT_OPERATORS(BlockImpl) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/eigen3/Eigen/Core:461, from /usr/include/eigen3/Eigen/Dense:1, from /usr/include/eigen3/Eigen/Eigen:1, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/matrix.h:41, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/cartesiancoordinates.h:45, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/cartesiancoordinates.cpp:36: /usr/include/eigen3/Eigen/src/Core/CwiseBinaryOp.h: In instantiation of ‘Eigen::CwiseBinaryOp::CwiseBinaryOp(const Lhs&, const Rhs&, const BinaryOp&) [with BinaryOp = Eigen::internal::scalar_product_op; LhsType = const Eigen::Transpose >, 1, -1, true> >; RhsType = const Eigen::Block, -1, 1, true>; Eigen::CwiseBinaryOp::Lhs = Eigen::Transpose >, 1, -1, true> >; Eigen::CwiseBinaryOp::Rhs = Eigen::Block, -1, 1, true>]’: /usr/include/eigen3/Eigen/src/Core/../plugins/MatrixCwiseBinaryOps.h:25:10: required from ‘const Eigen::CwiseBinaryOp::Scalar, typename Eigen::internal::traits::Scalar>, const Derived, const OtherDerived> Eigen::MatrixBase::cwiseProduct(const Eigen::MatrixBase&) const [with OtherDerived = Eigen::Block, -1, 1, true>; Derived = Eigen::Transpose >, 1, -1, true> >; typename Eigen::internal::traits::Scalar = double; typename Eigen::internal::traits::Scalar = double]’ /usr/include/eigen3/Eigen/src/Core/ProductEvaluators.h:552:72: required from ‘const CoeffReturnType Eigen::internal::product_evaluator, ProductTag, Eigen::DenseShape, Eigen::DenseShape>::coeff(Eigen::Index, Eigen::Index) const [with Lhs = Eigen::Transpose >; Rhs = Eigen::Matrix; int ProductTag = 8; typename Eigen::internal::traits::Rhs>::Scalar = double; typename Eigen::internal::traits::Lhs>::Scalar = double; Eigen::internal::product_evaluator, ProductTag, Eigen::DenseShape, Eigen::DenseShape>::CoeffReturnType = double; Eigen::Index = long int]’ /usr/include/eigen3/Eigen/src/Core/AssignEvaluator.h:631:5: required from ‘void Eigen::internal::generic_dense_assignment_kernel::assignCoeff(Eigen::Index, Eigen::Index) [with DstEvaluatorTypeT = Eigen::internal::evaluator >; SrcEvaluatorTypeT = Eigen::internal::evaluator >, Eigen::Matrix, 1> >; Functor = Eigen::internal::assign_op; int Version = 0; Eigen::Index = long int]’ /usr/include/eigen3/Eigen/src/Core/AssignEvaluator.h:645:5: required from ‘void Eigen::internal::generic_dense_assignment_kernel::assignCoeffByOuterInner(Eigen::Index, Eigen::Index) [with DstEvaluatorTypeT = Eigen::internal::evaluator >; SrcEvaluatorTypeT = Eigen::internal::evaluator >, Eigen::Matrix, 1> >; Functor = Eigen::internal::assign_op; int Version = 0; Eigen::Index = long int]’ /usr/include/eigen3/Eigen/src/Core/AssignEvaluator.h:326:9: required from ‘static void Eigen::internal::dense_assignment_loop::run(Kernel&) [with Kernel = Eigen::internal::generic_dense_assignment_kernel >, Eigen::internal::evaluator >, Eigen::Matrix, 1> >, Eigen::internal::assign_op, 0>]’ /usr/include/eigen3/Eigen/src/Core/AssignEvaluator.h:741:37: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /usr/include/eigen3/Eigen/src/Core/ProductEvaluators.h:148:43: required from ‘static void Eigen::internal::Assignment, Eigen::internal::assign_op, Eigen::internal::Dense2Dense, typename Eigen::internal::enable_if<((Options == Eigen::DefaultProduct) || (Options == Eigen::AliasFreeProduct))>::type>::run(DstXprType&, const SrcXprType&, const Eigen::internal::assign_op&) [with DstXprType = Eigen::Matrix; Lhs = Eigen::Transpose >; Rhs = Eigen::Matrix; int Options = 0; Scalar = double; Eigen::internal::Assignment, Eigen::internal::assign_op, Eigen::internal::Dense2Dense, typename Eigen::internal::enable_if<((Options == Eigen::DefaultProduct) || (Options == Eigen::AliasFreeProduct))>::type>::SrcXprType = Eigen::Product >, Eigen::Matrix, 0>]’ /usr/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:49: required from ‘void Eigen::internal::call_assignment_no_alias(Dst&, const Src&, const Func&) [with Dst = Eigen::Matrix; Src = Eigen::Product >, Eigen::Matrix, 0>; Func = Eigen::internal::assign_op]’ /usr/include/eigen3/Eigen/src/Core/PlainObjectBase.h:732:41: required from ‘Derived& Eigen::PlainObjectBase::_set_noalias(const Eigen::DenseBase&) [with OtherDerived = Eigen::Product >, Eigen::Matrix, 0>; Derived = Eigen::Matrix]’ /usr/include/eigen3/Eigen/src/Core/PlainObjectBase.h:537:7: required from ‘Eigen::PlainObjectBase::PlainObjectBase(const Eigen::DenseBase&) [with OtherDerived = Eigen::Product >, Eigen::Matrix, 0>; Derived = Eigen::Matrix]’ /usr/include/eigen3/Eigen/src/Core/Matrix.h:377:29: required from ‘Eigen::Matrix<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>::Matrix(const Eigen::EigenBase&) [with OtherDerived = Eigen::Product >, Eigen::Matrix, 0>; _Scalar = double; int _Rows = 3; int _Cols = 3; int _Options = 0; int _MaxRows = 3; int _MaxCols = 3]’ /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/cartesiancoordinates.cpp:433:59: required from here /usr/include/eigen3/Eigen/src/Core/CwiseBinaryOp.h:105:49: warning: implicitly-declared ‘Eigen::Transpose >, 1, -1, true> >::Transpose(const Eigen::Transpose >, 1, -1, true> >&)’ is deprecated [-Wdeprecated-copy] 105 | : m_lhs(aLhs), m_rhs(aRhs), m_functor(func) | ^ In file included from /usr/include/eigen3/Eigen/Core:445, from /usr/include/eigen3/Eigen/Dense:1, from /usr/include/eigen3/Eigen/Eigen:1, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/matrix.h:41, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/cartesiancoordinates.h:45, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/cartesiancoordinates.cpp:36: /usr/include/eigen3/Eigen/src/Core/Assign.h:55:30: note: because ‘Eigen::Transpose >, 1, -1, true> >’ has user-provided ‘Derived& Eigen::MatrixBase::operator=(const Eigen::MatrixBase&) [with Derived = Eigen::Transpose >, 1, -1, true> >]’ 55 | EIGEN_STRONG_INLINE Derived& MatrixBase::operator=(const MatrixBase& other) | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/eigen3/Eigen/Core:461, from /usr/include/eigen3/Eigen/Dense:1, from /usr/include/eigen3/Eigen/Eigen:1, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/matrix.h:41, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/cartesiancoordinates.h:45, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/cartesiancoordinates.cpp:36: /usr/include/eigen3/Eigen/src/Core/CwiseBinaryOp.h:105:49: warning: implicitly-declared ‘Eigen::Block, -1, 1, true>::Block(const Eigen::Block, -1, 1, true>&)’ is deprecated [-Wdeprecated-copy] 105 | : m_lhs(aLhs), m_rhs(aRhs), m_functor(func) | ^ In file included from /usr/include/eigen3/Eigen/Core:88, from /usr/include/eigen3/Eigen/Dense:1, from /usr/include/eigen3/Eigen/Eigen:1, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/matrix.h:41, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/cartesiancoordinates.h:45, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/cartesiancoordinates.cpp:36: /usr/include/eigen3/Eigen/src/Core/util/Macros.h:830:52: note: because ‘Eigen::Block, -1, 1, true>’ has user-provided ‘Eigen::BlockImpl& Eigen::BlockImpl::operator=(const Eigen::BlockImpl&) [with XprType = const Eigen::Matrix; int BlockRows = -1; int BlockCols = 1; bool InnerPanel = true]’ 830 | EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Derived& operator=(const Derived& other) \ | ^~~~~~~~ /usr/include/eigen3/Eigen/src/Core/util/Macros.h:842:53: note: in expansion of macro ‘EIGEN_INHERIT_ASSIGNMENT_EQUAL_OPERATOR’ 842 | #define EIGEN_INHERIT_ASSIGNMENT_OPERATORS(Derived) EIGEN_INHERIT_ASSIGNMENT_EQUAL_OPERATOR(Derived) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/eigen3/Eigen/src/Core/Block.h:161:5: note: in expansion of macro ‘EIGEN_INHERIT_ASSIGNMENT_OPERATORS’ 161 | EIGEN_INHERIT_ASSIGNMENT_OPERATORS(BlockImpl) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/eigen3/Eigen/Core:472, from /usr/include/eigen3/Eigen/Dense:1, from /usr/include/eigen3/Eigen/Eigen:1, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/matrix.h:41, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/cartesiancoordinates.h:45, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/cartesiancoordinates.cpp:36: /usr/include/eigen3/Eigen/src/Core/Block.h: In instantiation of ‘Eigen::internal::BlockImpl_dense::BlockImpl_dense(XprType&, Eigen::Index) [with XprType = const Eigen::Transpose >; int BlockRows = 1; int BlockCols = -1; bool InnerPanel = true; Eigen::Index = long int]’: /usr/include/eigen3/Eigen/src/Core/Block.h:162:75: required from ‘Eigen::BlockImpl::BlockImpl(XprType&, Eigen::Index) [with XprType = const Eigen::Transpose >; int BlockRows = 1; int BlockCols = -1; bool InnerPanel = true; Eigen::Index = long int]’ /usr/include/eigen3/Eigen/src/Core/Block.h:118:53: required from ‘Eigen::Block::Block(XprType&, Eigen::Index) [with XprType = const Eigen::Transpose >; int BlockRows = 1; int BlockCols = -1; bool InnerPanel = true; Eigen::Index = long int]’ /usr/include/eigen3/Eigen/src/Core/../plugins/BlockMethods.h:868:10: required from ‘Eigen::DenseBase::ConstRowXpr Eigen::DenseBase::row(Eigen::Index) const [with Derived = Eigen::Transpose >; Eigen::DenseBase::ConstRowXpr = const Eigen::Block >, 1, -1, true>; Eigen::Index = long int]’ /usr/include/eigen3/Eigen/src/Core/ProductEvaluators.h:552:28: required from ‘const CoeffReturnType Eigen::internal::product_evaluator, ProductTag, Eigen::DenseShape, Eigen::DenseShape>::coeff(Eigen::Index, Eigen::Index) const [with Lhs = Eigen::Transpose >; Rhs = Eigen::Matrix; int ProductTag = 8; typename Eigen::internal::traits::Rhs>::Scalar = double; typename Eigen::internal::traits::Lhs>::Scalar = double; Eigen::internal::product_evaluator, ProductTag, Eigen::DenseShape, Eigen::DenseShape>::CoeffReturnType = double; Eigen::Index = long int]’ /usr/include/eigen3/Eigen/src/Core/AssignEvaluator.h:631:5: required from ‘void Eigen::internal::generic_dense_assignment_kernel::assignCoeff(Eigen::Index, Eigen::Index) [with DstEvaluatorTypeT = Eigen::internal::evaluator >; SrcEvaluatorTypeT = Eigen::internal::evaluator >, Eigen::Matrix, 1> >; Functor = Eigen::internal::assign_op; int Version = 0; Eigen::Index = long int]’ /usr/include/eigen3/Eigen/src/Core/AssignEvaluator.h:645:5: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /usr/include/eigen3/Eigen/src/Core/ProductEvaluators.h:148:43: required from ‘static void Eigen::internal::Assignment, Eigen::internal::assign_op, Eigen::internal::Dense2Dense, typename Eigen::internal::enable_if<((Options == Eigen::DefaultProduct) || (Options == Eigen::AliasFreeProduct))>::type>::run(DstXprType&, const SrcXprType&, const Eigen::internal::assign_op&) [with DstXprType = Eigen::Matrix; Lhs = Eigen::Transpose >; Rhs = Eigen::Matrix; int Options = 0; Scalar = double; Eigen::internal::Assignment, Eigen::internal::assign_op, Eigen::internal::Dense2Dense, typename Eigen::internal::enable_if<((Options == Eigen::DefaultProduct) || (Options == Eigen::AliasFreeProduct))>::type>::SrcXprType = Eigen::Product >, Eigen::Matrix, 0>]’ /usr/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:49: required from ‘void Eigen::internal::call_assignment_no_alias(Dst&, const Src&, const Func&) [with Dst = Eigen::Matrix; Src = Eigen::Product >, Eigen::Matrix, 0>; Func = Eigen::internal::assign_op]’ /usr/include/eigen3/Eigen/src/Core/PlainObjectBase.h:732:41: required from ‘Derived& Eigen::PlainObjectBase::_set_noalias(const Eigen::DenseBase&) [with OtherDerived = Eigen::Product >, Eigen::Matrix, 0>; Derived = Eigen::Matrix]’ /usr/include/eigen3/Eigen/src/Core/PlainObjectBase.h:537:7: required from ‘Eigen::PlainObjectBase::PlainObjectBase(const Eigen::DenseBase&) [with OtherDerived = Eigen::Product >, Eigen::Matrix, 0>; Derived = Eigen::Matrix]’ /usr/include/eigen3/Eigen/src/Core/Matrix.h:377:29: required from ‘Eigen::Matrix<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>::Matrix(const Eigen::EigenBase&) [with OtherDerived = Eigen::Product >, Eigen::Matrix, 0>; _Scalar = double; int _Rows = 3; int _Cols = 3; int _Options = 0; int _MaxRows = 3; int _MaxCols = 3]’ /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/cartesiancoordinates.cpp:433:59: required from here /usr/include/eigen3/Eigen/src/Core/Block.h:353:86: warning: implicitly-declared ‘constexpr Eigen::Transpose >::Transpose(const Eigen::Transpose >&)’ is deprecated [-Wdeprecated-copy] 353 | ckRows==XprType::RowsAtCompileTime) && (BlockCols==1) ? i : 0) | ^ In file included from /usr/include/eigen3/Eigen/Core:445, from /usr/include/eigen3/Eigen/Dense:1, from /usr/include/eigen3/Eigen/Eigen:1, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/matrix.h:41, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/cartesiancoordinates.h:45, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/cartesiancoordinates.cpp:36: /usr/include/eigen3/Eigen/src/Core/Assign.h:55:30: note: because ‘Eigen::Transpose >’ has user-provided ‘Derived& Eigen::MatrixBase::operator=(const Eigen::MatrixBase&) [with Derived = Eigen::Transpose >]’ 55 | EIGEN_STRONG_INLINE Derived& MatrixBase::operator=(const MatrixBase& other) | ^~~~~~~~~~~~~~~~~~~ [ 4%] Building CXX object src/chemkit/CMakeFiles/chemkit.dir/chemkit.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit && /usr/bin/x86_64-pc-linux-gnu-g++ -DCHEMKIT_LIBRARY -Dchemkit_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/chemkit.dir/chemkit.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/chemkit.cpp [ 5%] Building CXX object src/chemkit/CMakeFiles/chemkit.dir/coordinatepredictor.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit && /usr/bin/x86_64-pc-linux-gnu-g++ -DCHEMKIT_LIBRARY -Dchemkit_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/chemkit.dir/coordinatepredictor.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/coordinatepredictor.cpp [ 5%] Building CXX object src/chemkit/CMakeFiles/chemkit.dir/coordinateset.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit && /usr/bin/x86_64-pc-linux-gnu-g++ -DCHEMKIT_LIBRARY -Dchemkit_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/chemkit.dir/coordinateset.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/coordinateset.cpp [ 5%] Building CXX object src/chemkit/CMakeFiles/chemkit.dir/delaunaytriangulation.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit && /usr/bin/x86_64-pc-linux-gnu-g++ -DCHEMKIT_LIBRARY -Dchemkit_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/chemkit.dir/delaunaytriangulation.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/delaunaytriangulation.cpp /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/delaunaytriangulation.cpp:100:6: warning: ‘bool chemkit::{anonymous}::Tetrahedron::contains(int) const’ defined but not used [-Wunused-function] 100 | bool Tetrahedron::contains(int vertex) const | ^~~~~~~~~~~ [ 6%] Building CXX object src/chemkit/CMakeFiles/chemkit.dir/diagramcoordinates.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit && /usr/bin/x86_64-pc-linux-gnu-g++ -DCHEMKIT_LIBRARY -Dchemkit_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/chemkit.dir/diagramcoordinates.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/diagramcoordinates.cpp [ 6%] Building CXX object src/chemkit/CMakeFiles/chemkit.dir/dynamiclibrary.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit && /usr/bin/x86_64-pc-linux-gnu-g++ -DCHEMKIT_LIBRARY -Dchemkit_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/chemkit.dir/dynamiclibrary.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/dynamiclibrary.cpp [ 7%] Building CXX object src/chemkit/CMakeFiles/chemkit.dir/element.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit && /usr/bin/x86_64-pc-linux-gnu-g++ -DCHEMKIT_LIBRARY -Dchemkit_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/chemkit.dir/element.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/element.cpp [ 7%] Building CXX object src/chemkit/CMakeFiles/chemkit.dir/fingerprint.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit && /usr/bin/x86_64-pc-linux-gnu-g++ -DCHEMKIT_LIBRARY -Dchemkit_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/chemkit.dir/fingerprint.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/fingerprint.cpp [ 8%] Building CXX object src/chemkit/CMakeFiles/chemkit.dir/fingerprintsimilaritydescriptor.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit && /usr/bin/x86_64-pc-linux-gnu-g++ -DCHEMKIT_LIBRARY -Dchemkit_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/chemkit.dir/fingerprintsimilaritydescriptor.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/fingerprintsimilaritydescriptor.cpp [ 8%] Building CXX object src/chemkit/CMakeFiles/chemkit.dir/fragment.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit && /usr/bin/x86_64-pc-linux-gnu-g++ -DCHEMKIT_LIBRARY -Dchemkit_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/chemkit.dir/fragment.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/fragment.cpp [ 9%] Building CXX object src/chemkit/CMakeFiles/chemkit.dir/geometry.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit && /usr/bin/x86_64-pc-linux-gnu-g++ -DCHEMKIT_LIBRARY -Dchemkit_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/chemkit.dir/geometry.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/geometry.cpp [ 9%] Building CXX object src/chemkit/CMakeFiles/chemkit.dir/internalcoordinates.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit && /usr/bin/x86_64-pc-linux-gnu-g++ -DCHEMKIT_LIBRARY -Dchemkit_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/chemkit.dir/internalcoordinates.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/internalcoordinates.cpp In file included from /usr/include/eigen3/Eigen/Core:461, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/point3.h:41, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/internalcoordinates.h:43, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/internalcoordinates.cpp:36: /usr/include/eigen3/Eigen/src/Core/CwiseBinaryOp.h: In instantiation of ‘const PlainObject Eigen::MatrixBase::normalized() const [with Derived = Eigen::CwiseBinaryOp, const Eigen::Matrix, const Eigen::Matrix >; Eigen::MatrixBase::PlainObject = Eigen::Matrix]’: /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/internalcoordinates.cpp:256:41: required from here /usr/include/eigen3/Eigen/src/Core/CwiseBinaryOp.h:77:7: warning: implicitly-declared ‘constexpr Eigen::internal::no_assignment_operator::no_assignment_operator(const Eigen::internal::no_assignment_operator&)’ is deprecated [-Wdeprecated-copy] 77 | class CwiseBinaryOp : | ^~~~~~~~~~~~~ In file included from /usr/include/eigen3/Eigen/Core:367, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/point3.h:41, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/internalcoordinates.h:43, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/internalcoordinates.cpp:36: /usr/include/eigen3/Eigen/src/Core/util/XprHelper.h:92:29: note: because ‘Eigen::internal::no_assignment_operator’ has user-provided ‘Eigen::internal::no_assignment_operator& Eigen::internal::no_assignment_operator::operator=(const Eigen::internal::no_assignment_operator&)’ 92 | no_assignment_operator& operator=(const no_assignment_operator&); | ^~~~~~~~ In file included from /usr/include/eigen3/Eigen/Core:466, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/point3.h:41, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/internalcoordinates.h:43, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/internalcoordinates.cpp:36: /usr/include/eigen3/Eigen/src/Core/Dot.h:127:11: note: synthesized method ‘Eigen::CwiseBinaryOp, const Eigen::Matrix, const Eigen::Matrix >::CwiseBinaryOp(const Eigen::CwiseBinaryOp, const Eigen::Matrix, const Eigen::Matrix >&)’ first required here 127 | _Nested n(derived()); | ^ In file included from /usr/include/eigen3/Eigen/Core:474, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/point3.h:41, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/internalcoordinates.h:43, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/internalcoordinates.cpp:36: /usr/include/eigen3/Eigen/src/Core/Transpose.h: In instantiation of ‘Eigen::Transpose::Transpose(MatrixType&) [with MatrixType = const Eigen::Block, 1, 3, false>]’: /usr/include/eigen3/Eigen/src/Core/Transpose.h:186:10: required from ‘Eigen::DenseBase::ConstTransposeReturnType Eigen::DenseBase::transpose() const [with Derived = Eigen::Block, 1, 3, false>; Eigen::DenseBase::ConstTransposeReturnType = const Eigen::Transpose, 1, 3, false> >]’ /usr/include/eigen3/Eigen/src/Core/ProductEvaluators.h:552:40: required from ‘const CoeffReturnType Eigen::internal::product_evaluator, ProductTag, Eigen::DenseShape, Eigen::DenseShape>::coeff(Eigen::Index, Eigen::Index) const [with Lhs = Eigen::Matrix; Rhs = Eigen::Matrix; int ProductTag = 3; typename Eigen::internal::traits::Rhs>::Scalar = double; typename Eigen::internal::traits::Lhs>::Scalar = double; Eigen::internal::product_evaluator, ProductTag, Eigen::DenseShape, Eigen::DenseShape>::CoeffReturnType = double; Eigen::Index = long int]’ /usr/include/eigen3/Eigen/src/Core/AssignEvaluator.h:631:5: required from ‘void Eigen::internal::generic_dense_assignment_kernel::assignCoeff(Eigen::Index, Eigen::Index) [with DstEvaluatorTypeT = Eigen::internal::evaluator >; SrcEvaluatorTypeT = Eigen::internal::evaluator, Eigen::Matrix, 1> >; Functor = Eigen::internal::assign_op; int Version = 0; Eigen::Index = long int]’ /usr/include/eigen3/Eigen/src/Core/AssignEvaluator.h:645:5: required from ‘void Eigen::internal::generic_dense_assignment_kernel::assignCoeffByOuterInner(Eigen::Index, Eigen::Index) [with DstEvaluatorTypeT = Eigen::internal::evaluator >; SrcEvaluatorTypeT = Eigen::internal::evaluator, Eigen::Matrix, 1> >; Functor = Eigen::internal::assign_op; int Version = 0; Eigen::Index = long int]’ /usr/include/eigen3/Eigen/src/Core/AssignEvaluator.h:206:5: required from ‘static void Eigen::internal::copy_using_evaluator_DefaultTraversal_CompleteUnrolling::run(Kernel&) [with Kernel = Eigen::internal::generic_dense_assignment_kernel >, Eigen::internal::evaluator, Eigen::Matrix, 1> >, Eigen::internal::assign_op, 0>; int Index = 2; int Stop = 3]’ /usr/include/eigen3/Eigen/src/Core/AssignEvaluator.h:435:92: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /usr/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:31: required from ‘static void Eigen::internal::Assignment::run(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen::Matrix; SrcXprType = Eigen::CwiseBinaryOp, const Eigen::Product, Eigen::Matrix, 0>, const Eigen::Matrix >; Functor = Eigen::internal::assign_op; Weak = void]’ /usr/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:49: required from ‘void Eigen::internal::call_assignment_no_alias(Dst&, const Src&, const Func&) [with Dst = Eigen::Matrix; Src = Eigen::CwiseBinaryOp, const Eigen::Product, Eigen::Matrix, 0>, const Eigen::Matrix >; Func = Eigen::internal::assign_op]’ /usr/include/eigen3/Eigen/src/Core/PlainObjectBase.h:732:41: required from ‘Derived& Eigen::PlainObjectBase::_set_noalias(const Eigen::DenseBase&) [with OtherDerived = Eigen::CwiseBinaryOp, const Eigen::Product, Eigen::Matrix, 0>, const Eigen::Matrix >; Derived = Eigen::Matrix]’ /usr/include/eigen3/Eigen/src/Core/PlainObjectBase.h:537:7: required from ‘Eigen::PlainObjectBase::PlainObjectBase(const Eigen::DenseBase&) [with OtherDerived = Eigen::CwiseBinaryOp, const Eigen::Product, Eigen::Matrix, 0>, const Eigen::Matrix >; Derived = Eigen::Matrix]’ /usr/include/eigen3/Eigen/src/Core/Matrix.h:377:29: required from ‘Eigen::Matrix<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>::Matrix(const Eigen::EigenBase&) [with OtherDerived = Eigen::CwiseBinaryOp, const Eigen::Product, Eigen::Matrix, 0>, const Eigen::Matrix >; _Scalar = double; int _Rows = 3; int _Cols = 1; int _Options = 0; int _MaxRows = 3; int _MaxCols = 1]’ /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/internalcoordinates.cpp:265:45: required from here /usr/include/eigen3/Eigen/src/Core/Transpose.h:64:68: warning: implicitly-declared ‘Eigen::Block, 1, 3, false>::Block(const Eigen::Block, 1, 3, false>&)’ is deprecated [-Wdeprecated-copy] 64 | explicit inline Transpose(MatrixType& matrix) : m_matrix(matrix) {} | ^ In file included from /usr/include/eigen3/Eigen/Core:88, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/point3.h:41, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/internalcoordinates.h:43, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/internalcoordinates.cpp:36: /usr/include/eigen3/Eigen/src/Core/util/Macros.h:830:52: note: because ‘Eigen::Block, 1, 3, false>’ has user-provided ‘Eigen::BlockImpl& Eigen::BlockImpl::operator=(const Eigen::BlockImpl&) [with XprType = const Eigen::Matrix; int BlockRows = 1; int BlockCols = 3; bool InnerPanel = false]’ 830 | EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Derived& operator=(const Derived& other) \ | ^~~~~~~~ /usr/include/eigen3/Eigen/src/Core/util/Macros.h:842:53: note: in expansion of macro ‘EIGEN_INHERIT_ASSIGNMENT_EQUAL_OPERATOR’ 842 | #define EIGEN_INHERIT_ASSIGNMENT_OPERATORS(Derived) EIGEN_INHERIT_ASSIGNMENT_EQUAL_OPERATOR(Derived) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/eigen3/Eigen/src/Core/Block.h:161:5: note: in expansion of macro ‘EIGEN_INHERIT_ASSIGNMENT_OPERATORS’ 161 | EIGEN_INHERIT_ASSIGNMENT_OPERATORS(BlockImpl) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/eigen3/Eigen/Core:461, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/point3.h:41, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/internalcoordinates.h:43, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/internalcoordinates.cpp:36: /usr/include/eigen3/Eigen/src/Core/CwiseBinaryOp.h: In instantiation of ‘Eigen::CwiseBinaryOp::CwiseBinaryOp(const Lhs&, const Rhs&, const BinaryOp&) [with BinaryOp = Eigen::internal::scalar_product_op; LhsType = const Eigen::Transpose, 1, 3, false> >; RhsType = const Eigen::Block, 3, 1, true>; Eigen::CwiseBinaryOp::Lhs = Eigen::Transpose, 1, 3, false> >; Eigen::CwiseBinaryOp::Rhs = Eigen::Block, 3, 1, true>]’: /usr/include/eigen3/Eigen/src/Core/../plugins/MatrixCwiseBinaryOps.h:25:10: required from ‘const Eigen::CwiseBinaryOp::Scalar, typename Eigen::internal::traits::Scalar>, const Derived, const OtherDerived> Eigen::MatrixBase::cwiseProduct(const Eigen::MatrixBase&) const [with OtherDerived = Eigen::Block, 3, 1, true>; Derived = Eigen::Transpose, 1, 3, false> >; typename Eigen::internal::traits::Scalar = double; typename Eigen::internal::traits::Scalar = double]’ /usr/include/eigen3/Eigen/src/Core/ProductEvaluators.h:552:72: required from ‘const CoeffReturnType Eigen::internal::product_evaluator, ProductTag, Eigen::DenseShape, Eigen::DenseShape>::coeff(Eigen::Index, Eigen::Index) const [with Lhs = Eigen::Matrix; Rhs = Eigen::Matrix; int ProductTag = 3; typename Eigen::internal::traits::Rhs>::Scalar = double; typename Eigen::internal::traits::Lhs>::Scalar = double; Eigen::internal::product_evaluator, ProductTag, Eigen::DenseShape, Eigen::DenseShape>::CoeffReturnType = double; Eigen::Index = long int]’ /usr/include/eigen3/Eigen/src/Core/AssignEvaluator.h:631:5: required from ‘void Eigen::internal::generic_dense_assignment_kernel::assignCoeff(Eigen::Index, Eigen::Index) [with DstEvaluatorTypeT = Eigen::internal::evaluator >; SrcEvaluatorTypeT = Eigen::internal::evaluator, Eigen::Matrix, 1> >; Functor = Eigen::internal::assign_op; int Version = 0; Eigen::Index = long int]’ /usr/include/eigen3/Eigen/src/Core/AssignEvaluator.h:645:5: required from ‘void Eigen::internal::generic_dense_assignment_kernel::assignCoeffByOuterInner(Eigen::Index, Eigen::Index) [with DstEvaluatorTypeT = Eigen::internal::evaluator >; SrcEvaluatorTypeT = Eigen::internal::evaluator, Eigen::Matrix, 1> >; Functor = Eigen::internal::assign_op; int Version = 0; Eigen::Index = long int]’ /usr/include/eigen3/Eigen/src/Core/AssignEvaluator.h:206:5: required from ‘static void Eigen::internal::copy_using_evaluator_DefaultTraversal_CompleteUnrolling::run(Kernel&) [with Kernel = Eigen::internal::generic_dense_assignment_kernel >, Eigen::internal::evaluator, Eigen::Matrix, 1> >, Eigen::internal::assign_op, 0>; int Index = 2; int Stop = 3]’ /usr/include/eigen3/Eigen/src/Core/AssignEvaluator.h:435:92: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /usr/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:31: required from ‘static void Eigen::internal::Assignment::run(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen::Matrix; SrcXprType = Eigen::CwiseBinaryOp, const Eigen::Product, Eigen::Matrix, 0>, const Eigen::Matrix >; Functor = Eigen::internal::assign_op; Weak = void]’ /usr/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:49: required from ‘void Eigen::internal::call_assignment_no_alias(Dst&, const Src&, const Func&) [with Dst = Eigen::Matrix; Src = Eigen::CwiseBinaryOp, const Eigen::Product, Eigen::Matrix, 0>, const Eigen::Matrix >; Func = Eigen::internal::assign_op]’ /usr/include/eigen3/Eigen/src/Core/PlainObjectBase.h:732:41: required from ‘Derived& Eigen::PlainObjectBase::_set_noalias(const Eigen::DenseBase&) [with OtherDerived = Eigen::CwiseBinaryOp, const Eigen::Product, Eigen::Matrix, 0>, const Eigen::Matrix >; Derived = Eigen::Matrix]’ /usr/include/eigen3/Eigen/src/Core/PlainObjectBase.h:537:7: required from ‘Eigen::PlainObjectBase::PlainObjectBase(const Eigen::DenseBase&) [with OtherDerived = Eigen::CwiseBinaryOp, const Eigen::Product, Eigen::Matrix, 0>, const Eigen::Matrix >; Derived = Eigen::Matrix]’ /usr/include/eigen3/Eigen/src/Core/Matrix.h:377:29: required from ‘Eigen::Matrix<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>::Matrix(const Eigen::EigenBase&) [with OtherDerived = Eigen::CwiseBinaryOp, const Eigen::Product, Eigen::Matrix, 0>, const Eigen::Matrix >; _Scalar = double; int _Rows = 3; int _Cols = 1; int _Options = 0; int _MaxRows = 3; int _MaxCols = 1]’ /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/internalcoordinates.cpp:265:45: required from here /usr/include/eigen3/Eigen/src/Core/CwiseBinaryOp.h:105:49: warning: implicitly-declared ‘Eigen::Transpose, 1, 3, false> >::Transpose(const Eigen::Transpose, 1, 3, false> >&)’ is deprecated [-Wdeprecated-copy] 105 | : m_lhs(aLhs), m_rhs(aRhs), m_functor(func) | ^ In file included from /usr/include/eigen3/Eigen/Core:445, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/point3.h:41, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/internalcoordinates.h:43, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/internalcoordinates.cpp:36: /usr/include/eigen3/Eigen/src/Core/Assign.h:55:30: note: because ‘Eigen::Transpose, 1, 3, false> >’ has user-provided ‘Derived& Eigen::MatrixBase::operator=(const Eigen::MatrixBase&) [with Derived = Eigen::Transpose, 1, 3, false> >]’ 55 | EIGEN_STRONG_INLINE Derived& MatrixBase::operator=(const MatrixBase& other) | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/eigen3/Eigen/Core:461, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/point3.h:41, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/internalcoordinates.h:43, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/internalcoordinates.cpp:36: /usr/include/eigen3/Eigen/src/Core/CwiseBinaryOp.h:105:49: warning: implicitly-declared ‘Eigen::Block, 3, 1, true>::Block(const Eigen::Block, 3, 1, true>&)’ is deprecated [-Wdeprecated-copy] 105 | : m_lhs(aLhs), m_rhs(aRhs), m_functor(func) | ^ In file included from /usr/include/eigen3/Eigen/Core:88, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/point3.h:41, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/internalcoordinates.h:43, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/internalcoordinates.cpp:36: /usr/include/eigen3/Eigen/src/Core/util/Macros.h:830:52: note: because ‘Eigen::Block, 3, 1, true>’ has user-provided ‘Eigen::BlockImpl& Eigen::BlockImpl::operator=(const Eigen::BlockImpl&) [with XprType = const Eigen::Matrix; int BlockRows = 3; int BlockCols = 1; bool InnerPanel = true]’ 830 | EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Derived& operator=(const Derived& other) \ | ^~~~~~~~ /usr/include/eigen3/Eigen/src/Core/util/Macros.h:842:53: note: in expansion of macro ‘EIGEN_INHERIT_ASSIGNMENT_EQUAL_OPERATOR’ 842 | #define EIGEN_INHERIT_ASSIGNMENT_OPERATORS(Derived) EIGEN_INHERIT_ASSIGNMENT_EQUAL_OPERATOR(Derived) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/eigen3/Eigen/src/Core/Block.h:161:5: note: in expansion of macro ‘EIGEN_INHERIT_ASSIGNMENT_OPERATORS’ 161 | EIGEN_INHERIT_ASSIGNMENT_OPERATORS(BlockImpl) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 10%] Building CXX object src/chemkit/CMakeFiles/chemkit.dir/isotope.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit && /usr/bin/x86_64-pc-linux-gnu-g++ -DCHEMKIT_LIBRARY -Dchemkit_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/chemkit.dir/isotope.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/isotope.cpp [ 10%] Building CXX object src/chemkit/CMakeFiles/chemkit.dir/lineformat.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit && /usr/bin/x86_64-pc-linux-gnu-g++ -DCHEMKIT_LIBRARY -Dchemkit_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/chemkit.dir/lineformat.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/lineformat.cpp [ 11%] Building CXX object src/chemkit/CMakeFiles/chemkit.dir/moiety.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit && /usr/bin/x86_64-pc-linux-gnu-g++ -DCHEMKIT_LIBRARY -Dchemkit_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/chemkit.dir/moiety.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moiety.cpp [ 11%] Building CXX object src/chemkit/CMakeFiles/chemkit.dir/moleculardescriptor.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit && /usr/bin/x86_64-pc-linux-gnu-g++ -DCHEMKIT_LIBRARY -Dchemkit_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/chemkit.dir/moleculardescriptor.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculardescriptor.cpp [ 11%] Building CXX object src/chemkit/CMakeFiles/chemkit.dir/molecularsurface.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit && /usr/bin/x86_64-pc-linux-gnu-g++ -DCHEMKIT_LIBRARY -Dchemkit_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/chemkit.dir/molecularsurface.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/molecularsurface.cpp [ 12%] Building CXX object src/chemkit/CMakeFiles/chemkit.dir/molecule.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit && /usr/bin/x86_64-pc-linux-gnu-g++ -DCHEMKIT_LIBRARY -Dchemkit_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/chemkit.dir/molecule.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/molecule.cpp [ 12%] Building CXX object src/chemkit/CMakeFiles/chemkit.dir/moleculealigner.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit && /usr/bin/x86_64-pc-linux-gnu-g++ -DCHEMKIT_LIBRARY -Dchemkit_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/chemkit.dir/moleculealigner.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculealigner.cpp In file included from /usr/include/eigen3/Eigen/Core:439, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculealigner.h:43, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculealigner.cpp:36: /usr/include/eigen3/Eigen/src/Core/Product.h: In instantiation of ‘Eigen::Product::Product(const Lhs&, const Rhs&) [with _Lhs = Eigen::Product, Eigen::Matrix, 0>; _Rhs = Eigen::Transpose >; int Option = 0; Eigen::Product::Lhs = Eigen::Product, Eigen::Matrix, 0>; Eigen::Product::Rhs = Eigen::Transpose >]’: /usr/include/eigen3/Eigen/src/Core/GeneralProduct.h:415:10: required from ‘const Eigen::Product Eigen::MatrixBase::operator*(const Eigen::MatrixBase&) const [with OtherDerived = Eigen::Transpose >; Derived = Eigen::Product, Eigen::Matrix, 0>]’ /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculealigner.cpp:198:79: required from here /usr/include/eigen3/Eigen/src/Core/Product.h:93:86: warning: implicitly-declared ‘constexpr Eigen::Transpose >::Transpose(const Eigen::Transpose >&)’ is deprecated [-Wdeprecated-copy] 93 | oduct(const Lhs& lhs, const Rhs& rhs) : m_lhs(lhs), m_rhs(rhs) | ^ In file included from /usr/include/eigen3/Eigen/Core:445, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculealigner.h:43, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculealigner.cpp:36: /usr/include/eigen3/Eigen/src/Core/Assign.h:55:30: note: because ‘Eigen::Transpose >’ has user-provided ‘Derived& Eigen::MatrixBase::operator=(const Eigen::MatrixBase&) [with Derived = Eigen::Transpose >]’ 55 | EIGEN_STRONG_INLINE Derived& MatrixBase::operator=(const MatrixBase& other) | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/eigen3/Eigen/Core:461, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculealigner.h:43, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculealigner.cpp:36: /usr/include/eigen3/Eigen/src/Core/CwiseBinaryOp.h: In instantiation of ‘Eigen::CwiseBinaryOp::CwiseBinaryOp(const Lhs&, const Rhs&, const BinaryOp&) [with BinaryOp = Eigen::internal::scalar_quotient_op; LhsType = const Eigen::Block, -1, -1, false>; RhsType = const Eigen::CwiseNullaryOp, const Eigen::Matrix >; Eigen::CwiseBinaryOp::Lhs = Eigen::Block, -1, -1, false>; Eigen::CwiseBinaryOp::Rhs = Eigen::CwiseNullaryOp, const Eigen::Matrix >]’: /usr/include/eigen3/Eigen/src/Core/../plugins/CommonCwiseBinaryOps.h:69:1: required from ‘typename Eigen::internal::enable_if::Scalar, typename Eigen::internal::promote_scalar_arg::Scalar, T, Eigen::internal::has_ReturnType::Scalar, T, Eigen::internal::scalar_quotient_op::Scalar, T> > >::value>::type>, const Derived, const typename Eigen::internal::plain_constant_type::Scalar, T, Eigen::internal::has_ReturnType::Scalar, T, Eigen::internal::scalar_quotient_op::Scalar, T> > >::value>::type>::type> >::type Eigen::MatrixBase::operator/(const T&) const [with T = double; Derived = Eigen::Block, -1, -1, false>; typename Eigen::internal::enable_if::Scalar, typename Eigen::internal::promote_scalar_arg::Scalar, T, Eigen::internal::has_ReturnType::Scalar, T, Eigen::internal::scalar_quotient_op::Scalar, T> > >::value>::type>, const Derived, const typename Eigen::internal::plain_constant_type::Scalar, T, Eigen::internal::has_ReturnType::Scalar, T, Eigen::internal::scalar_quotient_op::Scalar, T> > >::value>::type>::type> >::type = const Eigen::CwiseBinaryOp, const Eigen::Block, -1, -1, false>, const Eigen::CwiseNullaryOp, const Eigen::Matrix > >]’ /usr/include/eigen3/Eigen/src/SVD/JacobiSVD.h:689:60: required from ‘Eigen::JacobiSVD& Eigen::JacobiSVD::compute(const MatrixType&, unsigned int) [with _MatrixType = Eigen::Matrix; int QRPreconditioner = 2; Eigen::JacobiSVD::MatrixType = Eigen::Matrix]’ /usr/include/eigen3/Eigen/src/SVD/JacobiSVD.h:548:7: required from ‘Eigen::JacobiSVD::JacobiSVD(const MatrixType&, unsigned int) [with _MatrixType = Eigen::Matrix; int QRPreconditioner = 2; Eigen::JacobiSVD::MatrixType = Eigen::Matrix]’ /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculealigner.cpp:196:113: required from here /usr/include/eigen3/Eigen/src/Core/CwiseBinaryOp.h:105:49: warning: implicitly-declared ‘constexpr Eigen::Block, -1, -1, false>::Block(const Eigen::Block, -1, -1, false>&)’ is deprecated [-Wdeprecated-copy] 105 | : m_lhs(aLhs), m_rhs(aRhs), m_functor(func) | ^ In file included from /usr/include/eigen3/Eigen/Core:88, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculealigner.h:43, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculealigner.cpp:36: /usr/include/eigen3/Eigen/src/Core/util/Macros.h:830:52: note: because ‘Eigen::Block, -1, -1, false>’ has user-provided ‘Eigen::BlockImpl& Eigen::BlockImpl::operator=(const Eigen::BlockImpl&) [with XprType = const Eigen::Matrix; int BlockRows = -1; int BlockCols = -1; bool InnerPanel = false]’ 830 | EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Derived& operator=(const Derived& other) \ | ^~~~~~~~ /usr/include/eigen3/Eigen/src/Core/util/Macros.h:842:53: note: in expansion of macro ‘EIGEN_INHERIT_ASSIGNMENT_EQUAL_OPERATOR’ 842 | #define EIGEN_INHERIT_ASSIGNMENT_OPERATORS(Derived) EIGEN_INHERIT_ASSIGNMENT_EQUAL_OPERATOR(Derived) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/eigen3/Eigen/src/Core/Block.h:161:5: note: in expansion of macro ‘EIGEN_INHERIT_ASSIGNMENT_OPERATORS’ 161 | EIGEN_INHERIT_ASSIGNMENT_OPERATORS(BlockImpl) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/eigen3/Eigen/Core:462, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculealigner.h:43, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculealigner.cpp:36: /usr/include/eigen3/Eigen/src/Core/CwiseUnaryOp.h: In instantiation of ‘Eigen::CwiseUnaryOp::CwiseUnaryOp(const XprType&, const UnaryOp&) [with UnaryOp = Eigen::internal::scalar_opposite_op; XprType = const Eigen::Block, 3, 1, true>]’: /usr/include/eigen3/Eigen/src/Core/../plugins/CommonCwiseUnaryOps.h:45:28: required from ‘const NegativeReturnType Eigen::MatrixBase::operator-() const [with Derived = Eigen::Block, 3, 1, true>; Eigen::MatrixBase::NegativeReturnType = Eigen::CwiseUnaryOp, const Eigen::Block, 3, 1, true> >; typename Eigen::internal::traits::Scalar = double]’ /usr/include/eigen3/Eigen/src/SVD/JacobiSVD.h:757:62: required from ‘Eigen::JacobiSVD& Eigen::JacobiSVD::compute(const MatrixType&, unsigned int) [with _MatrixType = Eigen::Matrix; int QRPreconditioner = 2; Eigen::JacobiSVD::MatrixType = Eigen::Matrix]’ /usr/include/eigen3/Eigen/src/SVD/JacobiSVD.h:548:7: required from ‘Eigen::JacobiSVD::JacobiSVD(const MatrixType&, unsigned int) [with _MatrixType = Eigen::Matrix; int QRPreconditioner = 2; Eigen::JacobiSVD::MatrixType = Eigen::Matrix]’ /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculealigner.cpp:196:113: required from here /usr/include/eigen3/Eigen/src/Core/CwiseUnaryOp.h:66:35: warning: implicitly-declared ‘Eigen::Block, 3, 1, true>::Block(const Eigen::Block, 3, 1, true>&)’ is deprecated [-Wdeprecated-copy] 66 | : m_xpr(xpr), m_functor(func) {} | ^ In file included from /usr/include/eigen3/Eigen/Core:88, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculealigner.h:43, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculealigner.cpp:36: /usr/include/eigen3/Eigen/src/Core/util/Macros.h:830:52: note: because ‘Eigen::Block, 3, 1, true>’ has user-provided ‘Eigen::BlockImpl& Eigen::BlockImpl::operator=(const Eigen::BlockImpl&) [with XprType = Eigen::Matrix; int BlockRows = 3; int BlockCols = 1; bool InnerPanel = true]’ 830 | EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Derived& operator=(const Derived& other) \ | ^~~~~~~~ /usr/include/eigen3/Eigen/src/Core/util/Macros.h:842:53: note: in expansion of macro ‘EIGEN_INHERIT_ASSIGNMENT_EQUAL_OPERATOR’ 842 | #define EIGEN_INHERIT_ASSIGNMENT_OPERATORS(Derived) EIGEN_INHERIT_ASSIGNMENT_EQUAL_OPERATOR(Derived) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/eigen3/Eigen/src/Core/Block.h:161:5: note: in expansion of macro ‘EIGEN_INHERIT_ASSIGNMENT_OPERATORS’ 161 | EIGEN_INHERIT_ASSIGNMENT_OPERATORS(BlockImpl) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/eigen3/Eigen/Core:439, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculealigner.h:43, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculealigner.cpp:36: /usr/include/eigen3/Eigen/src/Core/Product.h: In instantiation of ‘Eigen::Product::Product(const Lhs&, const Rhs&) [with _Lhs = Eigen::Product, Eigen::Matrix, 0>; _Rhs = Eigen::Transpose >; int Option = 1; Eigen::Product::Lhs = Eigen::Product, Eigen::Matrix, 0>; Eigen::Product::Rhs = Eigen::Transpose >]’: /usr/include/eigen3/Eigen/src/Core/GeneralProduct.h:450:10: required from ‘const Eigen::Product Eigen::MatrixBase::lazyProduct(const Eigen::MatrixBase&) const [with OtherDerived = Eigen::Transpose >; Derived = Eigen::Product, Eigen::Matrix, 0>]’ /usr/include/eigen3/Eigen/src/Core/ProductEvaluators.h:397:29: required from ‘static void Eigen::internal::generic_product_impl::evalTo(Dst&, const Lhs&, const Rhs&) [with Dst = Eigen::Matrix; Lhs = Eigen::Product, Eigen::Matrix, 0>; Rhs = Eigen::Transpose >]’ /usr/include/eigen3/Eigen/src/Core/ProductEvaluators.h:148:43: required from ‘static void Eigen::internal::Assignment, Eigen::internal::assign_op, Eigen::internal::Dense2Dense, typename Eigen::internal::enable_if<((Options == Eigen::DefaultProduct) || (Options == Eigen::AliasFreeProduct))>::type>::run(DstXprType&, const SrcXprType&, const Eigen::internal::assign_op&) [with DstXprType = Eigen::Matrix; Lhs = Eigen::Product, Eigen::Matrix, 0>; Rhs = Eigen::Transpose >; int Options = 0; Scalar = double; Eigen::internal::Assignment, Eigen::internal::assign_op, Eigen::internal::Dense2Dense, typename Eigen::internal::enable_if<((Options == Eigen::DefaultProduct) || (Options == Eigen::AliasFreeProduct))>::type>::SrcXprType = Eigen::Product, Eigen::Matrix, 0>, Eigen::Transpose >, 0>]’ /usr/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:49: required from ‘void Eigen::internal::call_assignment_no_alias(Dst&, const Src&, const Func&) [with Dst = Eigen::Matrix; Src = Eigen::Product, Eigen::Matrix, 0>, Eigen::Transpose >, 0>; Func = Eigen::internal::assign_op]’ /usr/include/eigen3/Eigen/src/Core/PlainObjectBase.h:732:41: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /usr/include/eigen3/Eigen/src/Core/Matrix.h:294:31: required from ‘Eigen::Matrix<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>::Matrix(const T&) [with T = Eigen::Product, Eigen::Matrix, 0>, Eigen::Transpose >, 0>; _Scalar = double; int _Rows = 3; int _Cols = 3; int _Options = 1; int _MaxRows = 3; int _MaxCols = 3]’ /usr/include/eigen3/Eigen/src/Core/AssignEvaluator.h:796:41: required from ‘void Eigen::internal::call_assignment(Dst&, const Src&, const Func&, typename Eigen::internal::enable_if::value, void*>::type) [with Dst = Eigen::Matrix; Src = Eigen::Product, Eigen::Matrix, 0>, Eigen::Transpose >, 0>; Func = Eigen::internal::assign_op; typename Eigen::internal::enable_if::value, void*>::type = void*]’ /usr/include/eigen3/Eigen/src/Core/AssignEvaluator.h:782:18: required from ‘void Eigen::internal::call_assignment(Dst&, const Src&) [with Dst = Eigen::Matrix; Src = Eigen::Product, Eigen::Matrix, 0>, Eigen::Transpose >, 0>]’ /usr/include/eigen3/Eigen/src/Core/PlainObjectBase.h:714:32: required from ‘Derived& Eigen::PlainObjectBase::_set(const Eigen::DenseBase&) [with OtherDerived = Eigen::Product, Eigen::Matrix, 0>, Eigen::Transpose >, 0>; Derived = Eigen::Matrix]’ /usr/include/eigen3/Eigen/src/Core/Matrix.h:225:24: required from ‘Eigen::Matrix<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>& Eigen::Matrix<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>::operator=(const Eigen::DenseBase&) [with OtherDerived = Eigen::Product, Eigen::Matrix, 0>, Eigen::Transpose >, 0>; _Scalar = double; int _Rows = 3; int _Cols = 3; int _Options = 0; int _MaxRows = 3; int _MaxCols = 3]’ /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculealigner.cpp:198:79: required from here /usr/include/eigen3/Eigen/src/Core/Product.h:93:86: warning: implicitly-declared ‘constexpr Eigen::Transpose >::Transpose(const Eigen::Transpose >&)’ is deprecated [-Wdeprecated-copy] 93 | oduct(const Lhs& lhs, const Rhs& rhs) : m_lhs(lhs), m_rhs(rhs) | ^ In file included from /usr/include/eigen3/Eigen/Core:445, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculealigner.h:43, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculealigner.cpp:36: /usr/include/eigen3/Eigen/src/Core/Assign.h:55:30: note: because ‘Eigen::Transpose >’ has user-provided ‘Derived& Eigen::MatrixBase::operator=(const Eigen::MatrixBase&) [with Derived = Eigen::Transpose >]’ 55 | EIGEN_STRONG_INLINE Derived& MatrixBase::operator=(const MatrixBase& other) | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/eigen3/Eigen/Core:493, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculealigner.h:43, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculealigner.cpp:36: /usr/include/eigen3/Eigen/src/Core/ProductEvaluators.h: In instantiation of ‘Eigen::internal::product_evaluator, ProductTag, Eigen::DenseShape, Eigen::DenseShape>::product_evaluator(const XprType&) [with Lhs = Eigen::Product, Eigen::Matrix, 0>; Rhs = Eigen::Transpose >; int ProductTag = 3; typename Eigen::internal::traits::Rhs>::Scalar = double; typename Eigen::internal::traits::Lhs>::Scalar = double; Eigen::internal::product_evaluator, ProductTag, Eigen::DenseShape, Eigen::DenseShape>::XprType = Eigen::Product, Eigen::Matrix, 0>, Eigen::Transpose >, 1>]’: /usr/include/eigen3/Eigen/src/Core/ProductEvaluators.h:35:90: required from ‘Eigen::internal::evaluator >::evaluator(const XprType&) [with Lhs = Eigen::Product, Eigen::Matrix, 0>; Rhs = Eigen::Transpose >; int Options = 1; Eigen::internal::evaluator >::XprType = Eigen::Product, Eigen::Matrix, 0>, Eigen::Transpose >, 1>]’ /usr/include/eigen3/Eigen/src/Core/AssignEvaluator.h:730:20: required from ‘void Eigen::internal::call_dense_assignment_loop(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen::Matrix; SrcXprType = Eigen::Product, Eigen::Matrix, 0>, Eigen::Transpose >, 1>; Functor = Eigen::internal::assign_op]’ /usr/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:31: required from ‘static void Eigen::internal::Assignment::run(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen::Matrix; SrcXprType = Eigen::Product, Eigen::Matrix, 0>, Eigen::Transpose >, 1>; Functor = Eigen::internal::assign_op; Weak = void]’ /usr/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:49: required from ‘void Eigen::internal::call_assignment_no_alias(Dst&, const Src&, const Func&) [with Dst = Eigen::Matrix; Src = Eigen::Product, Eigen::Matrix, 0>, Eigen::Transpose >, 1>; Func = Eigen::internal::assign_op]’ /usr/include/eigen3/Eigen/src/Core/ProductEvaluators.h:397:29: required from ‘static void Eigen::internal::generic_product_impl::evalTo(Dst&, const Lhs&, const Rhs&) [with Dst = Eigen::Matrix; Lhs = Eigen::Product, Eigen::Matrix, 0>; Rhs = Eigen::Transpose >]’ /usr/include/eigen3/Eigen/src/Core/ProductEvaluators.h:148:43: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /usr/include/eigen3/Eigen/src/Core/Matrix.h:294:31: required from ‘Eigen::Matrix<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>::Matrix(const T&) [with T = Eigen::Product, Eigen::Matrix, 0>, Eigen::Transpose >, 0>; _Scalar = double; int _Rows = 3; int _Cols = 3; int _Options = 1; int _MaxRows = 3; int _MaxCols = 3]’ /usr/include/eigen3/Eigen/src/Core/AssignEvaluator.h:796:41: required from ‘void Eigen::internal::call_assignment(Dst&, const Src&, const Func&, typename Eigen::internal::enable_if::value, void*>::type) [with Dst = Eigen::Matrix; Src = Eigen::Product, Eigen::Matrix, 0>, Eigen::Transpose >, 0>; Func = Eigen::internal::assign_op; typename Eigen::internal::enable_if::value, void*>::type = void*]’ /usr/include/eigen3/Eigen/src/Core/AssignEvaluator.h:782:18: required from ‘void Eigen::internal::call_assignment(Dst&, const Src&) [with Dst = Eigen::Matrix; Src = Eigen::Product, Eigen::Matrix, 0>, Eigen::Transpose >, 0>]’ /usr/include/eigen3/Eigen/src/Core/PlainObjectBase.h:714:32: required from ‘Derived& Eigen::PlainObjectBase::_set(const Eigen::DenseBase&) [with OtherDerived = Eigen::Product, Eigen::Matrix, 0>, Eigen::Transpose >, 0>; Derived = Eigen::Matrix]’ /usr/include/eigen3/Eigen/src/Core/Matrix.h:225:24: required from ‘Eigen::Matrix<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>& Eigen::Matrix<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>::operator=(const Eigen::DenseBase&) [with OtherDerived = Eigen::Product, Eigen::Matrix, 0>, Eigen::Transpose >, 0>; _Scalar = double; int _Rows = 3; int _Cols = 3; int _Options = 0; int _MaxRows = 3; int _MaxCols = 3]’ /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculealigner.cpp:198:79: required from here /usr/include/eigen3/Eigen/src/Core/ProductEvaluators.h:451:34: warning: implicitly-declared ‘constexpr Eigen::Transpose >::Transpose(const Eigen::Transpose >&)’ is deprecated [-Wdeprecated-copy] 451 | m_innerDim(xpr.lhs().cols()) | ^ In file included from /usr/include/eigen3/Eigen/Core:445, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculealigner.h:43, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculealigner.cpp:36: /usr/include/eigen3/Eigen/src/Core/Assign.h:55:30: note: because ‘Eigen::Transpose >’ has user-provided ‘Derived& Eigen::MatrixBase::operator=(const Eigen::MatrixBase&) [with Derived = Eigen::Transpose >]’ 55 | EIGEN_STRONG_INLINE Derived& MatrixBase::operator=(const MatrixBase& other) | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/eigen3/Eigen/Core:474, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculealigner.h:43, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculealigner.cpp:36: /usr/include/eigen3/Eigen/src/Core/Transpose.h: In instantiation of ‘Eigen::Transpose::Transpose(MatrixType&) [with MatrixType = const Eigen::Block, 1, 3, false>]’: /usr/include/eigen3/Eigen/src/Core/Transpose.h:186:10: required from ‘Eigen::DenseBase::ConstTransposeReturnType Eigen::DenseBase::transpose() const [with Derived = Eigen::Block, 1, 3, false>; Eigen::DenseBase::ConstTransposeReturnType = const Eigen::Transpose, 1, 3, false> >]’ /usr/include/eigen3/Eigen/src/Core/ProductEvaluators.h:552:40: required from ‘const CoeffReturnType Eigen::internal::product_evaluator, ProductTag, Eigen::DenseShape, Eigen::DenseShape>::coeff(Eigen::Index, Eigen::Index) const [with Lhs = Eigen::Matrix; Rhs = Eigen::Matrix; int ProductTag = 3; typename Eigen::internal::traits::Rhs>::Scalar = double; typename Eigen::internal::traits::Lhs>::Scalar = double; Eigen::internal::product_evaluator, ProductTag, Eigen::DenseShape, Eigen::DenseShape>::CoeffReturnType = double; Eigen::Index = long int]’ /usr/include/eigen3/Eigen/src/Core/AssignEvaluator.h:631:5: required from ‘void Eigen::internal::generic_dense_assignment_kernel::assignCoeff(Eigen::Index, Eigen::Index) [with DstEvaluatorTypeT = Eigen::internal::evaluator >; SrcEvaluatorTypeT = Eigen::internal::evaluator, Eigen::Matrix, 1> >; Functor = Eigen::internal::assign_op; int Version = 0; Eigen::Index = long int]’ /usr/include/eigen3/Eigen/src/Core/AssignEvaluator.h:645:5: required from ‘void Eigen::internal::generic_dense_assignment_kernel::assignCoeffByOuterInner(Eigen::Index, Eigen::Index) [with DstEvaluatorTypeT = Eigen::internal::evaluator >; SrcEvaluatorTypeT = Eigen::internal::evaluator, Eigen::Matrix, 1> >; Functor = Eigen::internal::assign_op; int Version = 0; Eigen::Index = long int]’ /usr/include/eigen3/Eigen/src/Core/AssignEvaluator.h:206:5: required from ‘static void Eigen::internal::copy_using_evaluator_DefaultTraversal_CompleteUnrolling::run(Kernel&) [with Kernel = Eigen::internal::generic_dense_assignment_kernel >, Eigen::internal::evaluator, Eigen::Matrix, 1> >, Eigen::internal::assign_op, 0>; int Index = 2; int Stop = 3]’ /usr/include/eigen3/Eigen/src/Core/AssignEvaluator.h:435:92: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /usr/include/eigen3/Eigen/src/Core/ProductEvaluators.h:148:43: required from ‘static void Eigen::internal::Assignment, Eigen::internal::assign_op, Eigen::internal::Dense2Dense, typename Eigen::internal::enable_if<((Options == Eigen::DefaultProduct) || (Options == Eigen::AliasFreeProduct))>::type>::run(DstXprType&, const SrcXprType&, const Eigen::internal::assign_op&) [with DstXprType = Eigen::Matrix; Lhs = Eigen::Matrix; Rhs = Eigen::Matrix; int Options = 0; Scalar = double; Eigen::internal::Assignment, Eigen::internal::assign_op, Eigen::internal::Dense2Dense, typename Eigen::internal::enable_if<((Options == Eigen::DefaultProduct) || (Options == Eigen::AliasFreeProduct))>::type>::SrcXprType = Eigen::Product, Eigen::Matrix, 0>]’ /usr/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:49: required from ‘void Eigen::internal::call_assignment_no_alias(Dst&, const Src&, const Func&) [with Dst = Eigen::Matrix; Src = Eigen::Product, Eigen::Matrix, 0>; Func = Eigen::internal::assign_op]’ /usr/include/eigen3/Eigen/src/Core/PlainObjectBase.h:732:41: required from ‘Derived& Eigen::PlainObjectBase::_set_noalias(const Eigen::DenseBase&) [with OtherDerived = Eigen::Product, Eigen::Matrix, 0>; Derived = Eigen::Matrix]’ /usr/include/eigen3/Eigen/src/Core/PlainObjectBase.h:537:7: required from ‘Eigen::PlainObjectBase::PlainObjectBase(const Eigen::DenseBase&) [with OtherDerived = Eigen::Product, Eigen::Matrix, 0>; Derived = Eigen::Matrix]’ /usr/include/eigen3/Eigen/src/Core/Matrix.h:377:29: required from ‘Eigen::Matrix<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>::Matrix(const Eigen::EigenBase&) [with OtherDerived = Eigen::Product, Eigen::Matrix, 0>; _Scalar = double; int _Rows = 3; int _Cols = 1; int _Options = 0; int _MaxRows = 3; int _MaxCols = 1]’ /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculealigner.cpp:225:52: required from here /usr/include/eigen3/Eigen/src/Core/Transpose.h:64:68: warning: implicitly-declared ‘Eigen::Block, 1, 3, false>::Block(const Eigen::Block, 1, 3, false>&)’ is deprecated [-Wdeprecated-copy] 64 | explicit inline Transpose(MatrixType& matrix) : m_matrix(matrix) {} | ^ In file included from /usr/include/eigen3/Eigen/Core:88, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculealigner.h:43, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculealigner.cpp:36: /usr/include/eigen3/Eigen/src/Core/util/Macros.h:830:52: note: because ‘Eigen::Block, 1, 3, false>’ has user-provided ‘Eigen::BlockImpl& Eigen::BlockImpl::operator=(const Eigen::BlockImpl&) [with XprType = const Eigen::Matrix; int BlockRows = 1; int BlockCols = 3; bool InnerPanel = false]’ 830 | EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Derived& operator=(const Derived& other) \ | ^~~~~~~~ /usr/include/eigen3/Eigen/src/Core/util/Macros.h:842:53: note: in expansion of macro ‘EIGEN_INHERIT_ASSIGNMENT_EQUAL_OPERATOR’ 842 | #define EIGEN_INHERIT_ASSIGNMENT_OPERATORS(Derived) EIGEN_INHERIT_ASSIGNMENT_EQUAL_OPERATOR(Derived) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/eigen3/Eigen/src/Core/Block.h:161:5: note: in expansion of macro ‘EIGEN_INHERIT_ASSIGNMENT_OPERATORS’ 161 | EIGEN_INHERIT_ASSIGNMENT_OPERATORS(BlockImpl) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/eigen3/Eigen/Core:461, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculealigner.h:43, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculealigner.cpp:36: /usr/include/eigen3/Eigen/src/Core/CwiseBinaryOp.h: In instantiation of ‘Eigen::CwiseBinaryOp::CwiseBinaryOp(const Lhs&, const Rhs&, const BinaryOp&) [with BinaryOp = Eigen::internal::scalar_product_op; LhsType = const Eigen::Transpose, 1, 3, false> >; RhsType = const Eigen::Block, 3, 1, true>; Eigen::CwiseBinaryOp::Lhs = Eigen::Transpose, 1, 3, false> >; Eigen::CwiseBinaryOp::Rhs = Eigen::Block, 3, 1, true>]’: /usr/include/eigen3/Eigen/src/Core/../plugins/MatrixCwiseBinaryOps.h:25:10: required from ‘const Eigen::CwiseBinaryOp::Scalar, typename Eigen::internal::traits::Scalar>, const Derived, const OtherDerived> Eigen::MatrixBase::cwiseProduct(const Eigen::MatrixBase&) const [with OtherDerived = Eigen::Block, 3, 1, true>; Derived = Eigen::Transpose, 1, 3, false> >; typename Eigen::internal::traits::Scalar = double; typename Eigen::internal::traits::Scalar = double]’ /usr/include/eigen3/Eigen/src/Core/ProductEvaluators.h:552:72: required from ‘const CoeffReturnType Eigen::internal::product_evaluator, ProductTag, Eigen::DenseShape, Eigen::DenseShape>::coeff(Eigen::Index, Eigen::Index) const [with Lhs = Eigen::Matrix; Rhs = Eigen::Matrix; int ProductTag = 3; typename Eigen::internal::traits::Rhs>::Scalar = double; typename Eigen::internal::traits::Lhs>::Scalar = double; Eigen::internal::product_evaluator, ProductTag, Eigen::DenseShape, Eigen::DenseShape>::CoeffReturnType = double; Eigen::Index = long int]’ /usr/include/eigen3/Eigen/src/Core/AssignEvaluator.h:631:5: required from ‘void Eigen::internal::generic_dense_assignment_kernel::assignCoeff(Eigen::Index, Eigen::Index) [with DstEvaluatorTypeT = Eigen::internal::evaluator >; SrcEvaluatorTypeT = Eigen::internal::evaluator, Eigen::Matrix, 1> >; Functor = Eigen::internal::assign_op; int Version = 0; Eigen::Index = long int]’ /usr/include/eigen3/Eigen/src/Core/AssignEvaluator.h:645:5: required from ‘void Eigen::internal::generic_dense_assignment_kernel::assignCoeffByOuterInner(Eigen::Index, Eigen::Index) [with DstEvaluatorTypeT = Eigen::internal::evaluator >; SrcEvaluatorTypeT = Eigen::internal::evaluator, Eigen::Matrix, 1> >; Functor = Eigen::internal::assign_op; int Version = 0; Eigen::Index = long int]’ /usr/include/eigen3/Eigen/src/Core/AssignEvaluator.h:206:5: required from ‘static void Eigen::internal::copy_using_evaluator_DefaultTraversal_CompleteUnrolling::run(Kernel&) [with Kernel = Eigen::internal::generic_dense_assignment_kernel >, Eigen::internal::evaluator, Eigen::Matrix, 1> >, Eigen::internal::assign_op, 0>; int Index = 2; int Stop = 3]’ /usr/include/eigen3/Eigen/src/Core/AssignEvaluator.h:435:92: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /usr/include/eigen3/Eigen/src/Core/ProductEvaluators.h:148:43: required from ‘static void Eigen::internal::Assignment, Eigen::internal::assign_op, Eigen::internal::Dense2Dense, typename Eigen::internal::enable_if<((Options == Eigen::DefaultProduct) || (Options == Eigen::AliasFreeProduct))>::type>::run(DstXprType&, const SrcXprType&, const Eigen::internal::assign_op&) [with DstXprType = Eigen::Matrix; Lhs = Eigen::Matrix; Rhs = Eigen::Matrix; int Options = 0; Scalar = double; Eigen::internal::Assignment, Eigen::internal::assign_op, Eigen::internal::Dense2Dense, typename Eigen::internal::enable_if<((Options == Eigen::DefaultProduct) || (Options == Eigen::AliasFreeProduct))>::type>::SrcXprType = Eigen::Product, Eigen::Matrix, 0>]’ /usr/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:49: required from ‘void Eigen::internal::call_assignment_no_alias(Dst&, const Src&, const Func&) [with Dst = Eigen::Matrix; Src = Eigen::Product, Eigen::Matrix, 0>; Func = Eigen::internal::assign_op]’ /usr/include/eigen3/Eigen/src/Core/PlainObjectBase.h:732:41: required from ‘Derived& Eigen::PlainObjectBase::_set_noalias(const Eigen::DenseBase&) [with OtherDerived = Eigen::Product, Eigen::Matrix, 0>; Derived = Eigen::Matrix]’ /usr/include/eigen3/Eigen/src/Core/PlainObjectBase.h:537:7: required from ‘Eigen::PlainObjectBase::PlainObjectBase(const Eigen::DenseBase&) [with OtherDerived = Eigen::Product, Eigen::Matrix, 0>; Derived = Eigen::Matrix]’ /usr/include/eigen3/Eigen/src/Core/Matrix.h:377:29: required from ‘Eigen::Matrix<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>::Matrix(const Eigen::EigenBase&) [with OtherDerived = Eigen::Product, Eigen::Matrix, 0>; _Scalar = double; int _Rows = 3; int _Cols = 1; int _Options = 0; int _MaxRows = 3; int _MaxCols = 1]’ /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculealigner.cpp:225:52: required from here /usr/include/eigen3/Eigen/src/Core/CwiseBinaryOp.h:105:49: warning: implicitly-declared ‘Eigen::Transpose, 1, 3, false> >::Transpose(const Eigen::Transpose, 1, 3, false> >&)’ is deprecated [-Wdeprecated-copy] 105 | : m_lhs(aLhs), m_rhs(aRhs), m_functor(func) | ^ In file included from /usr/include/eigen3/Eigen/Core:445, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculealigner.h:43, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculealigner.cpp:36: /usr/include/eigen3/Eigen/src/Core/Assign.h:55:30: note: because ‘Eigen::Transpose, 1, 3, false> >’ has user-provided ‘Derived& Eigen::MatrixBase::operator=(const Eigen::MatrixBase&) [with Derived = Eigen::Transpose, 1, 3, false> >]’ 55 | EIGEN_STRONG_INLINE Derived& MatrixBase::operator=(const MatrixBase& other) | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/eigen3/Eigen/Core:461, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculealigner.h:43, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculealigner.cpp:36: /usr/include/eigen3/Eigen/src/Core/CwiseBinaryOp.h:105:49: warning: implicitly-declared ‘Eigen::Block, 3, 1, true>::Block(const Eigen::Block, 3, 1, true>&)’ is deprecated [-Wdeprecated-copy] 105 | : m_lhs(aLhs), m_rhs(aRhs), m_functor(func) | ^ In file included from /usr/include/eigen3/Eigen/Core:88, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculealigner.h:43, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculealigner.cpp:36: /usr/include/eigen3/Eigen/src/Core/util/Macros.h:830:52: note: because ‘Eigen::Block, 3, 1, true>’ has user-provided ‘Eigen::BlockImpl& Eigen::BlockImpl::operator=(const Eigen::BlockImpl&) [with XprType = const Eigen::Matrix; int BlockRows = 3; int BlockCols = 1; bool InnerPanel = true]’ 830 | EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Derived& operator=(const Derived& other) \ | ^~~~~~~~ /usr/include/eigen3/Eigen/src/Core/util/Macros.h:842:53: note: in expansion of macro ‘EIGEN_INHERIT_ASSIGNMENT_EQUAL_OPERATOR’ 842 | #define EIGEN_INHERIT_ASSIGNMENT_OPERATORS(Derived) EIGEN_INHERIT_ASSIGNMENT_EQUAL_OPERATOR(Derived) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/eigen3/Eigen/src/Core/Block.h:161:5: note: in expansion of macro ‘EIGEN_INHERIT_ASSIGNMENT_OPERATORS’ 161 | EIGEN_INHERIT_ASSIGNMENT_OPERATORS(BlockImpl) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/eigen3/Eigen/Core:461, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculealigner.h:43, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculealigner.cpp:36: /usr/include/eigen3/Eigen/src/Core/CwiseBinaryOp.h: In instantiation of ‘Eigen::CwiseBinaryOp::CwiseBinaryOp(const Lhs&, const Rhs&, const BinaryOp&) [with BinaryOp = Eigen::internal::scalar_product_op; LhsType = const Eigen::Transpose, 1, 3, false> >; RhsType = const Eigen::Block >, 3, 1, false>; Eigen::CwiseBinaryOp::Lhs = Eigen::Transpose, 1, 3, false> >; Eigen::CwiseBinaryOp::Rhs = Eigen::Block >, 3, 1, false>]’: /usr/include/eigen3/Eigen/src/Core/../plugins/MatrixCwiseBinaryOps.h:25:10: required from ‘const Eigen::CwiseBinaryOp::Scalar, typename Eigen::internal::traits::Scalar>, const Derived, const OtherDerived> Eigen::MatrixBase::cwiseProduct(const Eigen::MatrixBase&) const [with OtherDerived = Eigen::Block >, 3, 1, false>; Derived = Eigen::Transpose, 1, 3, false> >; typename Eigen::internal::traits::Scalar = double; typename Eigen::internal::traits::Scalar = double]’ /usr/include/eigen3/Eigen/src/Core/ProductEvaluators.h:552:72: required from ‘const CoeffReturnType Eigen::internal::product_evaluator, ProductTag, Eigen::DenseShape, Eigen::DenseShape>::coeff(Eigen::Index, Eigen::Index) const [with Lhs = Eigen::Product, Eigen::Matrix, 0>; Rhs = Eigen::Transpose >; int ProductTag = 3; typename Eigen::internal::traits::Rhs>::Scalar = double; typename Eigen::internal::traits::Lhs>::Scalar = double; Eigen::internal::product_evaluator, ProductTag, Eigen::DenseShape, Eigen::DenseShape>::CoeffReturnType = double; Eigen::Index = long int]’ /usr/include/eigen3/Eigen/src/Core/AssignEvaluator.h:631:5: required from ‘void Eigen::internal::generic_dense_assignment_kernel::assignCoeff(Eigen::Index, Eigen::Index) [with DstEvaluatorTypeT = Eigen::internal::evaluator >; SrcEvaluatorTypeT = Eigen::internal::evaluator, Eigen::Matrix, 0>, Eigen::Transpose >, 1> >; Functor = Eigen::internal::assign_op; int Version = 0; Eigen::Index = long int]’ /usr/include/eigen3/Eigen/src/Core/AssignEvaluator.h:645:5: required from ‘void Eigen::internal::generic_dense_assignment_kernel::assignCoeffByOuterInner(Eigen::Index, Eigen::Index) [with DstEvaluatorTypeT = Eigen::internal::evaluator >; SrcEvaluatorTypeT = Eigen::internal::evaluator, Eigen::Matrix, 0>, Eigen::Transpose >, 1> >; Functor = Eigen::internal::assign_op; int Version = 0; Eigen::Index = long int]’ /usr/include/eigen3/Eigen/src/Core/AssignEvaluator.h:222:5: required from ‘static void Eigen::internal::copy_using_evaluator_DefaultTraversal_InnerUnrolling::run(Kernel&, Eigen::Index) [with Kernel = Eigen::internal::generic_dense_assignment_kernel >, Eigen::internal::evaluator, Eigen::Matrix, 0>, Eigen::Transpose >, 1> >, Eigen::internal::assign_op, 0>; int Index_ = 0; int Stop = 3; Eigen::Index = long int]’ /usr/include/eigen3/Eigen/src/Core/AssignEvaluator.h:351:111: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /usr/include/eigen3/Eigen/src/Core/Matrix.h:294:31: required from ‘Eigen::Matrix<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>::Matrix(const T&) [with T = Eigen::Product, Eigen::Matrix, 0>, Eigen::Transpose >, 0>; _Scalar = double; int _Rows = 3; int _Cols = 3; int _Options = 1; int _MaxRows = 3; int _MaxCols = 3]’ /usr/include/eigen3/Eigen/src/Core/AssignEvaluator.h:796:41: required from ‘void Eigen::internal::call_assignment(Dst&, const Src&, const Func&, typename Eigen::internal::enable_if::value, void*>::type) [with Dst = Eigen::Matrix; Src = Eigen::Product, Eigen::Matrix, 0>, Eigen::Transpose >, 0>; Func = Eigen::internal::assign_op; typename Eigen::internal::enable_if::value, void*>::type = void*]’ /usr/include/eigen3/Eigen/src/Core/AssignEvaluator.h:782:18: required from ‘void Eigen::internal::call_assignment(Dst&, const Src&) [with Dst = Eigen::Matrix; Src = Eigen::Product, Eigen::Matrix, 0>, Eigen::Transpose >, 0>]’ /usr/include/eigen3/Eigen/src/Core/PlainObjectBase.h:714:32: required from ‘Derived& Eigen::PlainObjectBase::_set(const Eigen::DenseBase&) [with OtherDerived = Eigen::Product, Eigen::Matrix, 0>, Eigen::Transpose >, 0>; Derived = Eigen::Matrix]’ /usr/include/eigen3/Eigen/src/Core/Matrix.h:225:24: required from ‘Eigen::Matrix<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>& Eigen::Matrix<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>::operator=(const Eigen::DenseBase&) [with OtherDerived = Eigen::Product, Eigen::Matrix, 0>, Eigen::Transpose >, 0>; _Scalar = double; int _Rows = 3; int _Cols = 3; int _Options = 0; int _MaxRows = 3; int _MaxCols = 3]’ /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculealigner.cpp:198:79: required from here /usr/include/eigen3/Eigen/src/Core/CwiseBinaryOp.h:105:49: warning: implicitly-declared ‘Eigen::Transpose, 1, 3, false> >::Transpose(const Eigen::Transpose, 1, 3, false> >&)’ is deprecated [-Wdeprecated-copy] 105 | : m_lhs(aLhs), m_rhs(aRhs), m_functor(func) | ^ In file included from /usr/include/eigen3/Eigen/Core:445, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculealigner.h:43, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculealigner.cpp:36: /usr/include/eigen3/Eigen/src/Core/Assign.h:55:30: note: because ‘Eigen::Transpose, 1, 3, false> >’ has user-provided ‘Derived& Eigen::MatrixBase::operator=(const Eigen::MatrixBase&) [with Derived = Eigen::Transpose, 1, 3, false> >]’ 55 | EIGEN_STRONG_INLINE Derived& MatrixBase::operator=(const MatrixBase& other) | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/eigen3/Eigen/Core:461, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculealigner.h:43, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculealigner.cpp:36: /usr/include/eigen3/Eigen/src/Core/CwiseBinaryOp.h:105:49: warning: implicitly-declared ‘Eigen::Block >, 3, 1, false>::Block(const Eigen::Block >, 3, 1, false>&)’ is deprecated [-Wdeprecated-copy] 105 | : m_lhs(aLhs), m_rhs(aRhs), m_functor(func) | ^ In file included from /usr/include/eigen3/Eigen/Core:88, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculealigner.h:43, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculealigner.cpp:36: /usr/include/eigen3/Eigen/src/Core/util/Macros.h:830:52: note: because ‘Eigen::Block >, 3, 1, false>’ has user-provided ‘Eigen::BlockImpl& Eigen::BlockImpl::operator=(const Eigen::BlockImpl&) [with XprType = const Eigen::Transpose >; int BlockRows = 3; int BlockCols = 1; bool InnerPanel = false]’ 830 | EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Derived& operator=(const Derived& other) \ | ^~~~~~~~ /usr/include/eigen3/Eigen/src/Core/util/Macros.h:842:53: note: in expansion of macro ‘EIGEN_INHERIT_ASSIGNMENT_EQUAL_OPERATOR’ 842 | #define EIGEN_INHERIT_ASSIGNMENT_OPERATORS(Derived) EIGEN_INHERIT_ASSIGNMENT_EQUAL_OPERATOR(Derived) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/eigen3/Eigen/src/Core/Block.h:161:5: note: in expansion of macro ‘EIGEN_INHERIT_ASSIGNMENT_OPERATORS’ 161 | EIGEN_INHERIT_ASSIGNMENT_OPERATORS(BlockImpl) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/eigen3/Eigen/Core:472, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculealigner.h:43, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculealigner.cpp:36: /usr/include/eigen3/Eigen/src/Core/Block.h: In instantiation of ‘Eigen::internal::BlockImpl_dense::BlockImpl_dense(XprType&, Eigen::Index) [with XprType = const Eigen::Transpose >; int BlockRows = 3; int BlockCols = 1; bool InnerPanel = false; Eigen::Index = long int]’: /usr/include/eigen3/Eigen/src/Core/Block.h:162:75: required from ‘Eigen::BlockImpl::BlockImpl(XprType&, Eigen::Index) [with XprType = const Eigen::Transpose >; int BlockRows = 3; int BlockCols = 1; bool InnerPanel = false; Eigen::Index = long int]’ /usr/include/eigen3/Eigen/src/Core/Block.h:118:53: required from ‘Eigen::Block::Block(XprType&, Eigen::Index) [with XprType = const Eigen::Transpose >; int BlockRows = 3; int BlockCols = 1; bool InnerPanel = false; Eigen::Index = long int]’ /usr/include/eigen3/Eigen/src/Core/../plugins/BlockMethods.h:847:10: required from ‘Eigen::DenseBase::ConstColXpr Eigen::DenseBase::col(Eigen::Index) const [with Derived = Eigen::Transpose >; Eigen::DenseBase::ConstColXpr = const Eigen::Block >, 3, 1, false>; Eigen::Index = long int]’ /usr/include/eigen3/Eigen/src/Core/ProductEvaluators.h:552:72: required from ‘const CoeffReturnType Eigen::internal::product_evaluator, ProductTag, Eigen::DenseShape, Eigen::DenseShape>::coeff(Eigen::Index, Eigen::Index) const [with Lhs = Eigen::Product, Eigen::Matrix, 0>; Rhs = Eigen::Transpose >; int ProductTag = 3; typename Eigen::internal::traits::Rhs>::Scalar = double; typename Eigen::internal::traits::Lhs>::Scalar = double; Eigen::internal::product_evaluator, ProductTag, Eigen::DenseShape, Eigen::DenseShape>::CoeffReturnType = double; Eigen::Index = long int]’ /usr/include/eigen3/Eigen/src/Core/AssignEvaluator.h:631:5: required from ‘void Eigen::internal::generic_dense_assignment_kernel::assignCoeff(Eigen::Index, Eigen::Index) [with DstEvaluatorTypeT = Eigen::internal::evaluator >; SrcEvaluatorTypeT = Eigen::internal::evaluator, Eigen::Matrix, 0>, Eigen::Transpose >, 1> >; Functor = Eigen::internal::assign_op; int Version = 0; Eigen::Index = long int]’ /usr/include/eigen3/Eigen/src/Core/AssignEvaluator.h:645:5: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /usr/include/eigen3/Eigen/src/Core/Matrix.h:294:31: required from ‘Eigen::Matrix<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>::Matrix(const T&) [with T = Eigen::Product, Eigen::Matrix, 0>, Eigen::Transpose >, 0>; _Scalar = double; int _Rows = 3; int _Cols = 3; int _Options = 1; int _MaxRows = 3; int _MaxCols = 3]’ /usr/include/eigen3/Eigen/src/Core/AssignEvaluator.h:796:41: required from ‘void Eigen::internal::call_assignment(Dst&, const Src&, const Func&, typename Eigen::internal::enable_if::value, void*>::type) [with Dst = Eigen::Matrix; Src = Eigen::Product, Eigen::Matrix, 0>, Eigen::Transpose >, 0>; Func = Eigen::internal::assign_op; typename Eigen::internal::enable_if::value, void*>::type = void*]’ /usr/include/eigen3/Eigen/src/Core/AssignEvaluator.h:782:18: required from ‘void Eigen::internal::call_assignment(Dst&, const Src&) [with Dst = Eigen::Matrix; Src = Eigen::Product, Eigen::Matrix, 0>, Eigen::Transpose >, 0>]’ /usr/include/eigen3/Eigen/src/Core/PlainObjectBase.h:714:32: required from ‘Derived& Eigen::PlainObjectBase::_set(const Eigen::DenseBase&) [with OtherDerived = Eigen::Product, Eigen::Matrix, 0>, Eigen::Transpose >, 0>; Derived = Eigen::Matrix]’ /usr/include/eigen3/Eigen/src/Core/Matrix.h:225:24: required from ‘Eigen::Matrix<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>& Eigen::Matrix<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>::operator=(const Eigen::DenseBase&) [with OtherDerived = Eigen::Product, Eigen::Matrix, 0>, Eigen::Transpose >, 0>; _Scalar = double; int _Rows = 3; int _Cols = 3; int _Options = 0; int _MaxRows = 3; int _MaxCols = 3]’ /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculealigner.cpp:198:79: required from here /usr/include/eigen3/Eigen/src/Core/Block.h:353:86: warning: implicitly-declared ‘constexpr Eigen::Transpose >::Transpose(const Eigen::Transpose >&)’ is deprecated [-Wdeprecated-copy] 353 | ckRows==XprType::RowsAtCompileTime) && (BlockCols==1) ? i : 0) | ^ In file included from /usr/include/eigen3/Eigen/Core:445, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculealigner.h:43, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculealigner.cpp:36: /usr/include/eigen3/Eigen/src/Core/Assign.h:55:30: note: because ‘Eigen::Transpose >’ has user-provided ‘Derived& Eigen::MatrixBase::operator=(const Eigen::MatrixBase&) [with Derived = Eigen::Transpose >]’ 55 | EIGEN_STRONG_INLINE Derived& MatrixBase::operator=(const MatrixBase& other) | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/eigen3/Eigen/Core:461, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculealigner.h:43, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculealigner.cpp:36: /usr/include/eigen3/Eigen/src/Core/CwiseBinaryOp.h: In instantiation of ‘Eigen::CwiseBinaryOp::CwiseBinaryOp(const Lhs&, const Rhs&, const BinaryOp&) [with BinaryOp = Eigen::internal::scalar_product_op; LhsType = const Eigen::Transpose, 1, 3, false> >; RhsType = const Eigen::Block, 3, 1, true>; Eigen::CwiseBinaryOp::Lhs = Eigen::Transpose, 1, 3, false> >; Eigen::CwiseBinaryOp::Rhs = Eigen::Block, 3, 1, true>]’: /usr/include/eigen3/Eigen/src/Core/../plugins/MatrixCwiseBinaryOps.h:25:10: required from ‘const Eigen::CwiseBinaryOp::Scalar, typename Eigen::internal::traits::Scalar>, const Derived, const OtherDerived> Eigen::MatrixBase::cwiseProduct(const Eigen::MatrixBase&) const [with OtherDerived = Eigen::Block, 3, 1, true>; Derived = Eigen::Transpose, 1, 3, false> >; typename Eigen::internal::traits::Scalar = double; typename Eigen::internal::traits::Scalar = double]’ /usr/include/eigen3/Eigen/src/Core/ProductEvaluators.h:552:72: required from ‘const CoeffReturnType Eigen::internal::product_evaluator, ProductTag, Eigen::DenseShape, Eigen::DenseShape>::coeff(Eigen::Index, Eigen::Index) const [with Lhs = Eigen::Matrix; Rhs = Eigen::Matrix; int ProductTag = 3; typename Eigen::internal::traits::Rhs>::Scalar = double; typename Eigen::internal::traits::Lhs>::Scalar = double; Eigen::internal::product_evaluator, ProductTag, Eigen::DenseShape, Eigen::DenseShape>::CoeffReturnType = double; Eigen::Index = long int]’ /usr/include/eigen3/Eigen/src/Core/AssignEvaluator.h:631:5: required from ‘void Eigen::internal::generic_dense_assignment_kernel::assignCoeff(Eigen::Index, Eigen::Index) [with DstEvaluatorTypeT = Eigen::internal::evaluator >; SrcEvaluatorTypeT = Eigen::internal::evaluator, Eigen::Matrix, 1> >; Functor = Eigen::internal::assign_op; int Version = 0; Eigen::Index = long int]’ /usr/include/eigen3/Eigen/src/Core/AssignEvaluator.h:645:5: required from ‘void Eigen::internal::generic_dense_assignment_kernel::assignCoeffByOuterInner(Eigen::Index, Eigen::Index) [with DstEvaluatorTypeT = Eigen::internal::evaluator >; SrcEvaluatorTypeT = Eigen::internal::evaluator, Eigen::Matrix, 1> >; Functor = Eigen::internal::assign_op; int Version = 0; Eigen::Index = long int]’ /usr/include/eigen3/Eigen/src/Core/AssignEvaluator.h:222:5: required from ‘static void Eigen::internal::copy_using_evaluator_DefaultTraversal_InnerUnrolling::run(Kernel&, Eigen::Index) [with Kernel = Eigen::internal::generic_dense_assignment_kernel >, Eigen::internal::evaluator, Eigen::Matrix, 1> >, Eigen::internal::assign_op, 0>; int Index_ = 2; int Stop = 3; Eigen::Index = long int]’ /usr/include/eigen3/Eigen/src/Core/AssignEvaluator.h:578:96: [ skipping 20 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /usr/include/eigen3/Eigen/src/Core/Matrix.h:294:31: required from ‘Eigen::Matrix<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>::Matrix(const T&) [with T = Eigen::Product, Eigen::Matrix, 0>, Eigen::Transpose >, 0>; _Scalar = double; int _Rows = 3; int _Cols = 3; int _Options = 1; int _MaxRows = 3; int _MaxCols = 3]’ /usr/include/eigen3/Eigen/src/Core/AssignEvaluator.h:796:41: required from ‘void Eigen::internal::call_assignment(Dst&, const Src&, const Func&, typename Eigen::internal::enable_if::value, void*>::type) [with Dst = Eigen::Matrix; Src = Eigen::Product, Eigen::Matrix, 0>, Eigen::Transpose >, 0>; Func = Eigen::internal::assign_op; typename Eigen::internal::enable_if::value, void*>::type = void*]’ /usr/include/eigen3/Eigen/src/Core/AssignEvaluator.h:782:18: required from ‘void Eigen::internal::call_assignment(Dst&, const Src&) [with Dst = Eigen::Matrix; Src = Eigen::Product, Eigen::Matrix, 0>, Eigen::Transpose >, 0>]’ /usr/include/eigen3/Eigen/src/Core/PlainObjectBase.h:714:32: required from ‘Derived& Eigen::PlainObjectBase::_set(const Eigen::DenseBase&) [with OtherDerived = Eigen::Product, Eigen::Matrix, 0>, Eigen::Transpose >, 0>; Derived = Eigen::Matrix]’ /usr/include/eigen3/Eigen/src/Core/Matrix.h:225:24: required from ‘Eigen::Matrix<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>& Eigen::Matrix<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>::operator=(const Eigen::DenseBase&) [with OtherDerived = Eigen::Product, Eigen::Matrix, 0>, Eigen::Transpose >, 0>; _Scalar = double; int _Rows = 3; int _Cols = 3; int _Options = 0; int _MaxRows = 3; int _MaxCols = 3]’ /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculealigner.cpp:198:79: required from here /usr/include/eigen3/Eigen/src/Core/CwiseBinaryOp.h:105:49: warning: implicitly-declared ‘Eigen::Transpose, 1, 3, false> >::Transpose(const Eigen::Transpose, 1, 3, false> >&)’ is deprecated [-Wdeprecated-copy] 105 | : m_lhs(aLhs), m_rhs(aRhs), m_functor(func) | ^ In file included from /usr/include/eigen3/Eigen/Core:445, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculealigner.h:43, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculealigner.cpp:36: /usr/include/eigen3/Eigen/src/Core/Assign.h:55:30: note: because ‘Eigen::Transpose, 1, 3, false> >’ has user-provided ‘Derived& Eigen::MatrixBase::operator=(const Eigen::MatrixBase&) [with Derived = Eigen::Transpose, 1, 3, false> >]’ 55 | EIGEN_STRONG_INLINE Derived& MatrixBase::operator=(const MatrixBase& other) | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/eigen3/Eigen/Core:461, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculealigner.h:43, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculealigner.cpp:36: /usr/include/eigen3/Eigen/src/Core/CwiseBinaryOp.h:105:49: warning: implicitly-declared ‘Eigen::Block, 3, 1, true>::Block(const Eigen::Block, 3, 1, true>&)’ is deprecated [-Wdeprecated-copy] 105 | : m_lhs(aLhs), m_rhs(aRhs), m_functor(func) | ^ In file included from /usr/include/eigen3/Eigen/Core:88, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculealigner.h:43, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculealigner.cpp:36: /usr/include/eigen3/Eigen/src/Core/util/Macros.h:830:52: note: because ‘Eigen::Block, 3, 1, true>’ has user-provided ‘Eigen::BlockImpl& Eigen::BlockImpl::operator=(const Eigen::BlockImpl&) [with XprType = const Eigen::Matrix; int BlockRows = 3; int BlockCols = 1; bool InnerPanel = true]’ 830 | EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Derived& operator=(const Derived& other) \ | ^~~~~~~~ /usr/include/eigen3/Eigen/src/Core/util/Macros.h:842:53: note: in expansion of macro ‘EIGEN_INHERIT_ASSIGNMENT_EQUAL_OPERATOR’ 842 | #define EIGEN_INHERIT_ASSIGNMENT_OPERATORS(Derived) EIGEN_INHERIT_ASSIGNMENT_EQUAL_OPERATOR(Derived) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/eigen3/Eigen/src/Core/Block.h:161:5: note: in expansion of macro ‘EIGEN_INHERIT_ASSIGNMENT_OPERATORS’ 161 | EIGEN_INHERIT_ASSIGNMENT_OPERATORS(BlockImpl) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 13%] Building CXX object src/chemkit/CMakeFiles/chemkit.dir/moleculeeditor.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit && /usr/bin/x86_64-pc-linux-gnu-g++ -DCHEMKIT_LIBRARY -Dchemkit_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/chemkit.dir/moleculeeditor.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculeeditor.cpp /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculeeditor.cpp:185:6: warning: ‘bool chemkit::{anonymous}::UndoStack::isEmpty() const’ defined but not used [-Wunused-function] 185 | bool UndoStack::isEmpty() const | ^~~~~~~~~ /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculeeditor.cpp:179:8: warning: ‘size_t chemkit::{anonymous}::UndoStack::size() const’ defined but not used [-Wunused-function] 179 | size_t UndoStack::size() const | ^~~~~~~~~ [ 13%] Building CXX object src/chemkit/CMakeFiles/chemkit.dir/moleculewatcher.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit && /usr/bin/x86_64-pc-linux-gnu-g++ -DCHEMKIT_LIBRARY -Dchemkit_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/chemkit.dir/moleculewatcher.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/moleculewatcher.cpp [ 14%] Building CXX object src/chemkit/CMakeFiles/chemkit.dir/nucleotide.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit && /usr/bin/x86_64-pc-linux-gnu-g++ -DCHEMKIT_LIBRARY -Dchemkit_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/chemkit.dir/nucleotide.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/nucleotide.cpp [ 14%] Building CXX object src/chemkit/CMakeFiles/chemkit.dir/partialchargemodel.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit && /usr/bin/x86_64-pc-linux-gnu-g++ -DCHEMKIT_LIBRARY -Dchemkit_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/chemkit.dir/partialchargemodel.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/partialchargemodel.cpp [ 15%] Building CXX object src/chemkit/CMakeFiles/chemkit.dir/plugin.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit && /usr/bin/x86_64-pc-linux-gnu-g++ -DCHEMKIT_LIBRARY -Dchemkit_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/chemkit.dir/plugin.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/plugin.cpp [ 15%] Building CXX object src/chemkit/CMakeFiles/chemkit.dir/pluginmanager.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit && /usr/bin/x86_64-pc-linux-gnu-g++ -DCHEMKIT_LIBRARY -Dchemkit_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/chemkit.dir/pluginmanager.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/pluginmanager.cpp [ 16%] Building CXX object src/chemkit/CMakeFiles/chemkit.dir/polymer.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit && /usr/bin/x86_64-pc-linux-gnu-g++ -DCHEMKIT_LIBRARY -Dchemkit_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/chemkit.dir/polymer.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/polymer.cpp [ 16%] Building CXX object src/chemkit/CMakeFiles/chemkit.dir/polymerchain.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit && /usr/bin/x86_64-pc-linux-gnu-g++ -DCHEMKIT_LIBRARY -Dchemkit_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/chemkit.dir/polymerchain.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/polymerchain.cpp [ 17%] Building CXX object src/chemkit/CMakeFiles/chemkit.dir/residue.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit && /usr/bin/x86_64-pc-linux-gnu-g++ -DCHEMKIT_LIBRARY -Dchemkit_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/chemkit.dir/residue.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/residue.cpp [ 17%] Building CXX object src/chemkit/CMakeFiles/chemkit.dir/ring.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit && /usr/bin/x86_64-pc-linux-gnu-g++ -DCHEMKIT_LIBRARY -Dchemkit_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/chemkit.dir/ring.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/ring.cpp [ 17%] Building CXX object src/chemkit/CMakeFiles/chemkit.dir/scalarfield.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit && /usr/bin/x86_64-pc-linux-gnu-g++ -DCHEMKIT_LIBRARY -Dchemkit_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/chemkit.dir/scalarfield.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/scalarfield.cpp [ 18%] Building CXX object src/chemkit/CMakeFiles/chemkit.dir/stereochemistry.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit && /usr/bin/x86_64-pc-linux-gnu-g++ -DCHEMKIT_LIBRARY -Dchemkit_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden 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CMakeFiles/chemkit.dir/coordinatepredictor.cpp.o CMakeFiles/chemkit.dir/coordinateset.cpp.o CMakeFiles/chemkit.dir/delaunaytriangulation.cpp.o CMakeFiles/chemkit.dir/diagramcoordinates.cpp.o CMakeFiles/chemkit.dir/dynamiclibrary.cpp.o CMakeFiles/chemkit.dir/element.cpp.o CMakeFiles/chemkit.dir/fingerprint.cpp.o CMakeFiles/chemkit.dir/fingerprintsimilaritydescriptor.cpp.o CMakeFiles/chemkit.dir/fragment.cpp.o CMakeFiles/chemkit.dir/geometry.cpp.o CMakeFiles/chemkit.dir/internalcoordinates.cpp.o CMakeFiles/chemkit.dir/isotope.cpp.o CMakeFiles/chemkit.dir/lineformat.cpp.o CMakeFiles/chemkit.dir/moiety.cpp.o CMakeFiles/chemkit.dir/moleculardescriptor.cpp.o CMakeFiles/chemkit.dir/molecularsurface.cpp.o CMakeFiles/chemkit.dir/molecule.cpp.o CMakeFiles/chemkit.dir/moleculealigner.cpp.o CMakeFiles/chemkit.dir/moleculeeditor.cpp.o CMakeFiles/chemkit.dir/moleculewatcher.cpp.o CMakeFiles/chemkit.dir/nucleotide.cpp.o CMakeFiles/chemkit.dir/partialchargemodel.cpp.o CMakeFiles/chemkit.dir/plugin.cpp.o CMakeFiles/chemkit.dir/pluginmanager.cpp.o CMakeFiles/chemkit.dir/polymer.cpp.o CMakeFiles/chemkit.dir/polymerchain.cpp.o CMakeFiles/chemkit.dir/residue.cpp.o CMakeFiles/chemkit.dir/ring.cpp.o CMakeFiles/chemkit.dir/scalarfield.cpp.o CMakeFiles/chemkit.dir/stereochemistry.cpp.o CMakeFiles/chemkit.dir/structuresimilaritydescriptor.cpp.o CMakeFiles/chemkit.dir/substructurequery.cpp.o CMakeFiles/chemkit.dir/unitcell.cpp.o -lboost_system-mt -lboost_filesystem-mt -lboost_thread-mt -lpthread -lboost_chrono-mt -lboost_date_time-mt -lboost_atomic-mt -ldl cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit && /usr/bin/cmake -E copy /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit/libchemkit.so /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/lib64/libchemkit.so make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 20%] Built target chemkit make -f 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Scanning dependencies of target chemkit-io make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' make -f src/io/CMakeFiles/chemkit-io.dir/build.make src/io/CMakeFiles/chemkit-io.dir/build make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 20%] Building CXX object src/io/CMakeFiles/chemkit-io.dir/io.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/io && /usr/bin/x86_64-pc-linux-gnu-g++ -DCHEMKIT_IO_LIBRARY -Dchemkit_io_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/chemkit-io.dir/io.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/io/io.cpp [ 21%] Building CXX object src/io/CMakeFiles/chemkit-io.dir/moleculefile.cpp.o cd 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-I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/chemkit-io.dir/polymerfileformat.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/io/polymerfileformat.cpp [ 23%] Linking CXX shared library libchemkit-io.so cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/io && /usr/bin/cmake -E cmake_link_script CMakeFiles/chemkit-io.dir/link.txt --verbose=1 /usr/bin/x86_64-pc-linux-gnu-g++ -fPIC -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -Wl,-O1 -Wl,--as-needed -shared -Wl,-soname,libchemkit-io.so -o libchemkit-io.so CMakeFiles/chemkit-io.dir/io.cpp.o CMakeFiles/chemkit-io.dir/moleculefile.cpp.o CMakeFiles/chemkit-io.dir/moleculefileformat.cpp.o CMakeFiles/chemkit-io.dir/polymerfile.cpp.o CMakeFiles/chemkit-io.dir/polymerfileformat.cpp.o -Wl,-rpath,/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit: ../chemkit/libchemkit.so -lboost_iostreams-mt -lboost_regex-mt -lboost_system-mt -lboost_filesystem-mt -lboost_thread-mt -lpthread -lboost_chrono-mt -lboost_date_time-mt -lboost_atomic-mt -ldl cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/io && /usr/bin/cmake -E copy /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/io/libchemkit-io.so /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/lib64/libchemkit-io.so make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 23%] Built target chemkit-io make -f src/md/CMakeFiles/chemkit-md.dir/build.make src/md/CMakeFiles/chemkit-md.dir/depend make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' cd 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Scanning dependencies of target chemkit-md make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' make -f src/md/CMakeFiles/chemkit-md.dir/build.make src/md/CMakeFiles/chemkit-md.dir/build make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 23%] Building CXX object src/md/CMakeFiles/chemkit-md.dir/forcefieldcalculation.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/md && /usr/bin/x86_64-pc-linux-gnu-g++ -DCHEMKIT_MD_LIBRARY -Dchemkit_md_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/chemkit-md.dir/forcefieldcalculation.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/md/forcefieldcalculation.cpp [ 23%] Building CXX object src/md/CMakeFiles/chemkit-md.dir/forcefield.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/md && /usr/bin/x86_64-pc-linux-gnu-g++ -DCHEMKIT_MD_LIBRARY -Dchemkit_md_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/chemkit-md.dir/forcefield.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/md/forcefield.cpp [ 24%] Building CXX object src/md/CMakeFiles/chemkit-md.dir/integrator.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/md && /usr/bin/x86_64-pc-linux-gnu-g++ -DCHEMKIT_MD_LIBRARY -Dchemkit_md_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden 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-I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/chemkit-md.dir/moleculegeometryoptimizer.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/md/moleculegeometryoptimizer.cpp [ 25%] Building CXX object src/md/CMakeFiles/chemkit-md.dir/potential.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/md && /usr/bin/x86_64-pc-linux-gnu-g++ -DCHEMKIT_MD_LIBRARY -Dchemkit_md_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/chemkit-md.dir/potential.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/md/potential.cpp [ 26%] Building CXX object src/md/CMakeFiles/chemkit-md.dir/topology.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/md && /usr/bin/x86_64-pc-linux-gnu-g++ -DCHEMKIT_MD_LIBRARY -Dchemkit_md_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/chemkit-md.dir/topology.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/md/topology.cpp [ 26%] Building CXX object src/md/CMakeFiles/chemkit-md.dir/topologybuilder.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/md && /usr/bin/x86_64-pc-linux-gnu-g++ -DCHEMKIT_MD_LIBRARY -Dchemkit_md_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden 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-DCHEMKIT_MD_LIBRARY -Dchemkit_md_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/chemkit-md.dir/trajectoryframe.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/md/trajectoryframe.cpp [ 28%] Linking CXX shared library libchemkit-md.so cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/md && /usr/bin/cmake -E cmake_link_script CMakeFiles/chemkit-md.dir/link.txt --verbose=1 /usr/bin/x86_64-pc-linux-gnu-g++ -fPIC -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -Wl,-O1 -Wl,--as-needed -shared -Wl,-soname,libchemkit-md.so -o libchemkit-md.so CMakeFiles/chemkit-md.dir/forcefieldcalculation.cpp.o CMakeFiles/chemkit-md.dir/forcefield.cpp.o CMakeFiles/chemkit-md.dir/integrator.cpp.o CMakeFiles/chemkit-md.dir/md.cpp.o CMakeFiles/chemkit-md.dir/moleculegeometryoptimizer.cpp.o CMakeFiles/chemkit-md.dir/potential.cpp.o CMakeFiles/chemkit-md.dir/topology.cpp.o CMakeFiles/chemkit-md.dir/topologybuilder.cpp.o CMakeFiles/chemkit-md.dir/trajectory.cpp.o CMakeFiles/chemkit-md.dir/trajectoryframe.cpp.o -Wl,-rpath,/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit: ../chemkit/libchemkit.so -lboost_system-mt -lboost_filesystem-mt -lboost_thread-mt -lpthread -lboost_chrono-mt -lboost_date_time-mt -lboost_atomic-mt -ldl cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/md && /usr/bin/cmake -E copy /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/md/libchemkit-md.so /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/lib64/libchemkit-md.so make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 28%] Built target chemkit-md make -f src/md-io/CMakeFiles/chemkit-md-io.dir/build.make src/md-io/CMakeFiles/chemkit-md-io.dir/depend make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/md-io /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/md-io /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/md-io/CMakeFiles/chemkit-md-io.dir/DependInfo.cmake Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/md-io/CMakeFiles/chemkit-md-io.dir/DependInfo.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/md-io/CMakeFiles/chemkit-md-io.dir/depend.internal". Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/md-io/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/md-io/CMakeFiles/chemkit-md-io.dir/depend.internal". Scanning dependencies of target chemkit-md-io make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' make -f src/md-io/CMakeFiles/chemkit-md-io.dir/build.make src/md-io/CMakeFiles/chemkit-md-io.dir/build make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 28%] Building CXX object src/md-io/CMakeFiles/chemkit-md-io.dir/topologyfile.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/md-io && /usr/bin/x86_64-pc-linux-gnu-g++ -DCHEMKIT_MD_IO_LIBRARY -Dchemkit_md_io_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/chemkit-md-io.dir/topologyfile.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/md-io/topologyfile.cpp [ 29%] Building CXX object src/md-io/CMakeFiles/chemkit-md-io.dir/topologyfileformat.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/md-io && /usr/bin/x86_64-pc-linux-gnu-g++ -DCHEMKIT_MD_IO_LIBRARY -Dchemkit_md_io_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/chemkit-md-io.dir/topologyfileformat.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/md-io/topologyfileformat.cpp [ 29%] Building CXX object src/md-io/CMakeFiles/chemkit-md-io.dir/trajectoryfile.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/md-io && /usr/bin/x86_64-pc-linux-gnu-g++ -DCHEMKIT_MD_IO_LIBRARY -Dchemkit_md_io_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/chemkit-md-io.dir/trajectoryfile.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/md-io/trajectoryfile.cpp [ 29%] Building CXX object src/md-io/CMakeFiles/chemkit-md-io.dir/trajectoryfileformat.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/md-io && /usr/bin/x86_64-pc-linux-gnu-g++ -DCHEMKIT_MD_IO_LIBRARY -Dchemkit_md_io_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/chemkit-md-io.dir/trajectoryfileformat.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/md-io/trajectoryfileformat.cpp [ 30%] Linking CXX shared library libchemkit-md-io.so cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/md-io && /usr/bin/cmake -E cmake_link_script CMakeFiles/chemkit-md-io.dir/link.txt --verbose=1 /usr/bin/x86_64-pc-linux-gnu-g++ -fPIC -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -Wl,-O1 -Wl,--as-needed -shared -Wl,-soname,libchemkit-md-io.so -o libchemkit-md-io.so CMakeFiles/chemkit-md-io.dir/topologyfile.cpp.o CMakeFiles/chemkit-md-io.dir/topologyfileformat.cpp.o CMakeFiles/chemkit-md-io.dir/trajectoryfile.cpp.o CMakeFiles/chemkit-md-io.dir/trajectoryfileformat.cpp.o -Wl,-rpath,/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/io:/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/md:/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit: ../io/libchemkit-io.so ../md/libchemkit-md.so -lboost_iostreams-mt -lboost_regex-mt ../chemkit/libchemkit.so -lboost_system-mt -lboost_filesystem-mt -lboost_thread-mt -lpthread -lboost_chrono-mt -lboost_date_time-mt -lboost_atomic-mt -ldl cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/md-io && /usr/bin/cmake -E copy /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/md-io/libchemkit-md-io.so /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/lib64/libchemkit-md-io.so make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 30%] Built target chemkit-md-io make -f src/plugins/amber/CMakeFiles/amber.dir/build.make src/plugins/amber/CMakeFiles/amber.dir/depend make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/amber 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Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/amber/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/amber/CMakeFiles/amber.dir/depend.internal". Scanning dependencies of target amber make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' make -f src/plugins/amber/CMakeFiles/amber.dir/build.make src/plugins/amber/CMakeFiles/amber.dir/build make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 30%] Building CXX object src/plugins/amber/CMakeFiles/amber.dir/amberatomtyper.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/amber && /usr/bin/x86_64-pc-linux-gnu-g++ -Damber_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/amber.dir/amberatomtyper.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/amber/amberatomtyper.cpp [ 30%] Building CXX object src/plugins/amber/CMakeFiles/amber.dir/ambercalculation.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/amber && /usr/bin/x86_64-pc-linux-gnu-g++ -Damber_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/amber.dir/ambercalculation.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/amber/ambercalculation.cpp [ 31%] Building CXX object src/plugins/amber/CMakeFiles/amber.dir/amberforcefield.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/amber && /usr/bin/x86_64-pc-linux-gnu-g++ -Damber_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/amber.dir/amberforcefield.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/amber/amberforcefield.cpp [ 31%] Building CXX object src/plugins/amber/CMakeFiles/amber.dir/amberparameters.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/amber && /usr/bin/x86_64-pc-linux-gnu-g++ -Damber_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/amber.dir/amberparameters.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/amber/amberparameters.cpp [ 32%] Building CXX object src/plugins/amber/CMakeFiles/amber.dir/amberplugin.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/amber && /usr/bin/x86_64-pc-linux-gnu-g++ -Damber_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/amber.dir/amberplugin.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/amber/amberplugin.cpp [ 32%] Building CXX object src/plugins/amber/CMakeFiles/amber.dir/mdcrdfileformat.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/amber && /usr/bin/x86_64-pc-linux-gnu-g++ -Damber_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/amber.dir/mdcrdfileformat.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/amber/mdcrdfileformat.cpp [ 33%] Linking CXX shared library amber.so cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/amber && /usr/bin/cmake -E cmake_link_script CMakeFiles/amber.dir/link.txt --verbose=1 /usr/bin/x86_64-pc-linux-gnu-g++ -fPIC -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -Wl,-O1 -Wl,--as-needed -shared -Wl,-soname,amber.so -o amber.so CMakeFiles/amber.dir/amberatomtyper.cpp.o CMakeFiles/amber.dir/ambercalculation.cpp.o CMakeFiles/amber.dir/amberforcefield.cpp.o CMakeFiles/amber.dir/amberparameters.cpp.o CMakeFiles/amber.dir/amberplugin.cpp.o CMakeFiles/amber.dir/mdcrdfileformat.cpp.o -Wl,-rpath,/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/md-io:/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/md:/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/io:/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit: ../../md-io/libchemkit-md-io.so ../../md/libchemkit-md.so ../../io/libchemkit-io.so ../../chemkit/libchemkit.so -lboost_system-mt -lboost_filesystem-mt -lboost_thread-mt -lpthread -lboost_chrono-mt -lboost_date_time-mt -lboost_atomic-mt -ldl -lboost_iostreams-mt -lboost_regex-mt cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/amber && /usr/bin/cmake -E copy /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/amber/amber.so /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/lib64/chemkit/plugins/amber.so make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 33%] Built target amber make -f src/plugins/apol/CMakeFiles/apol.dir/build.make src/plugins/apol/CMakeFiles/apol.dir/depend make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/apol /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/apol /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/apol/CMakeFiles/apol.dir/DependInfo.cmake Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/apol/CMakeFiles/apol.dir/DependInfo.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/apol/CMakeFiles/apol.dir/depend.internal". Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/apol/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/apol/CMakeFiles/apol.dir/depend.internal". Scanning dependencies of target apol make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' make -f src/plugins/apol/CMakeFiles/apol.dir/build.make src/plugins/apol/CMakeFiles/apol.dir/build make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 33%] Building CXX object src/plugins/apol/CMakeFiles/apol.dir/apoldescriptor.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/apol && /usr/bin/x86_64-pc-linux-gnu-g++ -Dapol_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/apol.dir/apoldescriptor.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/apol/apoldescriptor.cpp [ 34%] Building CXX object src/plugins/apol/CMakeFiles/apol.dir/apolplugin.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/apol && /usr/bin/x86_64-pc-linux-gnu-g++ -Dapol_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/apol.dir/apolplugin.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/apol/apolplugin.cpp [ 34%] Linking CXX shared library apol.so cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/apol && /usr/bin/cmake -E cmake_link_script CMakeFiles/apol.dir/link.txt --verbose=1 /usr/bin/x86_64-pc-linux-gnu-g++ -fPIC -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -Wl,-O1 -Wl,--as-needed -shared -Wl,-soname,apol.so -o apol.so CMakeFiles/apol.dir/apoldescriptor.cpp.o CMakeFiles/apol.dir/apolplugin.cpp.o -Wl,-rpath,/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit: ../../chemkit/libchemkit.so -lboost_system-mt -lboost_filesystem-mt -lboost_thread-mt -lpthread -lboost_chrono-mt -lboost_date_time-mt -lboost_atomic-mt -ldl cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/apol && /usr/bin/cmake -E copy /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/apol/apol.so /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/lib64/chemkit/plugins/apol.so make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 34%] Built target apol make -f src/plugins/chemjson/CMakeFiles/chemjson.dir/build.make src/plugins/chemjson/CMakeFiles/chemjson.dir/depend make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/chemjson /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/chemjson /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/chemjson/CMakeFiles/chemjson.dir/DependInfo.cmake Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/chemjson/CMakeFiles/chemjson.dir/DependInfo.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/chemjson/CMakeFiles/chemjson.dir/depend.internal". Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/chemjson/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/chemjson/CMakeFiles/chemjson.dir/depend.internal". Scanning dependencies of target chemjson make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' make -f src/plugins/chemjson/CMakeFiles/chemjson.dir/build.make src/plugins/chemjson/CMakeFiles/chemjson.dir/build make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 35%] Building CXX object src/plugins/chemjson/CMakeFiles/chemjson.dir/chemjsonfileformat.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/chemjson && /usr/bin/x86_64-pc-linux-gnu-g++ -Dchemjson_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/chemjson.dir/chemjsonfileformat.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/chemjson/chemjsonfileformat.cpp [ 35%] Building CXX object src/plugins/chemjson/CMakeFiles/chemjson.dir/chemjsonplugin.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/chemjson && /usr/bin/x86_64-pc-linux-gnu-g++ -Dchemjson_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/chemjson.dir/chemjsonplugin.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/chemjson/chemjsonplugin.cpp [ 35%] Building CXX object src/plugins/chemjson/CMakeFiles/chemjson.dir/__/__/3rdparty/jsoncpp/jsoncpp.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/chemjson && /usr/bin/x86_64-pc-linux-gnu-g++ -Dchemjson_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/chemjson.dir/__/__/3rdparty/jsoncpp/jsoncpp.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/3rdparty/jsoncpp/jsoncpp.cpp [ 36%] Linking CXX shared library chemjson.so cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/chemjson && /usr/bin/cmake -E cmake_link_script CMakeFiles/chemjson.dir/link.txt --verbose=1 /usr/bin/x86_64-pc-linux-gnu-g++ -fPIC -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -Wl,-O1 -Wl,--as-needed -shared -Wl,-soname,chemjson.so -o chemjson.so CMakeFiles/chemjson.dir/chemjsonfileformat.cpp.o CMakeFiles/chemjson.dir/chemjsonplugin.cpp.o CMakeFiles/chemjson.dir/__/__/3rdparty/jsoncpp/jsoncpp.cpp.o -Wl,-rpath,/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/io:/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit: ../../io/libchemkit-io.so ../../chemkit/libchemkit.so -lboost_system-mt -lboost_filesystem-mt -lboost_thread-mt -lpthread -lboost_chrono-mt -lboost_date_time-mt -lboost_atomic-mt -ldl -lboost_iostreams-mt -lboost_regex-mt cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/chemjson && /usr/bin/cmake -E copy /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/chemjson/chemjson.so /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/lib64/chemkit/plugins/chemjson.so make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 36%] Built target chemjson make -f src/plugins/cml/CMakeFiles/cml.dir/build.make src/plugins/cml/CMakeFiles/cml.dir/depend make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/cml /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/cml /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/cml/CMakeFiles/cml.dir/DependInfo.cmake Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/cml/CMakeFiles/cml.dir/DependInfo.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/cml/CMakeFiles/cml.dir/depend.internal". Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/cml/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/cml/CMakeFiles/cml.dir/depend.internal". Scanning dependencies of target cml make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' make -f src/plugins/cml/CMakeFiles/cml.dir/build.make src/plugins/cml/CMakeFiles/cml.dir/build make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 37%] Building CXX object src/plugins/cml/CMakeFiles/cml.dir/cmlfileformat.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/cml && /usr/bin/x86_64-pc-linux-gnu-g++ -Dcml_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/cml.dir/cmlfileformat.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/cml/cmlfileformat.cpp [ 37%] Building CXX object src/plugins/cml/CMakeFiles/cml.dir/cmlplugin.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/cml && /usr/bin/x86_64-pc-linux-gnu-g++ -Dcml_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/cml.dir/cmlplugin.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/cml/cmlplugin.cpp [ 38%] Linking CXX shared library cml.so cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/cml && /usr/bin/cmake -E cmake_link_script CMakeFiles/cml.dir/link.txt --verbose=1 /usr/bin/x86_64-pc-linux-gnu-g++ -fPIC -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -Wl,-O1 -Wl,--as-needed -shared -Wl,-soname,cml.so -o cml.so CMakeFiles/cml.dir/cmlfileformat.cpp.o CMakeFiles/cml.dir/cmlplugin.cpp.o -Wl,-rpath,/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/io:/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit: ../../io/libchemkit-io.so ../../chemkit/libchemkit.so -lboost_system-mt -lboost_filesystem-mt -lboost_thread-mt -lpthread -lboost_chrono-mt -lboost_date_time-mt -lboost_atomic-mt -ldl -lboost_iostreams-mt -lboost_regex-mt cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/cml && /usr/bin/cmake -E copy /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/cml/cml.so /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/lib64/chemkit/plugins/cml.so make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 38%] Built target cml make -f src/plugins/countdescriptors/CMakeFiles/countdescriptors.dir/build.make src/plugins/countdescriptors/CMakeFiles/countdescriptors.dir/depend make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/countdescriptors /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/countdescriptors /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/countdescriptors/CMakeFiles/countdescriptors.dir/DependInfo.cmake Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/countdescriptors/CMakeFiles/countdescriptors.dir/DependInfo.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/countdescriptors/CMakeFiles/countdescriptors.dir/depend.internal". Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/countdescriptors/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/countdescriptors/CMakeFiles/countdescriptors.dir/depend.internal". Scanning dependencies of target countdescriptors make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' make -f src/plugins/countdescriptors/CMakeFiles/countdescriptors.dir/build.make src/plugins/countdescriptors/CMakeFiles/countdescriptors.dir/build make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 38%] Building CXX object src/plugins/countdescriptors/CMakeFiles/countdescriptors.dir/countdescriptors.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/countdescriptors && /usr/bin/x86_64-pc-linux-gnu-g++ -Dcountdescriptors_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/countdescriptors.dir/countdescriptors.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/countdescriptors/countdescriptors.cpp [ 39%] Building CXX object src/plugins/countdescriptors/CMakeFiles/countdescriptors.dir/countdescriptorsplugin.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/countdescriptors && /usr/bin/x86_64-pc-linux-gnu-g++ -Dcountdescriptors_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/countdescriptors.dir/countdescriptorsplugin.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/countdescriptors/countdescriptorsplugin.cpp [ 39%] Linking CXX shared library countdescriptors.so cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/countdescriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/countdescriptors.dir/link.txt --verbose=1 /usr/bin/x86_64-pc-linux-gnu-g++ -fPIC -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -Wl,-O1 -Wl,--as-needed -shared -Wl,-soname,countdescriptors.so -o countdescriptors.so CMakeFiles/countdescriptors.dir/countdescriptors.cpp.o CMakeFiles/countdescriptors.dir/countdescriptorsplugin.cpp.o -Wl,-rpath,/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit: ../../chemkit/libchemkit.so -lboost_system-mt -lboost_filesystem-mt -lboost_thread-mt -lpthread -lboost_chrono-mt -lboost_date_time-mt -lboost_atomic-mt -ldl cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/countdescriptors && /usr/bin/cmake -E copy /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/countdescriptors/countdescriptors.so /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/lib64/chemkit/plugins/countdescriptors.so make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 39%] Built target countdescriptors make -f src/plugins/elementtypers/CMakeFiles/elementtypers.dir/build.make src/plugins/elementtypers/CMakeFiles/elementtypers.dir/depend make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/elementtypers /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/elementtypers /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/elementtypers/CMakeFiles/elementtypers.dir/DependInfo.cmake Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/elementtypers/CMakeFiles/elementtypers.dir/DependInfo.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/elementtypers/CMakeFiles/elementtypers.dir/depend.internal". Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/elementtypers/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/elementtypers/CMakeFiles/elementtypers.dir/depend.internal". Scanning dependencies of target elementtypers make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' make -f src/plugins/elementtypers/CMakeFiles/elementtypers.dir/build.make src/plugins/elementtypers/CMakeFiles/elementtypers.dir/build make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 40%] Building CXX object src/plugins/elementtypers/CMakeFiles/elementtypers.dir/atomicnumberatomtyper.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/elementtypers && /usr/bin/x86_64-pc-linux-gnu-g++ -Delementtypers_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/elementtypers.dir/atomicnumberatomtyper.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/elementtypers/atomicnumberatomtyper.cpp [ 40%] Building CXX object src/plugins/elementtypers/CMakeFiles/elementtypers.dir/elementnameatomtyper.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/elementtypers && /usr/bin/x86_64-pc-linux-gnu-g++ -Delementtypers_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/elementtypers.dir/elementnameatomtyper.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/elementtypers/elementnameatomtyper.cpp [ 40%] Building CXX object src/plugins/elementtypers/CMakeFiles/elementtypers.dir/elementsymbolatomtyper.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/elementtypers && /usr/bin/x86_64-pc-linux-gnu-g++ -Delementtypers_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/elementtypers.dir/elementsymbolatomtyper.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/elementtypers/elementsymbolatomtyper.cpp [ 41%] Building CXX object src/plugins/elementtypers/CMakeFiles/elementtypers.dir/elementtypersplugin.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/elementtypers && /usr/bin/x86_64-pc-linux-gnu-g++ -Delementtypers_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/elementtypers.dir/elementtypersplugin.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/elementtypers/elementtypersplugin.cpp [ 41%] Linking CXX shared library elementtypers.so cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/elementtypers && /usr/bin/cmake -E cmake_link_script CMakeFiles/elementtypers.dir/link.txt --verbose=1 /usr/bin/x86_64-pc-linux-gnu-g++ -fPIC -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -Wl,-O1 -Wl,--as-needed -shared -Wl,-soname,elementtypers.so -o elementtypers.so CMakeFiles/elementtypers.dir/atomicnumberatomtyper.cpp.o CMakeFiles/elementtypers.dir/elementnameatomtyper.cpp.o CMakeFiles/elementtypers.dir/elementsymbolatomtyper.cpp.o CMakeFiles/elementtypers.dir/elementtypersplugin.cpp.o -Wl,-rpath,/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit: ../../chemkit/libchemkit.so -lboost_system-mt -lboost_filesystem-mt -lboost_thread-mt -lpthread -lboost_chrono-mt -lboost_date_time-mt -lboost_atomic-mt -ldl cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/elementtypers && /usr/bin/cmake -E copy /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/elementtypers/elementtypers.so /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/lib64/chemkit/plugins/elementtypers.so make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 41%] Built target elementtypers make -f src/plugins/fhz/CMakeFiles/fhz.dir/build.make src/plugins/fhz/CMakeFiles/fhz.dir/depend make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/fhz /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/fhz /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/fhz/CMakeFiles/fhz.dir/DependInfo.cmake Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/fhz/CMakeFiles/fhz.dir/DependInfo.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/fhz/CMakeFiles/fhz.dir/depend.internal". Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/fhz/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/fhz/CMakeFiles/fhz.dir/depend.internal". Scanning dependencies of target fhz make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' make -f src/plugins/fhz/CMakeFiles/fhz.dir/build.make src/plugins/fhz/CMakeFiles/fhz.dir/build make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 42%] Building CXX object src/plugins/fhz/CMakeFiles/fhz.dir/fhzfileformat.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/fhz && /usr/bin/x86_64-pc-linux-gnu-g++ -Dfhz_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/fhz.dir/fhzfileformat.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/fhz/fhzfileformat.cpp /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/fhz/fhzfileformat.cpp: In member function ‘virtual bool FhzFileFormat::read(std::istream&, chemkit::MoleculeFile*)’: /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/fhz/fhzfileformat.cpp:94:57: warning: this statement may fall through [-Wimplicit-fallthrough=] 94 | phi = boost::lexical_cast(tokens[6]); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/fhz/fhzfileformat.cpp:95:13: note: here 95 | case 2: | ^~~~ /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/fhz/fhzfileformat.cpp:97:59: warning: this statement may fall through [-Wimplicit-fallthrough=] 97 | theta = boost::lexical_cast(tokens[4]); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/fhz/fhzfileformat.cpp:98:13: note: here 98 | case 1: | ^~~~ [ 42%] Building CXX object src/plugins/fhz/CMakeFiles/fhz.dir/fhzplugin.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/fhz && /usr/bin/x86_64-pc-linux-gnu-g++ -Dfhz_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/fhz.dir/fhzplugin.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/fhz/fhzplugin.cpp [ 43%] Linking CXX shared library fhz.so cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/fhz && /usr/bin/cmake -E cmake_link_script CMakeFiles/fhz.dir/link.txt --verbose=1 /usr/bin/x86_64-pc-linux-gnu-g++ -fPIC -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -Wl,-O1 -Wl,--as-needed -shared -Wl,-soname,fhz.so -o fhz.so CMakeFiles/fhz.dir/fhzfileformat.cpp.o CMakeFiles/fhz.dir/fhzplugin.cpp.o -Wl,-rpath,/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/io:/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit: ../../io/libchemkit-io.so ../../chemkit/libchemkit.so -lboost_system-mt -lboost_filesystem-mt -lboost_thread-mt -lpthread -lboost_chrono-mt -lboost_date_time-mt -lboost_atomic-mt -ldl -lboost_iostreams-mt -lboost_regex-mt cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/fhz && /usr/bin/cmake -E copy /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/fhz/fhz.so /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/lib64/chemkit/plugins/fhz.so make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 43%] Built target fhz make -f src/plugins/formula/CMakeFiles/formula.dir/build.make src/plugins/formula/CMakeFiles/formula.dir/depend make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/formula /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/formula /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/formula/CMakeFiles/formula.dir/DependInfo.cmake Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/formula/CMakeFiles/formula.dir/DependInfo.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/formula/CMakeFiles/formula.dir/depend.internal". Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/formula/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/formula/CMakeFiles/formula.dir/depend.internal". Scanning dependencies of target formula make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' make -f src/plugins/formula/CMakeFiles/formula.dir/build.make src/plugins/formula/CMakeFiles/formula.dir/build make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 43%] Building CXX object src/plugins/formula/CMakeFiles/formula.dir/formulalineformat.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/formula && /usr/bin/x86_64-pc-linux-gnu-g++ -Dformula_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/formula.dir/formulalineformat.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/formula/formulalineformat.cpp [ 44%] Building CXX object src/plugins/formula/CMakeFiles/formula.dir/formulaplugin.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/formula && /usr/bin/x86_64-pc-linux-gnu-g++ -Dformula_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/formula.dir/formulaplugin.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/formula/formulaplugin.cpp [ 44%] Building CXX object src/plugins/formula/CMakeFiles/formula.dir/htmlformulalineformat.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/formula && /usr/bin/x86_64-pc-linux-gnu-g++ -Dformula_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/formula.dir/htmlformulalineformat.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/formula/htmlformulalineformat.cpp [ 45%] Building CXX object src/plugins/formula/CMakeFiles/formula.dir/spacedformulalineformat.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/formula && /usr/bin/x86_64-pc-linux-gnu-g++ -Dformula_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/formula.dir/spacedformulalineformat.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/formula/spacedformulalineformat.cpp [ 45%] Linking CXX shared library formula.so cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/formula && /usr/bin/cmake -E cmake_link_script CMakeFiles/formula.dir/link.txt --verbose=1 /usr/bin/x86_64-pc-linux-gnu-g++ -fPIC -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -Wl,-O1 -Wl,--as-needed -shared -Wl,-soname,formula.so -o formula.so CMakeFiles/formula.dir/formulalineformat.cpp.o CMakeFiles/formula.dir/formulaplugin.cpp.o CMakeFiles/formula.dir/htmlformulalineformat.cpp.o CMakeFiles/formula.dir/spacedformulalineformat.cpp.o -Wl,-rpath,/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit: ../../chemkit/libchemkit.so -lboost_system-mt -lboost_filesystem-mt -lboost_thread-mt -lpthread -lboost_chrono-mt -lboost_date_time-mt -lboost_atomic-mt -ldl cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/formula && /usr/bin/cmake -E copy /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/formula/formula.so /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/lib64/chemkit/plugins/formula.so make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 45%] Built target formula make -f src/plugins/fp2/CMakeFiles/fp2.dir/build.make src/plugins/fp2/CMakeFiles/fp2.dir/depend make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/fp2 /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/fp2 /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/fp2/CMakeFiles/fp2.dir/DependInfo.cmake Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/fp2/CMakeFiles/fp2.dir/DependInfo.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/fp2/CMakeFiles/fp2.dir/depend.internal". Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/fp2/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/fp2/CMakeFiles/fp2.dir/depend.internal". Scanning dependencies of target fp2 make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' make -f src/plugins/fp2/CMakeFiles/fp2.dir/build.make src/plugins/fp2/CMakeFiles/fp2.dir/build make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 46%] Building CXX object src/plugins/fp2/CMakeFiles/fp2.dir/fp2fingerprint.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/fp2 && /usr/bin/x86_64-pc-linux-gnu-g++ -Dfp2_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/fp2.dir/fp2fingerprint.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/fp2/fp2fingerprint.cpp [ 46%] Building CXX object src/plugins/fp2/CMakeFiles/fp2.dir/fp2plugin.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/fp2 && /usr/bin/x86_64-pc-linux-gnu-g++ -Dfp2_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/fp2.dir/fp2plugin.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/fp2/fp2plugin.cpp [ 46%] Linking CXX shared library fp2.so cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/fp2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/fp2.dir/link.txt --verbose=1 /usr/bin/x86_64-pc-linux-gnu-g++ -fPIC -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -Wl,-O1 -Wl,--as-needed -shared -Wl,-soname,fp2.so -o fp2.so CMakeFiles/fp2.dir/fp2fingerprint.cpp.o CMakeFiles/fp2.dir/fp2plugin.cpp.o -Wl,-rpath,/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit: ../../chemkit/libchemkit.so -lboost_system-mt -lboost_filesystem-mt -lboost_thread-mt -lpthread -lboost_chrono-mt -lboost_date_time-mt -lboost_atomic-mt -ldl cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/fp2 && /usr/bin/cmake -E copy /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/fp2/fp2.so /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/lib64/chemkit/plugins/fp2.so make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 46%] Built target fp2 make -f src/plugins/fps/CMakeFiles/fps.dir/build.make src/plugins/fps/CMakeFiles/fps.dir/depend make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/fps /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/fps /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/fps/CMakeFiles/fps.dir/DependInfo.cmake Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/fps/CMakeFiles/fps.dir/DependInfo.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/fps/CMakeFiles/fps.dir/depend.internal". Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/fps/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/fps/CMakeFiles/fps.dir/depend.internal". Scanning dependencies of target fps make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' make -f src/plugins/fps/CMakeFiles/fps.dir/build.make src/plugins/fps/CMakeFiles/fps.dir/build make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 47%] Building CXX object src/plugins/fps/CMakeFiles/fps.dir/fpsfileformat.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/fps && /usr/bin/x86_64-pc-linux-gnu-g++ -Dfps_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/fps.dir/fpsfileformat.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/fps/fpsfileformat.cpp [ 47%] Building CXX object src/plugins/fps/CMakeFiles/fps.dir/fpsplugin.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/fps && /usr/bin/x86_64-pc-linux-gnu-g++ -Dfps_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/fps.dir/fpsplugin.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/fps/fpsplugin.cpp [ 48%] Linking CXX shared library fps.so cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/fps && /usr/bin/cmake -E cmake_link_script CMakeFiles/fps.dir/link.txt --verbose=1 /usr/bin/x86_64-pc-linux-gnu-g++ -fPIC -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -Wl,-O1 -Wl,--as-needed -shared -Wl,-soname,fps.so -o fps.so CMakeFiles/fps.dir/fpsfileformat.cpp.o CMakeFiles/fps.dir/fpsplugin.cpp.o -Wl,-rpath,/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/io:/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit: ../../io/libchemkit-io.so ../../chemkit/libchemkit.so -lboost_system-mt -lboost_filesystem-mt -lboost_thread-mt -lpthread -lboost_chrono-mt -lboost_date_time-mt -lboost_atomic-mt -ldl -lboost_iostreams-mt -lboost_regex-mt cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/fps && /usr/bin/cmake -E copy /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/fps/fps.so /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/lib64/chemkit/plugins/fps.so make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 48%] Built target fps make -f src/plugins/gasteiger/CMakeFiles/gasteiger.dir/build.make src/plugins/gasteiger/CMakeFiles/gasteiger.dir/depend make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/gasteiger /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/gasteiger /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/gasteiger/CMakeFiles/gasteiger.dir/DependInfo.cmake Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/gasteiger/CMakeFiles/gasteiger.dir/DependInfo.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/gasteiger/CMakeFiles/gasteiger.dir/depend.internal". Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/gasteiger/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/gasteiger/CMakeFiles/gasteiger.dir/depend.internal". Scanning dependencies of target gasteiger make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' make -f src/plugins/gasteiger/CMakeFiles/gasteiger.dir/build.make src/plugins/gasteiger/CMakeFiles/gasteiger.dir/build make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 48%] Building CXX object src/plugins/gasteiger/CMakeFiles/gasteiger.dir/gasteigerpartialchargemodel.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/gasteiger && /usr/bin/x86_64-pc-linux-gnu-g++ -Dgasteiger_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/gasteiger.dir/gasteigerpartialchargemodel.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/gasteiger/gasteigerpartialchargemodel.cpp [ 49%] Building CXX object src/plugins/gasteiger/CMakeFiles/gasteiger.dir/gasteigerplugin.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/gasteiger && /usr/bin/x86_64-pc-linux-gnu-g++ -Dgasteiger_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/gasteiger.dir/gasteigerplugin.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/gasteiger/gasteigerplugin.cpp [ 49%] Linking CXX shared library gasteiger.so cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/gasteiger && /usr/bin/cmake -E cmake_link_script CMakeFiles/gasteiger.dir/link.txt --verbose=1 /usr/bin/x86_64-pc-linux-gnu-g++ -fPIC -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -Wl,-O1 -Wl,--as-needed -shared -Wl,-soname,gasteiger.so -o gasteiger.so CMakeFiles/gasteiger.dir/gasteigerpartialchargemodel.cpp.o CMakeFiles/gasteiger.dir/gasteigerplugin.cpp.o -Wl,-rpath,/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit: ../../chemkit/libchemkit.so -lboost_system-mt -lboost_filesystem-mt -lboost_thread-mt -lpthread -lboost_chrono-mt -lboost_date_time-mt -lboost_atomic-mt -ldl cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/gasteiger && /usr/bin/cmake -E copy /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/gasteiger/gasteiger.so /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/lib64/chemkit/plugins/gasteiger.so make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 49%] Built target gasteiger make -f src/plugins/gaussian/CMakeFiles/gaussian.dir/build.make src/plugins/gaussian/CMakeFiles/gaussian.dir/depend make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/gaussian /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/gaussian /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/gaussian/CMakeFiles/gaussian.dir/DependInfo.cmake Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/gaussian/CMakeFiles/gaussian.dir/DependInfo.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/gaussian/CMakeFiles/gaussian.dir/depend.internal". Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/gaussian/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/gaussian/CMakeFiles/gaussian.dir/depend.internal". Scanning dependencies of target gaussian make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' make -f src/plugins/gaussian/CMakeFiles/gaussian.dir/build.make src/plugins/gaussian/CMakeFiles/gaussian.dir/build make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 50%] Building CXX object src/plugins/gaussian/CMakeFiles/gaussian.dir/cubefileformat.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/gaussian && /usr/bin/x86_64-pc-linux-gnu-g++ -Dgaussian_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/gaussian.dir/cubefileformat.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/gaussian/cubefileformat.cpp [ 50%] Building CXX object src/plugins/gaussian/CMakeFiles/gaussian.dir/gaussianplugin.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/gaussian && /usr/bin/x86_64-pc-linux-gnu-g++ -Dgaussian_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/gaussian.dir/gaussianplugin.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/gaussian/gaussianplugin.cpp [ 51%] Linking CXX shared library gaussian.so cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/gaussian && /usr/bin/cmake -E cmake_link_script CMakeFiles/gaussian.dir/link.txt --verbose=1 /usr/bin/x86_64-pc-linux-gnu-g++ -fPIC -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -Wl,-O1 -Wl,--as-needed -shared -Wl,-soname,gaussian.so -o gaussian.so CMakeFiles/gaussian.dir/cubefileformat.cpp.o CMakeFiles/gaussian.dir/gaussianplugin.cpp.o -Wl,-rpath,/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/io:/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit: ../../io/libchemkit-io.so ../../chemkit/libchemkit.so -lboost_system-mt -lboost_filesystem-mt -lboost_thread-mt -lpthread -lboost_chrono-mt -lboost_date_time-mt -lboost_atomic-mt -ldl -lboost_iostreams-mt -lboost_regex-mt cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/gaussian && /usr/bin/cmake -E copy /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/gaussian/gaussian.so /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/lib64/chemkit/plugins/gaussian.so make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 51%] Built target gaussian make -f src/plugins/graphdescriptors/CMakeFiles/graphdescriptors.dir/build.make src/plugins/graphdescriptors/CMakeFiles/graphdescriptors.dir/depend make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/graphdescriptors /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/graphdescriptors /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/graphdescriptors/CMakeFiles/graphdescriptors.dir/DependInfo.cmake Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/graphdescriptors/CMakeFiles/graphdescriptors.dir/DependInfo.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/graphdescriptors/CMakeFiles/graphdescriptors.dir/depend.internal". Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/graphdescriptors/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/graphdescriptors/CMakeFiles/graphdescriptors.dir/depend.internal". Scanning dependencies of target graphdescriptors make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' make -f src/plugins/graphdescriptors/CMakeFiles/graphdescriptors.dir/build.make src/plugins/graphdescriptors/CMakeFiles/graphdescriptors.dir/build make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 51%] Building CXX object src/plugins/graphdescriptors/CMakeFiles/graphdescriptors.dir/graphdescriptors.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/graphdescriptors && /usr/bin/x86_64-pc-linux-gnu-g++ -Dgraphdescriptors_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/graphdescriptors.dir/graphdescriptors.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/graphdescriptors/graphdescriptors.cpp [ 51%] Building CXX object src/plugins/graphdescriptors/CMakeFiles/graphdescriptors.dir/graphdescriptorsplugin.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/graphdescriptors && /usr/bin/x86_64-pc-linux-gnu-g++ -Dgraphdescriptors_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/graphdescriptors.dir/graphdescriptorsplugin.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/graphdescriptors/graphdescriptorsplugin.cpp [ 52%] Linking CXX shared library graphdescriptors.so cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/graphdescriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphdescriptors.dir/link.txt --verbose=1 /usr/bin/x86_64-pc-linux-gnu-g++ -fPIC -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -Wl,-O1 -Wl,--as-needed -shared -Wl,-soname,graphdescriptors.so -o graphdescriptors.so CMakeFiles/graphdescriptors.dir/graphdescriptors.cpp.o CMakeFiles/graphdescriptors.dir/graphdescriptorsplugin.cpp.o -Wl,-rpath,/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit: ../../chemkit/libchemkit.so -lboost_system-mt -lboost_filesystem-mt -lboost_thread-mt -lpthread -lboost_chrono-mt -lboost_date_time-mt -lboost_atomic-mt -ldl cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/graphdescriptors && /usr/bin/cmake -E copy /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/graphdescriptors/graphdescriptors.so /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/lib64/chemkit/plugins/graphdescriptors.so make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 52%] Built target graphdescriptors make -f src/plugins/gromacs/CMakeFiles/gromacs.dir/build.make src/plugins/gromacs/CMakeFiles/gromacs.dir/depend make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/gromacs /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/gromacs /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/gromacs/CMakeFiles/gromacs.dir/DependInfo.cmake Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/gromacs/CMakeFiles/gromacs.dir/DependInfo.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/gromacs/CMakeFiles/gromacs.dir/depend.internal". Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/gromacs/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/gromacs/CMakeFiles/gromacs.dir/depend.internal". Scanning dependencies of target gromacs make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' make -f src/plugins/gromacs/CMakeFiles/gromacs.dir/build.make src/plugins/gromacs/CMakeFiles/gromacs.dir/build make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 52%] Building CXX object src/plugins/gromacs/CMakeFiles/gromacs.dir/grofileformat.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/gromacs && /usr/bin/x86_64-pc-linux-gnu-g++ -Dgromacs_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/gromacs.dir/grofileformat.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/gromacs/grofileformat.cpp [ 53%] Building CXX object src/plugins/gromacs/CMakeFiles/gromacs.dir/gromacsplugin.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/gromacs && /usr/bin/x86_64-pc-linux-gnu-g++ -Dgromacs_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/gromacs.dir/gromacsplugin.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/gromacs/gromacsplugin.cpp [ 53%] Building CXX object src/plugins/gromacs/CMakeFiles/gromacs.dir/topfileformat.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/gromacs && /usr/bin/x86_64-pc-linux-gnu-g++ -Dgromacs_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/gromacs.dir/topfileformat.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/gromacs/topfileformat.cpp [ 54%] Linking CXX shared library gromacs.so cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/gromacs && /usr/bin/cmake -E cmake_link_script CMakeFiles/gromacs.dir/link.txt --verbose=1 /usr/bin/x86_64-pc-linux-gnu-g++ -fPIC -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -Wl,-O1 -Wl,--as-needed -shared -Wl,-soname,gromacs.so -o gromacs.so CMakeFiles/gromacs.dir/grofileformat.cpp.o CMakeFiles/gromacs.dir/gromacsplugin.cpp.o CMakeFiles/gromacs.dir/topfileformat.cpp.o -Wl,-rpath,/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/md-io:/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/io:/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/md:/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit: ../../md-io/libchemkit-md-io.so ../../io/libchemkit-io.so -lboost_iostreams-mt -lboost_regex-mt ../../md/libchemkit-md.so ../../chemkit/libchemkit.so -lboost_system-mt -lboost_filesystem-mt -lboost_thread-mt -lpthread -lboost_chrono-mt -lboost_date_time-mt -lboost_atomic-mt -ldl cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/gromacs && /usr/bin/cmake -E copy /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/gromacs/gromacs.so /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/lib64/chemkit/plugins/gromacs.so make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 54%] Built target gromacs make -f src/plugins/hydrogenbonds/CMakeFiles/hydrogenbonds.dir/build.make src/plugins/hydrogenbonds/CMakeFiles/hydrogenbonds.dir/depend make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/hydrogenbonds /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/hydrogenbonds /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/hydrogenbonds/CMakeFiles/hydrogenbonds.dir/DependInfo.cmake Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/hydrogenbonds/CMakeFiles/hydrogenbonds.dir/DependInfo.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/hydrogenbonds/CMakeFiles/hydrogenbonds.dir/depend.internal". Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/hydrogenbonds/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/hydrogenbonds/CMakeFiles/hydrogenbonds.dir/depend.internal". Scanning dependencies of target hydrogenbonds make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' make -f src/plugins/hydrogenbonds/CMakeFiles/hydrogenbonds.dir/build.make src/plugins/hydrogenbonds/CMakeFiles/hydrogenbonds.dir/build make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 54%] Building CXX object src/plugins/hydrogenbonds/CMakeFiles/hydrogenbonds.dir/hydrogenbondacceptorsdescriptor.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/hydrogenbonds && /usr/bin/x86_64-pc-linux-gnu-g++ -Dhydrogenbonds_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/hydrogenbonds.dir/hydrogenbondacceptorsdescriptor.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/hydrogenbonds/hydrogenbondacceptorsdescriptor.cpp [ 55%] Building CXX object src/plugins/hydrogenbonds/CMakeFiles/hydrogenbonds.dir/hydrogenbonddonorsdescriptor.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/hydrogenbonds && /usr/bin/x86_64-pc-linux-gnu-g++ -Dhydrogenbonds_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/hydrogenbonds.dir/hydrogenbonddonorsdescriptor.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/hydrogenbonds/hydrogenbonddonorsdescriptor.cpp [ 55%] Building CXX object src/plugins/hydrogenbonds/CMakeFiles/hydrogenbonds.dir/hydrogenbondsplugin.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/hydrogenbonds && /usr/bin/x86_64-pc-linux-gnu-g++ -Dhydrogenbonds_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/hydrogenbonds.dir/hydrogenbondsplugin.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/hydrogenbonds/hydrogenbondsplugin.cpp [ 56%] Linking CXX shared library hydrogenbonds.so cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/hydrogenbonds && /usr/bin/cmake -E cmake_link_script CMakeFiles/hydrogenbonds.dir/link.txt --verbose=1 /usr/bin/x86_64-pc-linux-gnu-g++ -fPIC -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -Wl,-O1 -Wl,--as-needed -shared -Wl,-soname,hydrogenbonds.so -o hydrogenbonds.so CMakeFiles/hydrogenbonds.dir/hydrogenbondacceptorsdescriptor.cpp.o CMakeFiles/hydrogenbonds.dir/hydrogenbonddonorsdescriptor.cpp.o CMakeFiles/hydrogenbonds.dir/hydrogenbondsplugin.cpp.o -Wl,-rpath,/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit: ../../chemkit/libchemkit.so -lboost_system-mt -lboost_filesystem-mt -lboost_thread-mt -lpthread -lboost_chrono-mt -lboost_date_time-mt -lboost_atomic-mt -ldl cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/hydrogenbonds && /usr/bin/cmake -E copy /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/hydrogenbonds/hydrogenbonds.so /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/lib64/chemkit/plugins/hydrogenbonds.so make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 56%] Built target hydrogenbonds make -f src/plugins/inchi/CMakeFiles/inchi.dir/build.make src/plugins/inchi/CMakeFiles/inchi.dir/depend make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/inchi /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/inchi /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/inchi/CMakeFiles/inchi.dir/DependInfo.cmake Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/inchi/CMakeFiles/inchi.dir/DependInfo.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/inchi/CMakeFiles/inchi.dir/depend.internal". Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/inchi/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/inchi/CMakeFiles/inchi.dir/depend.internal". Scanning dependencies of target inchi make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' make -f src/plugins/inchi/CMakeFiles/inchi.dir/build.make src/plugins/inchi/CMakeFiles/inchi.dir/build make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 56%] Building CXX object src/plugins/inchi/CMakeFiles/inchi.dir/inchikeylineformat.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/inchi && /usr/bin/x86_64-pc-linux-gnu-g++ -Dinchi_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/inchi.dir/inchikeylineformat.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/inchi/inchikeylineformat.cpp [ 57%] Building CXX object src/plugins/inchi/CMakeFiles/inchi.dir/inchilineformat.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/inchi && /usr/bin/x86_64-pc-linux-gnu-g++ -Dinchi_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/inchi.dir/inchilineformat.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/inchi/inchilineformat.cpp [ 57%] Building CXX object src/plugins/inchi/CMakeFiles/inchi.dir/inchiplugin.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/inchi && /usr/bin/x86_64-pc-linux-gnu-g++ -Dinchi_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/inchi.dir/inchiplugin.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/inchi/inchiplugin.cpp [ 57%] Linking CXX shared library inchi.so cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/inchi && /usr/bin/cmake -E cmake_link_script CMakeFiles/inchi.dir/link.txt --verbose=1 /usr/bin/x86_64-pc-linux-gnu-g++ -fPIC -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -Wl,-O1 -Wl,--as-needed -shared -Wl,-soname,inchi.so -o inchi.so CMakeFiles/inchi.dir/inchikeylineformat.cpp.o CMakeFiles/inchi.dir/inchilineformat.cpp.o CMakeFiles/inchi.dir/inchiplugin.cpp.o -Wl,-rpath,/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/io:/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit: ../../io/libchemkit-io.so ../../chemkit/libchemkit.so -lboost_system-mt -lboost_filesystem-mt -lboost_thread-mt -lpthread -lboost_chrono-mt -lboost_date_time-mt -lboost_atomic-mt -ldl -lboost_iostreams-mt -lboost_regex-mt cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/inchi && /usr/bin/cmake -E copy /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/inchi/inchi.so /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/lib64/chemkit/plugins/inchi.so make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 57%] Built target inchi make -f src/plugins/mannhold/CMakeFiles/mannhold.dir/build.make src/plugins/mannhold/CMakeFiles/mannhold.dir/depend make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/mannhold /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/mannhold /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/mannhold/CMakeFiles/mannhold.dir/DependInfo.cmake Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/mannhold/CMakeFiles/mannhold.dir/DependInfo.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/mannhold/CMakeFiles/mannhold.dir/depend.internal". Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/mannhold/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/mannhold/CMakeFiles/mannhold.dir/depend.internal". Scanning dependencies of target mannhold make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' make -f src/plugins/mannhold/CMakeFiles/mannhold.dir/build.make src/plugins/mannhold/CMakeFiles/mannhold.dir/build make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 58%] Building CXX object src/plugins/mannhold/CMakeFiles/mannhold.dir/mannholdlogpdescriptor.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/mannhold && /usr/bin/x86_64-pc-linux-gnu-g++ -Dmannhold_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/mannhold.dir/mannholdlogpdescriptor.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/mannhold/mannholdlogpdescriptor.cpp [ 58%] Building CXX object src/plugins/mannhold/CMakeFiles/mannhold.dir/mannholdplugin.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/mannhold && /usr/bin/x86_64-pc-linux-gnu-g++ -Dmannhold_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/mannhold.dir/mannholdplugin.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/mannhold/mannholdplugin.cpp [ 59%] Linking CXX shared library mannhold.so cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/mannhold && /usr/bin/cmake -E cmake_link_script CMakeFiles/mannhold.dir/link.txt --verbose=1 /usr/bin/x86_64-pc-linux-gnu-g++ -fPIC -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -Wl,-O1 -Wl,--as-needed -shared -Wl,-soname,mannhold.so -o mannhold.so CMakeFiles/mannhold.dir/mannholdlogpdescriptor.cpp.o CMakeFiles/mannhold.dir/mannholdplugin.cpp.o -Wl,-rpath,/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit: ../../chemkit/libchemkit.so -lboost_system-mt -lboost_filesystem-mt -lboost_thread-mt -lpthread -lboost_chrono-mt -lboost_date_time-mt -lboost_atomic-mt -ldl cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/mannhold && /usr/bin/cmake -E copy /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/mannhold/mannhold.so /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/lib64/chemkit/plugins/mannhold.so make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 59%] Built target mannhold make -f src/plugins/massdescriptors/CMakeFiles/massdescriptors.dir/build.make src/plugins/massdescriptors/CMakeFiles/massdescriptors.dir/depend make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/massdescriptors /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/massdescriptors /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/massdescriptors/CMakeFiles/massdescriptors.dir/DependInfo.cmake Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/massdescriptors/CMakeFiles/massdescriptors.dir/DependInfo.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/massdescriptors/CMakeFiles/massdescriptors.dir/depend.internal". Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/massdescriptors/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/massdescriptors/CMakeFiles/massdescriptors.dir/depend.internal". Scanning dependencies of target massdescriptors make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' make -f src/plugins/massdescriptors/CMakeFiles/massdescriptors.dir/build.make src/plugins/massdescriptors/CMakeFiles/massdescriptors.dir/build make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 59%] Building CXX object src/plugins/massdescriptors/CMakeFiles/massdescriptors.dir/massdescriptors.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/massdescriptors && /usr/bin/x86_64-pc-linux-gnu-g++ -Dmassdescriptors_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/massdescriptors.dir/massdescriptors.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/massdescriptors/massdescriptors.cpp [ 60%] Building CXX object src/plugins/massdescriptors/CMakeFiles/massdescriptors.dir/massdescriptorsplugin.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/massdescriptors && /usr/bin/x86_64-pc-linux-gnu-g++ -Dmassdescriptors_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/massdescriptors.dir/massdescriptorsplugin.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/massdescriptors/massdescriptorsplugin.cpp [ 60%] Linking CXX shared library massdescriptors.so cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/massdescriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/massdescriptors.dir/link.txt --verbose=1 /usr/bin/x86_64-pc-linux-gnu-g++ -fPIC -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -Wl,-O1 -Wl,--as-needed -shared -Wl,-soname,massdescriptors.so -o massdescriptors.so CMakeFiles/massdescriptors.dir/massdescriptors.cpp.o CMakeFiles/massdescriptors.dir/massdescriptorsplugin.cpp.o -Wl,-rpath,/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit: ../../chemkit/libchemkit.so -lboost_system-mt -lboost_filesystem-mt -lboost_thread-mt -lpthread -lboost_chrono-mt -lboost_date_time-mt -lboost_atomic-mt -ldl cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/massdescriptors && /usr/bin/cmake -E copy /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/massdescriptors/massdescriptors.so /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/lib64/chemkit/plugins/massdescriptors.so make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 60%] Built target massdescriptors make -f src/plugins/mcdl/CMakeFiles/mcdl.dir/build.make src/plugins/mcdl/CMakeFiles/mcdl.dir/depend make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/mcdl /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/mcdl /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/mcdl/CMakeFiles/mcdl.dir/DependInfo.cmake Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/mcdl/CMakeFiles/mcdl.dir/DependInfo.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/mcdl/CMakeFiles/mcdl.dir/depend.internal". Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/mcdl/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/mcdl/CMakeFiles/mcdl.dir/depend.internal". Scanning dependencies of target mcdl make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' make -f src/plugins/mcdl/CMakeFiles/mcdl.dir/build.make src/plugins/mcdl/CMakeFiles/mcdl.dir/build make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 61%] Building CXX object src/plugins/mcdl/CMakeFiles/mcdl.dir/mcdllineformat.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/mcdl && /usr/bin/x86_64-pc-linux-gnu-g++ -Dmcdl_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/mcdl.dir/mcdllineformat.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/mcdl/mcdllineformat.cpp [ 61%] Building CXX object src/plugins/mcdl/CMakeFiles/mcdl.dir/mcdlplugin.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/mcdl && /usr/bin/x86_64-pc-linux-gnu-g++ -Dmcdl_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/mcdl.dir/mcdlplugin.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/mcdl/mcdlplugin.cpp [ 62%] Building CXX object src/plugins/mcdl/CMakeFiles/mcdl.dir/mcdlreader.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/mcdl && /usr/bin/x86_64-pc-linux-gnu-g++ -Dmcdl_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/mcdl.dir/mcdlreader.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/mcdl/mcdlreader.cpp [ 62%] Linking CXX shared library mcdl.so cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/mcdl && /usr/bin/cmake -E cmake_link_script CMakeFiles/mcdl.dir/link.txt --verbose=1 /usr/bin/x86_64-pc-linux-gnu-g++ -fPIC -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -Wl,-O1 -Wl,--as-needed -shared -Wl,-soname,mcdl.so -o mcdl.so CMakeFiles/mcdl.dir/mcdllineformat.cpp.o CMakeFiles/mcdl.dir/mcdlplugin.cpp.o CMakeFiles/mcdl.dir/mcdlreader.cpp.o -Wl,-rpath,/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit: ../../chemkit/libchemkit.so -lboost_system-mt -lboost_filesystem-mt -lboost_thread-mt -lpthread -lboost_chrono-mt -lboost_date_time-mt -lboost_atomic-mt -ldl cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/mcdl && /usr/bin/cmake -E copy /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/mcdl/mcdl.so /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/lib64/chemkit/plugins/mcdl.so make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 62%] Built target mcdl make -f src/plugins/mdl/CMakeFiles/mdl.dir/build.make src/plugins/mdl/CMakeFiles/mdl.dir/depend make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/mdl /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/mdl /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/mdl/CMakeFiles/mdl.dir/DependInfo.cmake Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/mdl/CMakeFiles/mdl.dir/DependInfo.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/mdl/CMakeFiles/mdl.dir/depend.internal". Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/mdl/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/mdl/CMakeFiles/mdl.dir/depend.internal". Scanning dependencies of target mdl make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' make -f src/plugins/mdl/CMakeFiles/mdl.dir/build.make src/plugins/mdl/CMakeFiles/mdl.dir/build make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 63%] Building CXX object src/plugins/mdl/CMakeFiles/mdl.dir/mdlfileformat.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/mdl && /usr/bin/x86_64-pc-linux-gnu-g++ -Dmdl_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/mdl.dir/mdlfileformat.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/mdl/mdlfileformat.cpp /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/mdl/mdlfileformat.cpp: In member function ‘void MdlFileFormat::writeBondBlock(const chemkit::Molecule*, std::ostream&)’: /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/mdl/mdlfileformat.cpp:337:30: warning: ‘%3d’ directive writing 3 bytes into a region of size between 1 and 17 [-Wformat-overflow=] 337 | sprintf(line, "%3d%3d%3d 0 0 0 0\n", static_cast(bond->atom1()->index()) + 1, | ^~~ /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/mdl/mdlfileformat.cpp:337:23: note: directive argument in the range [0, 255] 337 | sprintf(line, "%3d%3d%3d 0 0 0 0\n", static_cast(bond->atom1()->index()) + 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from /usr/lib/gcc/x86_64-pc-linux-gnu/9.1.0/include/g++-v9/cstdio:42, from /usr/lib/gcc/x86_64-pc-linux-gnu/9.1.0/include/g++-v9/ext/string_conversions.h:43, from /usr/lib/gcc/x86_64-pc-linux-gnu/9.1.0/include/g++-v9/bits/basic_string.h:6493, from /usr/lib/gcc/x86_64-pc-linux-gnu/9.1.0/include/g++-v9/string:55, from /usr/lib/gcc/x86_64-pc-linux-gnu/9.1.0/include/g++-v9/stdexcept:39, from /usr/lib/gcc/x86_64-pc-linux-gnu/9.1.0/include/g++-v9/array:39, from /usr/lib/gcc/x86_64-pc-linux-gnu/9.1.0/include/g++-v9/tuple:39, from /usr/lib/gcc/x86_64-pc-linux-gnu/9.1.0/include/g++-v9/bits/stl_map.h:63, from /usr/lib/gcc/x86_64-pc-linux-gnu/9.1.0/include/g++-v9/map:61, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include/chemkit/../../src/chemkit/molecule.h:41, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include/chemkit/molecule.h:1, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/mdl/mdlfileformat.h:39, from /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/mdl/mdlfileformat.cpp:41: /usr/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 23 and 39 bytes into a destination of size 23 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 63%] Building CXX object src/plugins/mdl/CMakeFiles/mdl.dir/mdlplugin.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/mdl && /usr/bin/x86_64-pc-linux-gnu-g++ -Dmdl_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/mdl.dir/mdlplugin.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/mdl/mdlplugin.cpp [ 63%] Linking CXX shared library mdl.so cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/mdl && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdl.dir/link.txt --verbose=1 /usr/bin/x86_64-pc-linux-gnu-g++ -fPIC -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -Wl,-O1 -Wl,--as-needed -shared -Wl,-soname,mdl.so -o mdl.so CMakeFiles/mdl.dir/mdlfileformat.cpp.o CMakeFiles/mdl.dir/mdlplugin.cpp.o -Wl,-rpath,/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/io:/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit: ../../io/libchemkit-io.so ../../chemkit/libchemkit.so -lboost_system-mt -lboost_filesystem-mt -lboost_thread-mt -lpthread -lboost_chrono-mt -lboost_date_time-mt -lboost_atomic-mt -ldl -lboost_iostreams-mt -lboost_regex-mt cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/mdl && /usr/bin/cmake -E copy /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/mdl/mdl.so /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/lib64/chemkit/plugins/mdl.so make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 63%] Built target mdl make -f src/plugins/mmff/CMakeFiles/mmff.dir/build.make src/plugins/mmff/CMakeFiles/mmff.dir/depend make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/mmff /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/mmff /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/mmff/CMakeFiles/mmff.dir/DependInfo.cmake Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/mmff/CMakeFiles/mmff.dir/DependInfo.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/mmff/CMakeFiles/mmff.dir/depend.internal". Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/mmff/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/mmff/CMakeFiles/mmff.dir/depend.internal". Scanning dependencies of target mmff make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' make -f src/plugins/mmff/CMakeFiles/mmff.dir/build.make src/plugins/mmff/CMakeFiles/mmff.dir/build make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 64%] Building CXX object src/plugins/mmff/CMakeFiles/mmff.dir/mmffaromaticitymodel.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/mmff && /usr/bin/x86_64-pc-linux-gnu-g++ -Dmmff_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/mmff.dir/mmffaromaticitymodel.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/mmff/mmffaromaticitymodel.cpp [ 64%] Building CXX object src/plugins/mmff/CMakeFiles/mmff.dir/mmffatomtyper.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/mmff && /usr/bin/x86_64-pc-linux-gnu-g++ -Dmmff_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/mmff.dir/mmffatomtyper.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/mmff/mmffatomtyper.cpp [ 65%] Building CXX object src/plugins/mmff/CMakeFiles/mmff.dir/mmffcalculation.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/mmff && /usr/bin/x86_64-pc-linux-gnu-g++ -Dmmff_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/mmff.dir/mmffcalculation.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/mmff/mmffcalculation.cpp [ 65%] Building CXX object src/plugins/mmff/CMakeFiles/mmff.dir/mmffforcefield.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/mmff && /usr/bin/x86_64-pc-linux-gnu-g++ -Dmmff_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/mmff.dir/mmffforcefield.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/mmff/mmffforcefield.cpp [ 66%] Building CXX object src/plugins/mmff/CMakeFiles/mmff.dir/mmffparameters.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/mmff && /usr/bin/x86_64-pc-linux-gnu-g++ -Dmmff_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/mmff.dir/mmffparameters.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/mmff/mmffparameters.cpp [ 66%] Building CXX object src/plugins/mmff/CMakeFiles/mmff.dir/mmffparametersdata.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/mmff && /usr/bin/x86_64-pc-linux-gnu-g++ -Dmmff_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/mmff.dir/mmffparametersdata.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/mmff/mmffparametersdata.cpp [ 67%] Building CXX object src/plugins/mmff/CMakeFiles/mmff.dir/mmffpartialchargemodel.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/mmff && /usr/bin/x86_64-pc-linux-gnu-g++ -Dmmff_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/mmff.dir/mmffpartialchargemodel.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/mmff/mmffpartialchargemodel.cpp [ 67%] Building CXX object src/plugins/mmff/CMakeFiles/mmff.dir/mmffplugin.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/mmff && /usr/bin/x86_64-pc-linux-gnu-g++ -Dmmff_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/mmff.dir/mmffplugin.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/mmff/mmffplugin.cpp [ 68%] Linking CXX shared library mmff.so cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/mmff && /usr/bin/cmake -E cmake_link_script CMakeFiles/mmff.dir/link.txt --verbose=1 /usr/bin/x86_64-pc-linux-gnu-g++ -fPIC -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -Wl,-O1 -Wl,--as-needed -shared -Wl,-soname,mmff.so -o mmff.so CMakeFiles/mmff.dir/mmffaromaticitymodel.cpp.o CMakeFiles/mmff.dir/mmffatomtyper.cpp.o CMakeFiles/mmff.dir/mmffcalculation.cpp.o CMakeFiles/mmff.dir/mmffforcefield.cpp.o CMakeFiles/mmff.dir/mmffparameters.cpp.o CMakeFiles/mmff.dir/mmffparametersdata.cpp.o CMakeFiles/mmff.dir/mmffpartialchargemodel.cpp.o CMakeFiles/mmff.dir/mmffplugin.cpp.o -Wl,-rpath,/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/md:/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit: ../../md/libchemkit-md.so ../../chemkit/libchemkit.so -lboost_system-mt -lboost_filesystem-mt -lboost_thread-mt -lpthread -lboost_chrono-mt -lboost_date_time-mt -lboost_atomic-mt -ldl cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/mmff && /usr/bin/cmake -E copy /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/mmff/mmff.so /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/lib64/chemkit/plugins/mmff.so make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 68%] Built target mmff make -f src/plugins/mopac/CMakeFiles/mopac.dir/build.make src/plugins/mopac/CMakeFiles/mopac.dir/depend make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/mopac /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/mopac /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/mopac/CMakeFiles/mopac.dir/DependInfo.cmake Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/mopac/CMakeFiles/mopac.dir/DependInfo.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/mopac/CMakeFiles/mopac.dir/depend.internal". Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/mopac/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/mopac/CMakeFiles/mopac.dir/depend.internal". Scanning dependencies of target mopac make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' make -f src/plugins/mopac/CMakeFiles/mopac.dir/build.make src/plugins/mopac/CMakeFiles/mopac.dir/build make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 68%] Building CXX object src/plugins/mopac/CMakeFiles/mopac.dir/mopacplugin.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/mopac && /usr/bin/x86_64-pc-linux-gnu-g++ -Dmopac_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/mopac.dir/mopacplugin.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/mopac/mopacplugin.cpp [ 69%] Building CXX object src/plugins/mopac/CMakeFiles/mopac.dir/mopcrtfileformat.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/mopac && /usr/bin/x86_64-pc-linux-gnu-g++ -Dmopac_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/mopac.dir/mopcrtfileformat.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/mopac/mopcrtfileformat.cpp [ 69%] Building CXX object src/plugins/mopac/CMakeFiles/mopac.dir/mopinfileformat.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/mopac && /usr/bin/x86_64-pc-linux-gnu-g++ -Dmopac_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/mopac.dir/mopinfileformat.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/mopac/mopinfileformat.cpp [ 69%] Linking CXX shared library mopac.so cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/mopac && /usr/bin/cmake -E cmake_link_script CMakeFiles/mopac.dir/link.txt --verbose=1 /usr/bin/x86_64-pc-linux-gnu-g++ -fPIC -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -Wl,-O1 -Wl,--as-needed -shared -Wl,-soname,mopac.so -o mopac.so CMakeFiles/mopac.dir/mopacplugin.cpp.o CMakeFiles/mopac.dir/mopcrtfileformat.cpp.o CMakeFiles/mopac.dir/mopinfileformat.cpp.o -Wl,-rpath,/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/io:/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit: ../../io/libchemkit-io.so ../../chemkit/libchemkit.so -lboost_system-mt -lboost_filesystem-mt -lboost_thread-mt -lpthread -lboost_chrono-mt -lboost_date_time-mt -lboost_atomic-mt -ldl -lboost_iostreams-mt -lboost_regex-mt cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/mopac && /usr/bin/cmake -E copy /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/mopac/mopac.so /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/lib64/chemkit/plugins/mopac.so make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 69%] Built target mopac make -f src/plugins/moriguchi/CMakeFiles/moriguchi.dir/build.make src/plugins/moriguchi/CMakeFiles/moriguchi.dir/depend make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/moriguchi /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/moriguchi /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/moriguchi/CMakeFiles/moriguchi.dir/DependInfo.cmake Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/moriguchi/CMakeFiles/moriguchi.dir/DependInfo.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/moriguchi/CMakeFiles/moriguchi.dir/depend.internal". Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/moriguchi/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/moriguchi/CMakeFiles/moriguchi.dir/depend.internal". Scanning dependencies of target moriguchi make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' make -f src/plugins/moriguchi/CMakeFiles/moriguchi.dir/build.make src/plugins/moriguchi/CMakeFiles/moriguchi.dir/build make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 70%] Building CXX object src/plugins/moriguchi/CMakeFiles/moriguchi.dir/moriguchilogpdescriptor.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/moriguchi && /usr/bin/x86_64-pc-linux-gnu-g++ -Dmoriguchi_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/moriguchi.dir/moriguchilogpdescriptor.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/moriguchi/moriguchilogpdescriptor.cpp [ 70%] Building CXX object src/plugins/moriguchi/CMakeFiles/moriguchi.dir/moriguchiplugin.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/moriguchi && /usr/bin/x86_64-pc-linux-gnu-g++ -Dmoriguchi_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/moriguchi.dir/moriguchiplugin.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/moriguchi/moriguchiplugin.cpp [ 71%] Linking CXX shared library moriguchi.so cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/moriguchi && /usr/bin/cmake -E cmake_link_script CMakeFiles/moriguchi.dir/link.txt --verbose=1 /usr/bin/x86_64-pc-linux-gnu-g++ -fPIC -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -Wl,-O1 -Wl,--as-needed -shared -Wl,-soname,moriguchi.so -o moriguchi.so CMakeFiles/moriguchi.dir/moriguchilogpdescriptor.cpp.o CMakeFiles/moriguchi.dir/moriguchiplugin.cpp.o -Wl,-rpath,/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit: ../../chemkit/libchemkit.so -lboost_system-mt -lboost_filesystem-mt -lboost_thread-mt -lpthread -lboost_chrono-mt -lboost_date_time-mt -lboost_atomic-mt -ldl cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/moriguchi && /usr/bin/cmake -E copy /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/moriguchi/moriguchi.so /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/lib64/chemkit/plugins/moriguchi.so make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 71%] Built target moriguchi make -f src/plugins/opls/CMakeFiles/opls.dir/build.make src/plugins/opls/CMakeFiles/opls.dir/depend make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/opls /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/opls /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/opls/CMakeFiles/opls.dir/DependInfo.cmake Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/opls/CMakeFiles/opls.dir/DependInfo.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/opls/CMakeFiles/opls.dir/depend.internal". Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/opls/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/opls/CMakeFiles/opls.dir/depend.internal". Scanning dependencies of target opls make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' make -f src/plugins/opls/CMakeFiles/opls.dir/build.make src/plugins/opls/CMakeFiles/opls.dir/build make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 71%] Building CXX object src/plugins/opls/CMakeFiles/opls.dir/oplsatomtyper.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/opls && /usr/bin/x86_64-pc-linux-gnu-g++ -Dopls_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/opls.dir/oplsatomtyper.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/opls/oplsatomtyper.cpp [ 72%] Building CXX object src/plugins/opls/CMakeFiles/opls.dir/oplscalculation.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/opls && /usr/bin/x86_64-pc-linux-gnu-g++ -Dopls_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/opls.dir/oplscalculation.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/opls/oplscalculation.cpp [ 72%] Building CXX object src/plugins/opls/CMakeFiles/opls.dir/oplsforcefield.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/opls && /usr/bin/x86_64-pc-linux-gnu-g++ -Dopls_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/opls.dir/oplsforcefield.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/opls/oplsforcefield.cpp [ 73%] Building CXX object src/plugins/opls/CMakeFiles/opls.dir/oplsparameters.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/opls && /usr/bin/x86_64-pc-linux-gnu-g++ -Dopls_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/opls.dir/oplsparameters.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/opls/oplsparameters.cpp [ 73%] Building CXX object src/plugins/opls/CMakeFiles/opls.dir/oplsplugin.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/opls && /usr/bin/x86_64-pc-linux-gnu-g++ -Dopls_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/opls.dir/oplsplugin.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/opls/oplsplugin.cpp [ 74%] Linking CXX shared library opls.so cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/opls && /usr/bin/cmake -E cmake_link_script CMakeFiles/opls.dir/link.txt --verbose=1 /usr/bin/x86_64-pc-linux-gnu-g++ -fPIC -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -Wl,-O1 -Wl,--as-needed -shared -Wl,-soname,opls.so -o opls.so CMakeFiles/opls.dir/oplsatomtyper.cpp.o CMakeFiles/opls.dir/oplscalculation.cpp.o CMakeFiles/opls.dir/oplsforcefield.cpp.o CMakeFiles/opls.dir/oplsparameters.cpp.o CMakeFiles/opls.dir/oplsplugin.cpp.o -Wl,-rpath,/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/md:/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit: ../../md/libchemkit-md.so ../../chemkit/libchemkit.so -lboost_system-mt -lboost_filesystem-mt -lboost_thread-mt -lpthread -lboost_chrono-mt -lboost_date_time-mt -lboost_atomic-mt -ldl cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/opls && /usr/bin/cmake -E copy /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/opls/opls.so /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/lib64/chemkit/plugins/opls.so make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 74%] Built target opls make -f src/plugins/pdb/CMakeFiles/pdb.dir/build.make src/plugins/pdb/CMakeFiles/pdb.dir/depend make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/pdb /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/pdb /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/pdb/CMakeFiles/pdb.dir/DependInfo.cmake Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/pdb/CMakeFiles/pdb.dir/DependInfo.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/pdb/CMakeFiles/pdb.dir/depend.internal". Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/pdb/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/pdb/CMakeFiles/pdb.dir/depend.internal". Scanning dependencies of target pdb make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' make -f src/plugins/pdb/CMakeFiles/pdb.dir/build.make src/plugins/pdb/CMakeFiles/pdb.dir/build make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 74%] Building CXX object src/plugins/pdb/CMakeFiles/pdb.dir/pdbfileformat.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/pdb && /usr/bin/x86_64-pc-linux-gnu-g++ -Dpdb_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/pdb.dir/pdbfileformat.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/pdb/pdbfileformat.cpp /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/pdb/pdbfileformat.cpp:328:1: warning: ‘{anonymous}::PdbLigand::~PdbLigand()’ defined but not used [-Wunused-function] 328 | PdbLigand::~PdbLigand() | ^~~~~~~~~ /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/pdb/pdbfileformat.cpp:196:13: warning: ‘std::string {anonymous}::PdbChain::name() const’ defined but not used [-Wunused-function] 196 | std::string PdbChain::name() const | ^~~~~~~~ /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/pdb/pdbfileformat.cpp: In member function ‘void {anonymous}::PdbFile::writePolymerFile(chemkit::PolymerFile*)’: /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/pdb/pdbfileformat.cpp:571:22: warning: ‘symbol’ may be used uninitialized in this function [-Wmaybe-uninitialized] 571 | else if(symbol == 'U'){ | ^~ [ 75%] Building CXX object src/plugins/pdb/CMakeFiles/pdb.dir/pdbmlfileformat.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/pdb && /usr/bin/x86_64-pc-linux-gnu-g++ -Dpdb_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/pdb.dir/pdbmlfileformat.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/pdb/pdbmlfileformat.cpp [ 75%] Building CXX object src/plugins/pdb/CMakeFiles/pdb.dir/pdbplugin.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/pdb && /usr/bin/x86_64-pc-linux-gnu-g++ -Dpdb_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/pdb.dir/pdbplugin.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/pdb/pdbplugin.cpp [ 75%] Linking CXX shared library pdb.so cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/pdb && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb.dir/link.txt --verbose=1 /usr/bin/x86_64-pc-linux-gnu-g++ -fPIC -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -Wl,-O1 -Wl,--as-needed -shared -Wl,-soname,pdb.so -o pdb.so CMakeFiles/pdb.dir/pdbfileformat.cpp.o CMakeFiles/pdb.dir/pdbmlfileformat.cpp.o CMakeFiles/pdb.dir/pdbplugin.cpp.o -Wl,-rpath,/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/io:/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit: ../../io/libchemkit-io.so ../../chemkit/libchemkit.so -lboost_system-mt -lboost_filesystem-mt -lboost_thread-mt -lpthread -lboost_chrono-mt -lboost_date_time-mt -lboost_atomic-mt -ldl -lboost_iostreams-mt -lboost_regex-mt cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/pdb && /usr/bin/cmake -E copy /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/pdb/pdb.so /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/lib64/chemkit/plugins/pdb.so make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 75%] Built target pdb make -f src/plugins/pqr/CMakeFiles/pqr.dir/build.make src/plugins/pqr/CMakeFiles/pqr.dir/depend make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/pqr /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/pqr /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/pqr/CMakeFiles/pqr.dir/DependInfo.cmake Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/pqr/CMakeFiles/pqr.dir/DependInfo.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/pqr/CMakeFiles/pqr.dir/depend.internal". Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/pqr/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/pqr/CMakeFiles/pqr.dir/depend.internal". Scanning dependencies of target pqr make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' make -f src/plugins/pqr/CMakeFiles/pqr.dir/build.make src/plugins/pqr/CMakeFiles/pqr.dir/build make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 76%] Building CXX object src/plugins/pqr/CMakeFiles/pqr.dir/pqrfileformat.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/pqr && /usr/bin/x86_64-pc-linux-gnu-g++ -Dpqr_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/pqr.dir/pqrfileformat.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/pqr/pqrfileformat.cpp [ 76%] Building CXX object src/plugins/pqr/CMakeFiles/pqr.dir/pqrplugin.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/pqr && /usr/bin/x86_64-pc-linux-gnu-g++ -Dpqr_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/pqr.dir/pqrplugin.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/pqr/pqrplugin.cpp [ 77%] Linking CXX shared library pqr.so cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/pqr && /usr/bin/cmake -E cmake_link_script CMakeFiles/pqr.dir/link.txt --verbose=1 /usr/bin/x86_64-pc-linux-gnu-g++ -fPIC -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -Wl,-O1 -Wl,--as-needed -shared -Wl,-soname,pqr.so -o pqr.so CMakeFiles/pqr.dir/pqrfileformat.cpp.o CMakeFiles/pqr.dir/pqrplugin.cpp.o -Wl,-rpath,/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/io:/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit: ../../io/libchemkit-io.so ../../chemkit/libchemkit.so -lboost_system-mt -lboost_filesystem-mt -lboost_thread-mt -lpthread -lboost_chrono-mt -lboost_date_time-mt -lboost_atomic-mt -ldl -lboost_iostreams-mt -lboost_regex-mt cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/pqr && /usr/bin/cmake -E copy /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/pqr/pqr.so /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/lib64/chemkit/plugins/pqr.so make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 77%] Built target pqr make -f src/plugins/pubchem/CMakeFiles/pubchem.dir/build.make src/plugins/pubchem/CMakeFiles/pubchem.dir/depend make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/pubchem /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/pubchem /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/pubchem/CMakeFiles/pubchem.dir/DependInfo.cmake Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/pubchem/CMakeFiles/pubchem.dir/DependInfo.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/pubchem/CMakeFiles/pubchem.dir/depend.internal". Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/pubchem/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/pubchem/CMakeFiles/pubchem.dir/depend.internal". Scanning dependencies of target pubchem make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' make -f src/plugins/pubchem/CMakeFiles/pubchem.dir/build.make src/plugins/pubchem/CMakeFiles/pubchem.dir/build make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 77%] Building CXX object src/plugins/pubchem/CMakeFiles/pubchem.dir/pubchemfingerprint.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/pubchem && /usr/bin/x86_64-pc-linux-gnu-g++ -Dpubchem_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/pubchem.dir/pubchemfingerprint.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/pubchem/pubchemfingerprint.cpp [ 78%] Building CXX object src/plugins/pubchem/CMakeFiles/pubchem.dir/pubchemplugin.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/pubchem && /usr/bin/x86_64-pc-linux-gnu-g++ -Dpubchem_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/pubchem.dir/pubchemplugin.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/pubchem/pubchemplugin.cpp [ 78%] Linking CXX shared library pubchem.so cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/pubchem && /usr/bin/cmake -E cmake_link_script CMakeFiles/pubchem.dir/link.txt --verbose=1 /usr/bin/x86_64-pc-linux-gnu-g++ -fPIC -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -Wl,-O1 -Wl,--as-needed -shared -Wl,-soname,pubchem.so -o pubchem.so CMakeFiles/pubchem.dir/pubchemfingerprint.cpp.o CMakeFiles/pubchem.dir/pubchemplugin.cpp.o -Wl,-rpath,/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit: ../../chemkit/libchemkit.so -lboost_system-mt -lboost_filesystem-mt -lboost_thread-mt -lpthread -lboost_chrono-mt -lboost_date_time-mt -lboost_atomic-mt -ldl cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/pubchem && /usr/bin/cmake -E copy /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/pubchem/pubchem.so /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/lib64/chemkit/plugins/pubchem.so make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 78%] Built target pubchem make -f src/plugins/randicindex/CMakeFiles/randicindex.dir/build.make src/plugins/randicindex/CMakeFiles/randicindex.dir/depend make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/randicindex /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/randicindex /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/randicindex/CMakeFiles/randicindex.dir/DependInfo.cmake Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/randicindex/CMakeFiles/randicindex.dir/DependInfo.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/randicindex/CMakeFiles/randicindex.dir/depend.internal". Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/randicindex/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/randicindex/CMakeFiles/randicindex.dir/depend.internal". Scanning dependencies of target randicindex make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' make -f src/plugins/randicindex/CMakeFiles/randicindex.dir/build.make src/plugins/randicindex/CMakeFiles/randicindex.dir/build make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 79%] Building CXX object src/plugins/randicindex/CMakeFiles/randicindex.dir/randicindexdescriptor.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/randicindex && /usr/bin/x86_64-pc-linux-gnu-g++ -Drandicindex_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/randicindex.dir/randicindexdescriptor.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/randicindex/randicindexdescriptor.cpp [ 79%] Building CXX object src/plugins/randicindex/CMakeFiles/randicindex.dir/randicindexplugin.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/randicindex && /usr/bin/x86_64-pc-linux-gnu-g++ -Drandicindex_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/randicindex.dir/randicindexplugin.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/randicindex/randicindexplugin.cpp [ 80%] Linking CXX shared library randicindex.so cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/randicindex && /usr/bin/cmake -E cmake_link_script CMakeFiles/randicindex.dir/link.txt --verbose=1 /usr/bin/x86_64-pc-linux-gnu-g++ -fPIC -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -Wl,-O1 -Wl,--as-needed -shared -Wl,-soname,randicindex.so -o randicindex.so CMakeFiles/randicindex.dir/randicindexdescriptor.cpp.o CMakeFiles/randicindex.dir/randicindexplugin.cpp.o -Wl,-rpath,/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit: ../../chemkit/libchemkit.so -lboost_system-mt -lboost_filesystem-mt -lboost_thread-mt -lpthread -lboost_chrono-mt -lboost_date_time-mt -lboost_atomic-mt -ldl cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/randicindex && /usr/bin/cmake -E copy /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/randicindex/randicindex.so /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/lib64/chemkit/plugins/randicindex.so make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 80%] Built target randicindex make -f src/plugins/rof5/CMakeFiles/rof5.dir/build.make src/plugins/rof5/CMakeFiles/rof5.dir/depend make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/rof5 /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/rof5 /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/rof5/CMakeFiles/rof5.dir/DependInfo.cmake Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/rof5/CMakeFiles/rof5.dir/DependInfo.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/rof5/CMakeFiles/rof5.dir/depend.internal". Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/rof5/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/rof5/CMakeFiles/rof5.dir/depend.internal". Scanning dependencies of target rof5 make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' make -f src/plugins/rof5/CMakeFiles/rof5.dir/build.make src/plugins/rof5/CMakeFiles/rof5.dir/build make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 80%] Building CXX object src/plugins/rof5/CMakeFiles/rof5.dir/rof5plugin.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/rof5 && /usr/bin/x86_64-pc-linux-gnu-g++ -Drof5_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/rof5.dir/rof5plugin.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/rof5/rof5plugin.cpp [ 81%] Building CXX object src/plugins/rof5/CMakeFiles/rof5.dir/ruleoffivedescriptor.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/rof5 && /usr/bin/x86_64-pc-linux-gnu-g++ -Drof5_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/rof5.dir/ruleoffivedescriptor.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/rof5/ruleoffivedescriptor.cpp [ 81%] Building CXX object src/plugins/rof5/CMakeFiles/rof5.dir/ruleoffiveviolationsdescriptor.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/rof5 && /usr/bin/x86_64-pc-linux-gnu-g++ -Drof5_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/rof5.dir/ruleoffiveviolationsdescriptor.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/rof5/ruleoffiveviolationsdescriptor.cpp [ 81%] Linking CXX shared library rof5.so cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/rof5 && /usr/bin/cmake -E cmake_link_script CMakeFiles/rof5.dir/link.txt --verbose=1 /usr/bin/x86_64-pc-linux-gnu-g++ -fPIC -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -Wl,-O1 -Wl,--as-needed -shared -Wl,-soname,rof5.so -o rof5.so CMakeFiles/rof5.dir/rof5plugin.cpp.o CMakeFiles/rof5.dir/ruleoffivedescriptor.cpp.o CMakeFiles/rof5.dir/ruleoffiveviolationsdescriptor.cpp.o -Wl,-rpath,/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit: ../../chemkit/libchemkit.so -lboost_system-mt -lboost_filesystem-mt -lboost_thread-mt -lpthread -lboost_chrono-mt -lboost_date_time-mt -lboost_atomic-mt -ldl cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/rof5 && /usr/bin/cmake -E copy /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/rof5/rof5.so /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/lib64/chemkit/plugins/rof5.so make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 81%] Built target rof5 make -f src/plugins/rotatablebonds/CMakeFiles/rotatablebonds.dir/build.make src/plugins/rotatablebonds/CMakeFiles/rotatablebonds.dir/depend make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/rotatablebonds /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/rotatablebonds /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/rotatablebonds/CMakeFiles/rotatablebonds.dir/DependInfo.cmake Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/rotatablebonds/CMakeFiles/rotatablebonds.dir/DependInfo.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/rotatablebonds/CMakeFiles/rotatablebonds.dir/depend.internal". Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/rotatablebonds/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/rotatablebonds/CMakeFiles/rotatablebonds.dir/depend.internal". Scanning dependencies of target rotatablebonds make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' make -f src/plugins/rotatablebonds/CMakeFiles/rotatablebonds.dir/build.make src/plugins/rotatablebonds/CMakeFiles/rotatablebonds.dir/build make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 82%] Building CXX object src/plugins/rotatablebonds/CMakeFiles/rotatablebonds.dir/rotatablebondsdescriptor.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/rotatablebonds && /usr/bin/x86_64-pc-linux-gnu-g++ -Drotatablebonds_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/rotatablebonds.dir/rotatablebondsdescriptor.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/rotatablebonds/rotatablebondsdescriptor.cpp /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/rotatablebonds/rotatablebondsdescriptor.cpp: In member function ‘virtual chemkit::Variant RotatableBondsDescriptor::value(const chemkit::Molecule*) const’: /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/rotatablebonds/rotatablebondsdescriptor.cpp:58:27: warning: logical not is only applied to the left hand side of comparison [-Wlogical-not-parentheses] 58 | if(!bond->order() == chemkit::Bond::Single){ | ^~ /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/rotatablebonds/rotatablebondsdescriptor.cpp:58:12: note: add parentheses around left hand side expression to silence this warning 58 | if(!bond->order() == chemkit::Bond::Single){ | ^~~~~~~~~~~~~~ | ( ) [ 82%] Building CXX object src/plugins/rotatablebonds/CMakeFiles/rotatablebonds.dir/rotatablebondsplugin.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/rotatablebonds && /usr/bin/x86_64-pc-linux-gnu-g++ -Drotatablebonds_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/rotatablebonds.dir/rotatablebondsplugin.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/rotatablebonds/rotatablebondsplugin.cpp [ 83%] Linking CXX shared library rotatablebonds.so cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/rotatablebonds && /usr/bin/cmake -E cmake_link_script CMakeFiles/rotatablebonds.dir/link.txt --verbose=1 /usr/bin/x86_64-pc-linux-gnu-g++ -fPIC -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -Wl,-O1 -Wl,--as-needed -shared -Wl,-soname,rotatablebonds.so -o rotatablebonds.so CMakeFiles/rotatablebonds.dir/rotatablebondsdescriptor.cpp.o CMakeFiles/rotatablebonds.dir/rotatablebondsplugin.cpp.o -Wl,-rpath,/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit: ../../chemkit/libchemkit.so -lboost_system-mt -lboost_filesystem-mt -lboost_thread-mt -lpthread -lboost_chrono-mt -lboost_date_time-mt -lboost_atomic-mt -ldl cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/rotatablebonds && /usr/bin/cmake -E copy /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/rotatablebonds/rotatablebonds.so /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/lib64/chemkit/plugins/rotatablebonds.so make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 83%] Built target rotatablebonds make -f src/plugins/smiles/CMakeFiles/smiles.dir/build.make src/plugins/smiles/CMakeFiles/smiles.dir/depend make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/smiles /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/smiles /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/smiles/CMakeFiles/smiles.dir/DependInfo.cmake Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/smiles/CMakeFiles/smiles.dir/DependInfo.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/smiles/CMakeFiles/smiles.dir/depend.internal". Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/smiles/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/smiles/CMakeFiles/smiles.dir/depend.internal". Scanning dependencies of target smiles make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' make -f src/plugins/smiles/CMakeFiles/smiles.dir/build.make src/plugins/smiles/CMakeFiles/smiles.dir/build make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 83%] Building CXX object src/plugins/smiles/CMakeFiles/smiles.dir/daylightaromaticitymodel.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/smiles && /usr/bin/x86_64-pc-linux-gnu-g++ -Dsmiles_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/smiles/../../3rdparty/lemon -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/smiles.dir/daylightaromaticitymodel.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/smiles/daylightaromaticitymodel.cpp [ 84%] Building CXX object src/plugins/smiles/CMakeFiles/smiles.dir/kekulizer.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/smiles && /usr/bin/x86_64-pc-linux-gnu-g++ -Dsmiles_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/smiles/../../3rdparty/lemon -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/smiles.dir/kekulizer.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/smiles/kekulizer.cpp [ 84%] Building CXX object src/plugins/smiles/CMakeFiles/smiles.dir/smilesgraph.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/smiles && /usr/bin/x86_64-pc-linux-gnu-g++ -Dsmiles_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/smiles/../../3rdparty/lemon -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/smiles.dir/smilesgraph.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/smiles/smilesgraph.cpp [ 85%] Building CXX object src/plugins/smiles/CMakeFiles/smiles.dir/smileslineformat.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/smiles && /usr/bin/x86_64-pc-linux-gnu-g++ -Dsmiles_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/smiles/../../3rdparty/lemon -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/smiles.dir/smileslineformat.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/smiles/smileslineformat.cpp /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/smiles/smileslineformat.cpp:163:5: warning: ‘int {anonymous}::readCharge(const char**)’ defined but not used [-Wunused-function] 163 | int readCharge(const char **p) | ^~~~~~~~~~ [ 85%] Building CXX object src/plugins/smiles/CMakeFiles/smiles.dir/smilesplugin.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/smiles && /usr/bin/x86_64-pc-linux-gnu-g++ -Dsmiles_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/smiles/../../3rdparty/lemon -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/smiles.dir/smilesplugin.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/smiles/smilesplugin.cpp [ 86%] Linking CXX shared library smiles.so cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/smiles && /usr/bin/cmake -E cmake_link_script CMakeFiles/smiles.dir/link.txt --verbose=1 /usr/bin/x86_64-pc-linux-gnu-g++ -fPIC -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -Wl,-O1 -Wl,--as-needed -shared -Wl,-soname,smiles.so -o smiles.so CMakeFiles/smiles.dir/daylightaromaticitymodel.cpp.o CMakeFiles/smiles.dir/kekulizer.cpp.o CMakeFiles/smiles.dir/smilesgraph.cpp.o CMakeFiles/smiles.dir/smileslineformat.cpp.o CMakeFiles/smiles.dir/smilesplugin.cpp.o -Wl,-rpath,/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/io:/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit: ../../io/libchemkit-io.so ../../chemkit/libchemkit.so -lboost_system-mt -lboost_filesystem-mt -lboost_thread-mt -lpthread -lboost_chrono-mt -lboost_date_time-mt -lboost_atomic-mt -ldl -lboost_iostreams-mt -lboost_regex-mt cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/smiles && /usr/bin/cmake -E copy /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/smiles/smiles.so /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/lib64/chemkit/plugins/smiles.so make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 86%] Built target smiles make -f src/plugins/surfacedescriptors/CMakeFiles/surfacedescriptors.dir/build.make src/plugins/surfacedescriptors/CMakeFiles/surfacedescriptors.dir/depend make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/surfacedescriptors /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/surfacedescriptors /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/surfacedescriptors/CMakeFiles/surfacedescriptors.dir/DependInfo.cmake Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/surfacedescriptors/CMakeFiles/surfacedescriptors.dir/DependInfo.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/surfacedescriptors/CMakeFiles/surfacedescriptors.dir/depend.internal". Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/surfacedescriptors/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/surfacedescriptors/CMakeFiles/surfacedescriptors.dir/depend.internal". Scanning dependencies of target surfacedescriptors make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' make -f src/plugins/surfacedescriptors/CMakeFiles/surfacedescriptors.dir/build.make src/plugins/surfacedescriptors/CMakeFiles/surfacedescriptors.dir/build make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 86%] Building CXX object src/plugins/surfacedescriptors/CMakeFiles/surfacedescriptors.dir/surfacedescriptors.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/surfacedescriptors && /usr/bin/x86_64-pc-linux-gnu-g++ -Dsurfacedescriptors_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/surfacedescriptors.dir/surfacedescriptors.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/surfacedescriptors/surfacedescriptors.cpp [ 87%] Building CXX object src/plugins/surfacedescriptors/CMakeFiles/surfacedescriptors.dir/surfacedescriptorsplugin.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/surfacedescriptors && /usr/bin/x86_64-pc-linux-gnu-g++ -Dsurfacedescriptors_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/surfacedescriptors.dir/surfacedescriptorsplugin.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/surfacedescriptors/surfacedescriptorsplugin.cpp [ 87%] Linking CXX shared library surfacedescriptors.so cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/surfacedescriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/surfacedescriptors.dir/link.txt --verbose=1 /usr/bin/x86_64-pc-linux-gnu-g++ -fPIC -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -Wl,-O1 -Wl,--as-needed -shared -Wl,-soname,surfacedescriptors.so -o surfacedescriptors.so CMakeFiles/surfacedescriptors.dir/surfacedescriptors.cpp.o CMakeFiles/surfacedescriptors.dir/surfacedescriptorsplugin.cpp.o -Wl,-rpath,/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit: ../../chemkit/libchemkit.so -lboost_system-mt -lboost_filesystem-mt -lboost_thread-mt -lpthread -lboost_chrono-mt -lboost_date_time-mt -lboost_atomic-mt -ldl cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/surfacedescriptors && /usr/bin/cmake -E copy /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/surfacedescriptors/surfacedescriptors.so /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/lib64/chemkit/plugins/surfacedescriptors.so make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 87%] Built target surfacedescriptors make -f src/plugins/sybyl/CMakeFiles/sybyl.dir/build.make src/plugins/sybyl/CMakeFiles/sybyl.dir/depend make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/sybyl /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/sybyl /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/sybyl/CMakeFiles/sybyl.dir/DependInfo.cmake Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/sybyl/CMakeFiles/sybyl.dir/DependInfo.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/sybyl/CMakeFiles/sybyl.dir/depend.internal". Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/sybyl/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/sybyl/CMakeFiles/sybyl.dir/depend.internal". Scanning dependencies of target sybyl make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' make -f src/plugins/sybyl/CMakeFiles/sybyl.dir/build.make src/plugins/sybyl/CMakeFiles/sybyl.dir/build make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 87%] Building CXX object src/plugins/sybyl/CMakeFiles/sybyl.dir/sybylatomtyper.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/sybyl && /usr/bin/x86_64-pc-linux-gnu-g++ -Dsybyl_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/sybyl.dir/sybylatomtyper.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/sybyl/sybylatomtyper.cpp [ 88%] Building CXX object src/plugins/sybyl/CMakeFiles/sybyl.dir/sybylplugin.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/sybyl && /usr/bin/x86_64-pc-linux-gnu-g++ -Dsybyl_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/sybyl.dir/sybylplugin.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/sybyl/sybylplugin.cpp [ 88%] Building CXX object src/plugins/sybyl/CMakeFiles/sybyl.dir/mol2fileformat.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/sybyl && /usr/bin/x86_64-pc-linux-gnu-g++ -Dsybyl_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/sybyl.dir/mol2fileformat.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/sybyl/mol2fileformat.cpp [ 89%] Linking CXX shared library sybyl.so cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/sybyl && /usr/bin/cmake -E cmake_link_script CMakeFiles/sybyl.dir/link.txt --verbose=1 /usr/bin/x86_64-pc-linux-gnu-g++ -fPIC -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -Wl,-O1 -Wl,--as-needed -shared -Wl,-soname,sybyl.so -o sybyl.so CMakeFiles/sybyl.dir/sybylatomtyper.cpp.o CMakeFiles/sybyl.dir/sybylplugin.cpp.o CMakeFiles/sybyl.dir/mol2fileformat.cpp.o -Wl,-rpath,/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/io:/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit: ../../io/libchemkit-io.so ../../chemkit/libchemkit.so -lboost_system-mt -lboost_filesystem-mt -lboost_thread-mt -lpthread -lboost_chrono-mt -lboost_date_time-mt -lboost_atomic-mt -ldl -lboost_iostreams-mt -lboost_regex-mt cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/sybyl && /usr/bin/cmake -E copy /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/sybyl/sybyl.so /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/lib64/chemkit/plugins/sybyl.so make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 89%] Built target sybyl make -f src/plugins/tpsa/CMakeFiles/tpsa.dir/build.make src/plugins/tpsa/CMakeFiles/tpsa.dir/depend make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/tpsa /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/tpsa /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/tpsa/CMakeFiles/tpsa.dir/DependInfo.cmake Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/tpsa/CMakeFiles/tpsa.dir/DependInfo.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/tpsa/CMakeFiles/tpsa.dir/depend.internal". Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/tpsa/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/tpsa/CMakeFiles/tpsa.dir/depend.internal". Scanning dependencies of target tpsa make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' make -f src/plugins/tpsa/CMakeFiles/tpsa.dir/build.make src/plugins/tpsa/CMakeFiles/tpsa.dir/build make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 89%] Building CXX object src/plugins/tpsa/CMakeFiles/tpsa.dir/tpsadescriptor.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/tpsa && /usr/bin/x86_64-pc-linux-gnu-g++ -Dtpsa_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/tpsa.dir/tpsadescriptor.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/tpsa/tpsadescriptor.cpp [ 90%] Building CXX object src/plugins/tpsa/CMakeFiles/tpsa.dir/tpsaplugin.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/tpsa && /usr/bin/x86_64-pc-linux-gnu-g++ -Dtpsa_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/tpsa.dir/tpsaplugin.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/tpsa/tpsaplugin.cpp [ 90%] Linking CXX shared library tpsa.so cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/tpsa && /usr/bin/cmake -E cmake_link_script CMakeFiles/tpsa.dir/link.txt --verbose=1 /usr/bin/x86_64-pc-linux-gnu-g++ -fPIC -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -Wl,-O1 -Wl,--as-needed -shared -Wl,-soname,tpsa.so -o tpsa.so CMakeFiles/tpsa.dir/tpsadescriptor.cpp.o CMakeFiles/tpsa.dir/tpsaplugin.cpp.o -Wl,-rpath,/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit: ../../chemkit/libchemkit.so -lboost_system-mt -lboost_filesystem-mt -lboost_thread-mt -lpthread -lboost_chrono-mt -lboost_date_time-mt -lboost_atomic-mt -ldl cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/tpsa && /usr/bin/cmake -E copy /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/tpsa/tpsa.so /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/lib64/chemkit/plugins/tpsa.so make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 90%] Built target tpsa make -f src/plugins/txyz/CMakeFiles/txyz.dir/build.make src/plugins/txyz/CMakeFiles/txyz.dir/depend make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/txyz /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/txyz /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/txyz/CMakeFiles/txyz.dir/DependInfo.cmake Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/txyz/CMakeFiles/txyz.dir/DependInfo.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/txyz/CMakeFiles/txyz.dir/depend.internal". Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/txyz/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/txyz/CMakeFiles/txyz.dir/depend.internal". Scanning dependencies of target txyz make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' make -f src/plugins/txyz/CMakeFiles/txyz.dir/build.make src/plugins/txyz/CMakeFiles/txyz.dir/build make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 91%] Building CXX object src/plugins/txyz/CMakeFiles/txyz.dir/txyzfileformat.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/txyz && /usr/bin/x86_64-pc-linux-gnu-g++ -Dtxyz_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/txyz.dir/txyzfileformat.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/txyz/txyzfileformat.cpp [ 91%] Building CXX object src/plugins/txyz/CMakeFiles/txyz.dir/txyzplugin.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/txyz && /usr/bin/x86_64-pc-linux-gnu-g++ -Dtxyz_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/txyz.dir/txyzplugin.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/txyz/txyzplugin.cpp [ 92%] Linking CXX shared library txyz.so cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/txyz && /usr/bin/cmake -E cmake_link_script CMakeFiles/txyz.dir/link.txt --verbose=1 /usr/bin/x86_64-pc-linux-gnu-g++ -fPIC -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -Wl,-O1 -Wl,--as-needed -shared -Wl,-soname,txyz.so -o txyz.so CMakeFiles/txyz.dir/txyzfileformat.cpp.o CMakeFiles/txyz.dir/txyzplugin.cpp.o -Wl,-rpath,/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/io:/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit: ../../io/libchemkit-io.so ../../chemkit/libchemkit.so -lboost_system-mt -lboost_filesystem-mt -lboost_thread-mt -lpthread -lboost_chrono-mt -lboost_date_time-mt -lboost_atomic-mt -ldl -lboost_iostreams-mt -lboost_regex-mt cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/txyz && /usr/bin/cmake -E copy /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/txyz/txyz.so /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/lib64/chemkit/plugins/txyz.so make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 92%] Built target txyz make -f src/plugins/uff/CMakeFiles/uff.dir/build.make src/plugins/uff/CMakeFiles/uff.dir/depend make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/uff /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/uff /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/uff/CMakeFiles/uff.dir/DependInfo.cmake Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/uff/CMakeFiles/uff.dir/DependInfo.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/uff/CMakeFiles/uff.dir/depend.internal". Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/uff/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/uff/CMakeFiles/uff.dir/depend.internal". Scanning dependencies of target uff make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' make -f src/plugins/uff/CMakeFiles/uff.dir/build.make src/plugins/uff/CMakeFiles/uff.dir/build make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 92%] Building CXX object src/plugins/uff/CMakeFiles/uff.dir/uffatomtyper.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/uff && /usr/bin/x86_64-pc-linux-gnu-g++ -Duff_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/uff.dir/uffatomtyper.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/uff/uffatomtyper.cpp [ 93%] Building CXX object src/plugins/uff/CMakeFiles/uff.dir/uffplugin.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/uff && /usr/bin/x86_64-pc-linux-gnu-g++ -Duff_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/uff.dir/uffplugin.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/uff/uffplugin.cpp [ 93%] Building CXX object src/plugins/uff/CMakeFiles/uff.dir/uffcalculation.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/uff && /usr/bin/x86_64-pc-linux-gnu-g++ -Duff_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/uff.dir/uffcalculation.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/uff/uffcalculation.cpp [ 93%] Building CXX object src/plugins/uff/CMakeFiles/uff.dir/uffforcefield.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/uff && /usr/bin/x86_64-pc-linux-gnu-g++ -Duff_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/uff.dir/uffforcefield.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/uff/uffforcefield.cpp [ 94%] Building CXX object src/plugins/uff/CMakeFiles/uff.dir/uffparameters.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/uff && /usr/bin/x86_64-pc-linux-gnu-g++ -Duff_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/uff.dir/uffparameters.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/uff/uffparameters.cpp [ 94%] Linking CXX shared library uff.so cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/uff && /usr/bin/cmake -E cmake_link_script CMakeFiles/uff.dir/link.txt --verbose=1 /usr/bin/x86_64-pc-linux-gnu-g++ -fPIC -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -Wl,-O1 -Wl,--as-needed -shared -Wl,-soname,uff.so -o uff.so CMakeFiles/uff.dir/uffatomtyper.cpp.o CMakeFiles/uff.dir/uffplugin.cpp.o CMakeFiles/uff.dir/uffcalculation.cpp.o CMakeFiles/uff.dir/uffforcefield.cpp.o CMakeFiles/uff.dir/uffparameters.cpp.o -Wl,-rpath,/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/md:/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit: ../../md/libchemkit-md.so ../../chemkit/libchemkit.so -lboost_system-mt -lboost_filesystem-mt -lboost_thread-mt -lpthread -lboost_chrono-mt -lboost_date_time-mt -lboost_atomic-mt -ldl cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/uff && /usr/bin/cmake -E copy /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/uff/uff.so /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/lib64/chemkit/plugins/uff.so make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 94%] Built target uff make -f src/plugins/vabc/CMakeFiles/vabc.dir/build.make src/plugins/vabc/CMakeFiles/vabc.dir/depend make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/vabc /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/vabc /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/vabc/CMakeFiles/vabc.dir/DependInfo.cmake Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/vabc/CMakeFiles/vabc.dir/DependInfo.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/vabc/CMakeFiles/vabc.dir/depend.internal". Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/vabc/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/vabc/CMakeFiles/vabc.dir/depend.internal". Scanning dependencies of target vabc make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' make -f src/plugins/vabc/CMakeFiles/vabc.dir/build.make src/plugins/vabc/CMakeFiles/vabc.dir/build make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 95%] Building CXX object src/plugins/vabc/CMakeFiles/vabc.dir/vabcdescriptor.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/vabc && /usr/bin/x86_64-pc-linux-gnu-g++ -Dvabc_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/vabc.dir/vabcdescriptor.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/vabc/vabcdescriptor.cpp [ 95%] Building CXX object src/plugins/vabc/CMakeFiles/vabc.dir/vabcplugin.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/vabc && /usr/bin/x86_64-pc-linux-gnu-g++ -Dvabc_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/vabc.dir/vabcplugin.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/vabc/vabcplugin.cpp [ 96%] Linking CXX shared library vabc.so cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/vabc && /usr/bin/cmake -E cmake_link_script CMakeFiles/vabc.dir/link.txt --verbose=1 /usr/bin/x86_64-pc-linux-gnu-g++ -fPIC -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -Wl,-O1 -Wl,--as-needed -shared -Wl,-soname,vabc.so -o vabc.so CMakeFiles/vabc.dir/vabcdescriptor.cpp.o CMakeFiles/vabc.dir/vabcplugin.cpp.o -Wl,-rpath,/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit: ../../chemkit/libchemkit.so -lboost_system-mt -lboost_filesystem-mt -lboost_thread-mt -lpthread -lboost_chrono-mt -lboost_date_time-mt -lboost_atomic-mt -ldl cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/vabc && /usr/bin/cmake -E copy /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/vabc/vabc.so /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/lib64/chemkit/plugins/vabc.so make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 96%] Built target vabc make -f src/plugins/wienerindex/CMakeFiles/wienerindex.dir/build.make src/plugins/wienerindex/CMakeFiles/wienerindex.dir/depend make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/wienerindex /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/wienerindex /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/wienerindex/CMakeFiles/wienerindex.dir/DependInfo.cmake Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/wienerindex/CMakeFiles/wienerindex.dir/DependInfo.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/wienerindex/CMakeFiles/wienerindex.dir/depend.internal". Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/wienerindex/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/wienerindex/CMakeFiles/wienerindex.dir/depend.internal". Scanning dependencies of target wienerindex make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' make -f src/plugins/wienerindex/CMakeFiles/wienerindex.dir/build.make src/plugins/wienerindex/CMakeFiles/wienerindex.dir/build make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 96%] Building CXX object src/plugins/wienerindex/CMakeFiles/wienerindex.dir/wienerindexdescriptor.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/wienerindex && /usr/bin/x86_64-pc-linux-gnu-g++ -Dwienerindex_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/wienerindex.dir/wienerindexdescriptor.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/wienerindex/wienerindexdescriptor.cpp [ 97%] Building CXX object src/plugins/wienerindex/CMakeFiles/wienerindex.dir/wienerindexplugin.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/wienerindex && /usr/bin/x86_64-pc-linux-gnu-g++ -Dwienerindex_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/wienerindex.dir/wienerindexplugin.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/wienerindex/wienerindexplugin.cpp [ 97%] Linking CXX shared library wienerindex.so cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/wienerindex && /usr/bin/cmake -E cmake_link_script CMakeFiles/wienerindex.dir/link.txt --verbose=1 /usr/bin/x86_64-pc-linux-gnu-g++ -fPIC -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -Wl,-O1 -Wl,--as-needed -shared -Wl,-soname,wienerindex.so -o wienerindex.so CMakeFiles/wienerindex.dir/wienerindexdescriptor.cpp.o CMakeFiles/wienerindex.dir/wienerindexplugin.cpp.o -Wl,-rpath,/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit: ../../chemkit/libchemkit.so -lboost_system-mt -lboost_filesystem-mt -lboost_thread-mt -lpthread -lboost_chrono-mt -lboost_date_time-mt -lboost_atomic-mt -ldl cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/wienerindex && /usr/bin/cmake -E copy /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/wienerindex/wienerindex.so /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/lib64/chemkit/plugins/wienerindex.so make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 97%] Built target wienerindex make -f src/plugins/xyz/CMakeFiles/xyz.dir/build.make src/plugins/xyz/CMakeFiles/xyz.dir/depend make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/xyz /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/xyz /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/xyz/CMakeFiles/xyz.dir/DependInfo.cmake Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/xyz/CMakeFiles/xyz.dir/DependInfo.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/xyz/CMakeFiles/xyz.dir/depend.internal". Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/xyz/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/xyz/CMakeFiles/xyz.dir/depend.internal". Scanning dependencies of target xyz make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' make -f src/plugins/xyz/CMakeFiles/xyz.dir/build.make src/plugins/xyz/CMakeFiles/xyz.dir/build make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 98%] Building CXX object src/plugins/xyz/CMakeFiles/xyz.dir/xyzfileformat.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/xyz && /usr/bin/x86_64-pc-linux-gnu-g++ -Dxyz_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/xyz.dir/xyzfileformat.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/xyz/xyzfileformat.cpp [ 98%] Building CXX object src/plugins/xyz/CMakeFiles/xyz.dir/xyzplugin.cpp.o cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/xyz && /usr/bin/x86_64-pc-linux-gnu-g++ -Dxyz_EXPORTS -I/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC -o CMakeFiles/xyz.dir/xyzplugin.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/xyz/xyzplugin.cpp [ 99%] Linking CXX shared library xyz.so cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/xyz && /usr/bin/cmake -E cmake_link_script CMakeFiles/xyz.dir/link.txt --verbose=1 /usr/bin/x86_64-pc-linux-gnu-g++ -fPIC -O2 -pipe -march=native -DSYSTEM_INCHI -DSYSTEM_RAPIDXML -fvisibility=hidden -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -Wl,-O1 -Wl,--as-needed -shared -Wl,-soname,xyz.so -o xyz.so CMakeFiles/xyz.dir/xyzfileformat.cpp.o CMakeFiles/xyz.dir/xyzplugin.cpp.o -Wl,-rpath,/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/io:/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit: ../../io/libchemkit-io.so ../../chemkit/libchemkit.so -lboost_system-mt -lboost_filesystem-mt -lboost_thread-mt -lpthread -lboost_chrono-mt -lboost_date_time-mt -lboost_atomic-mt -ldl -lboost_iostreams-mt -lboost_regex-mt cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/xyz && /usr/bin/cmake -E copy /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/xyz/xyz.so /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/lib64/chemkit/plugins/xyz.so make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 99%] Built target xyz make -f bindings/python/CMakeFiles/chemkit-python.dir/build.make bindings/python/CMakeFiles/chemkit-python.dir/depend make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' [ 99%] Generating chemkit.cpp cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/bindings/python && /usr/bin/cython --cplus --fast-fail -o /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/bindings/python/chemkit.cpp /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/bindings/python/chemkit.pyx /usr/lib64/python2.7/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/bindings/python/chemkit.pyx tree = Parsing.p_module(s, pxd, full_module_name) Error compiling Cython file: ------------------------------------------------------------ ... self._atom.setPosition(x, y, z) def position(self): """Returns the position of the atom.""" cdef _Point3 p = self._atom.position() ^ ------------------------------------------------------------ /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/bindings/python/atom.pxi:253:13: Compiler crash in AnalyseExpressionsTransform ModuleNode.body = StatListNode(chemkit.pyx:36:0) StatListNode.stats[0] = StatListNode(atom.pxi:36:0) StatListNode.stats[2] = CClassDefNode(atom.pxi:43:5, as_name = u'Atom', class_name = u'Atom', doc = u'The Atom class represents an atom in a molecule.\n\n Atom objects are created with the\n :func:`~chemkit.Molecule.addAtom` method and destroyed with the\n :func:`~chemkit.Molecule.removeAtom` method.\n\n ') CClassDefNode.body = StatListNode(atom.pxi:44:4) StatListNode.stats[36] = DefNode(atom.pxi:250:4, doc = u'Returns the position of the atom.', modifiers = [...]/0, name = u'position', np_args_idx = [...]/0, num_required_args = 1, outer_attrs = [...]/2, py_wrapper_required = True, used = True) File 'Nodes.py', line 436, in analyse_expressions: StatListNode(atom.pxi:251:8, is_terminator = True) File 'Nodes.py', line 5159, in analyse_expressions: SingleAssignmentNode(atom.pxi:253:13, first = True) File 'Nodes.py', line 5301, in analyse_types: SingleAssignmentNode(atom.pxi:253:13, first = True) Compiler crash traceback from this point on: File "/usr/lib64/python2.7/site-packages/Cython/Compiler/Nodes.py", line 5301, in analyse_types op = env.lookup_operator_for_types(self.pos, '=', [self.lhs.type, self.rhs.type]) File "/usr/lib64/python2.7/site-packages/Cython/Compiler/Symtab.py", line 939, in lookup_operator_for_types return self.lookup_operator(operator, operands) File "/usr/lib64/python2.7/site-packages/Cython/Compiler/Symtab.py", line 921, in lookup_operator method = obj_type.scope.lookup("operator%s" % operator) AttributeError: 'NoneType' object has no attribute 'lookup' make[2]: *** [bindings/python/CMakeFiles/chemkit-python.dir/build.make:91: bindings/python/chemkit.cpp] Error 1 make[2]: *** Deleting file 'bindings/python/chemkit.cpp' make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' make[1]: *** [CMakeFiles/Makefile2:2422: bindings/python/CMakeFiles/chemkit-python.dir/all] Error 2 make[1]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' make: *** [Makefile:141: all] Error 2 * ERROR: sci-libs/chemkit-0.1-r2::gentoo failed (compile phase): * emake failed * * If you need support, post the output of `emerge --info '=sci-libs/chemkit-0.1-r2::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-libs/chemkit-0.1-r2::gentoo'`. * The complete build log is located at '/var/log/portage/sci-libs:chemkit-0.1-r2:20190726-172831.log'. * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-libs/chemkit-0.1-r2/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-libs/chemkit-0.1-r2/temp/environment'. * Working directory: '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build' * S: '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit'