sci-libs:chemkit-0.1-r2:20190726-172831.log

sci-libs:chemkit-0.1-r2:20190726-172831.log (text/plain), 419.84 KB, created by Toralf Förster on 2019-07-26 17:54:38 UTC

 * Package:    sci-libs/chemkit-0.1-r2
 * Repository: gentoo
 * Maintainer: [e-mail]
 * 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 $<TARGET_FILE>, 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 $<TARGET_FILE>, 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 $<TARGET_FILE>, 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 $<TARGET_FILE>, 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 $<TARGET_FILE>, 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 $<TARGET_FILE>, 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 $<TARGET_FILE>, 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
  $<TARGET_FILE>, 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 $<TARGET_FILE>, 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 $<TARGET_FILE>, 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
  $<TARGET_FILE>, 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 $<TARGET_FILE>, 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
  $<TARGET_FILE>, 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
  $<TARGET_FILE>, 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 $<TARGET_FILE>, 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 $<TARGET_FILE>, 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 $<TARGET_FILE>, 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 $<TARGET_FILE>, 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 $<TARGET_FILE>, 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 $<TARGET_FILE>, 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 $<TARGET_FILE>, 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 $<TARGET_FILE>, 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 $<TARGET_FILE>, 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
  $<TARGET_FILE>, 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 $<TARGET_FILE>, 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 $<TARGET_FILE>, 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 $<TARGET_FILE>, 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 $<TARGET_FILE>, 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
  $<TARGET_FILE>, 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
  $<TARGET_FILE>, 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 $<TARGET_FILE>, 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 $<TARGET_FILE>, 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 $<TARGET_FILE>, 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 $<TARGET_FILE>, 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 $<TARGET_FILE>, 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 $<TARGET_FILE>, 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 $<TARGET_FILE>, 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 $<TARGET_FILE>, 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 $<TARGET_FILE>, 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
  $<TARGET_FILE>, 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 $<TARGET_FILE>, 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 $<TARGET_FILE>, 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
  $<TARGET_FILE>, 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<Lhs, Rhs, Option>::Product(const Lhs&, const Rhs&) [with _Lhs = Eigen::Transpose<Eigen::Matrix<double, -1, -1> >; _Rhs = Eigen::Matrix<double, -1, -1>; int Option = 0; Eigen::Product<Lhs, Rhs, Option>::Lhs = Eigen::Transpose<Eigen::Matrix<double, -1, -1> >; Eigen::Product<Lhs, Rhs, Option>::Rhs = Eigen::Matrix<double, -1, -1>]’:
/usr/include/eigen3/Eigen/src/Core/GeneralProduct.h:415:10:   required from ‘const Eigen::Product<Derived, OtherDerived> Eigen::MatrixBase<Derived>::operator*(const Eigen::MatrixBase<OtherDerived>&) const [with OtherDerived = Eigen::Matrix<double, -1, -1>; Derived = Eigen::Transpose<Eigen::Matrix<double, -1, -1> >]’
/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<Eigen::Matrix<double, -1, -1> >::Transpose(const Eigen::Transpose<Eigen::Matrix<double, -1, -1> >&)’ 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<Eigen::Matrix<double, -1, -1> >’ has user-provided ‘Derived& Eigen::MatrixBase<Derived>::operator=(const Eigen::MatrixBase<Derived>&) [with Derived = Eigen::Transpose<Eigen::Matrix<double, -1, -1> >]’
   55 | EIGEN_STRONG_INLINE Derived& MatrixBase<Derived>::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<BinaryOp, Lhs, Rhs>::CwiseBinaryOp(const Lhs&, const Rhs&, const BinaryOp&) [with BinaryOp = Eigen::internal::scalar_sum_op<double, double>; LhsType = const Eigen::ArrayWrapper<const Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::Matrix<double, 3, 1>, const Eigen::Matrix<double, 3, 1> > >; RhsType = const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Array<double, 3, 1> >; Eigen::CwiseBinaryOp<BinaryOp, Lhs, Rhs>::Lhs = Eigen::ArrayWrapper<const Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::Matrix<double, 3, 1>, const Eigen::Matrix<double, 3, 1> > >; Eigen::CwiseBinaryOp<BinaryOp, Lhs, Rhs>::Rhs = Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Array<double, 3, 1> >]’:
/usr/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseBinaryOps.h:215:1:   required from ‘typename Eigen::internal::enable_if<true, const Eigen::CwiseBinaryOp<Eigen::internal::scalar_sum_op<typename Eigen::internal::traits<T>::Scalar, typename Eigen::internal::promote_scalar_arg<typename Eigen::internal::traits<T>::Scalar, T, Eigen::internal::has_ReturnType<Eigen::ScalarBinaryOpTraits<typename Eigen::internal::traits<T>::Scalar, T, Eigen::internal::scalar_sum_op<typename Eigen::internal::traits<T>::Scalar, T> > >::value>::type>, const Derived, const typename Eigen::internal::plain_constant_type<Derived, typename Eigen::internal::promote_scalar_arg<typename Eigen::internal::traits<T>::Scalar, T, Eigen::internal::has_ReturnType<Eigen::ScalarBinaryOpTraits<typename Eigen::internal::traits<T>::Scalar, T, Eigen::internal::scalar_sum_op<typename Eigen::internal::traits<T>::Scalar, T> > >::value>::type>::type> >::type Eigen::ArrayBase<Derived>::operator+(const T&) const [with T = double; Derived = Eigen::ArrayWrapper<const Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::Matrix<double, 3, 1>, const Eigen::Matrix<double, 3, 1> > >; typename Eigen::internal::enable_if<true, const Eigen::CwiseBinaryOp<Eigen::internal::scalar_sum_op<typename Eigen::internal::traits<T>::Scalar, typename Eigen::internal::promote_scalar_arg<typename Eigen::internal::traits<T>::Scalar, T, Eigen::internal::has_ReturnType<Eigen::ScalarBinaryOpTraits<typename Eigen::internal::traits<T>::Scalar, T, Eigen::internal::scalar_sum_op<typename Eigen::internal::traits<T>::Scalar, T> > >::value>::type>, const Derived, const typename Eigen::internal::plain_constant_type<Derived, typename Eigen::internal::promote_scalar_arg<typename Eigen::internal::traits<T>::Scalar, T, Eigen::internal::has_ReturnType<Eigen::ScalarBinaryOpTraits<typename Eigen::internal::traits<T>::Scalar, T, Eigen::internal::scalar_sum_op<typename Eigen::internal::traits<T>::Scalar, T> > >::value>::type>::type> >::type = const Eigen::CwiseBinaryOp<Eigen::internal::scalar_sum_op<double, double>, const Eigen::ArrayWrapper<const Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::Matrix<double, 3, 1>, const Eigen::Matrix<double, 3, 1> > >, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Array<double, 3, 1> > >]’
/usr/include/eigen3/Eigen/src/Geometry/AngleAxis.h:240:61:   required from ‘Eigen::AngleAxis<Scalar>::Matrix3 Eigen::AngleAxis<Scalar>::toRotationMatrix() const [with _Scalar = double; Eigen::AngleAxis<Scalar>::Matrix3 = Eigen::Matrix<double, 3, 3>]’
/usr/include/eigen3/Eigen/src/Geometry/RotationBase.h:45:110:   required from ‘Eigen::RotationBase<Derived, _Dim>::RotationMatrixType Eigen::RotationBase<Derived, _Dim>::toRotationMatrix() const [with Derived = Eigen::AngleAxis<double>; int _Dim = 3; Eigen::RotationBase<Derived, _Dim>::RotationMatrixType = Eigen::Matrix<double, 3, 3>; typename Eigen::internal::traits<T>::Scalar = double]’
/usr/include/eigen3/Eigen/src/Geometry/RotationBase.h:191:29:   required from ‘Eigen::Matrix<Scalar, Dim, Dim> Eigen::internal::toRotationMatrix(const Eigen::RotationBase<OtherDerived, Dim>&) [with Scalar = double; int Dim = 3; OtherDerived = Eigen::AngleAxis<double>]’
/usr/include/eigen3/Eigen/src/Geometry/Transform.h:1030:52:   required from ‘Eigen::Transform<Scalar, Dim, Mode, Options>& Eigen::Transform<Scalar, Dim, Mode, _Options>::operator=(const Eigen::RotationBase<Derived, Dim>&) [with Derived = Eigen::AngleAxis<double>; _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<Scalar, Dim, Mode, _Options>::Transform(const Eigen::RotationBase<Derived, Dim>&) [with Derived = Eigen::AngleAxis<double>; _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::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::Matrix<double, 3, 1>, const Eigen::Matrix<double, 3, 1> > >::ArrayWrapper(const Eigen::ArrayWrapper<const Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::Matrix<double, 3, 1>, const Eigen::Matrix<double, 3, 1> > >&)’ 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::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::Matrix<double, 3, 1>, const Eigen::Matrix<double, 3, 1> > >’ has user-provided ‘Derived& Eigen::ArrayBase<Derived>::operator=(const Eigen::ArrayBase<Derived>&) [with Derived = Eigen::ArrayWrapper<const Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::Matrix<double, 3, 1>, const Eigen::Matrix<double, 3, 1> > >]’
  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<Lhs, Rhs, Option>::Product(const Lhs&, const Rhs&) [with _Lhs = Eigen::Transpose<Eigen::Matrix<double, -1, -1> >; _Rhs = Eigen::Matrix<double, -1, -1>; int Option = 1; Eigen::Product<Lhs, Rhs, Option>::Lhs = Eigen::Transpose<Eigen::Matrix<double, -1, -1> >; Eigen::Product<Lhs, Rhs, Option>::Rhs = Eigen::Matrix<double, -1, -1>]’:
/usr/include/eigen3/Eigen/src/Core/GeneralProduct.h:450:10:   required from ‘const Eigen::Product<Derived, OtherDerived, 1> Eigen::MatrixBase<Derived>::lazyProduct(const Eigen::MatrixBase<OtherDerived>&) const [with OtherDerived = Eigen::Matrix<double, -1, -1>; Derived = Eigen::Transpose<Eigen::Matrix<double, -1, -1> >]’
/usr/include/eigen3/Eigen/src/Core/ProductEvaluators.h:397:29:   required from ‘static void Eigen::internal::generic_product_impl<Lhs, Rhs, Eigen::DenseShape, Eigen::DenseShape, 3>::evalTo(Dst&, const Lhs&, const Rhs&) [with Dst = Eigen::Matrix<double, 3, 3>; Lhs = Eigen::Transpose<Eigen::Matrix<double, -1, -1> >; Rhs = Eigen::Matrix<double, -1, -1>]’
/usr/include/eigen3/Eigen/src/Core/products/GeneralMatrixMatrix.h:431:26:   required from ‘static void Eigen::internal::generic_product_impl<Lhs, Rhs, Eigen::DenseShape, Eigen::DenseShape, 8>::evalTo(Dst&, const Lhs&, const Rhs&) [with Dst = Eigen::Matrix<double, 3, 3>; Lhs = Eigen::Transpose<Eigen::Matrix<double, -1, -1> >; Rhs = Eigen::Matrix<double, -1, -1>]’
/usr/include/eigen3/Eigen/src/Core/ProductEvaluators.h:148:43:   required from ‘static void Eigen::internal::Assignment<DstXprType, Eigen::Product<Lhs, Rhs, Options>, Eigen::internal::assign_op<Scalar, Scalar>, Eigen::internal::Dense2Dense, typename Eigen::internal::enable_if<((Options == Eigen::DefaultProduct) || (Options == Eigen::AliasFreeProduct))>::type>::run(DstXprType&, const SrcXprType&, const Eigen::internal::assign_op<Scalar, Scalar>&) [with DstXprType = Eigen::Matrix<double, 3, 3>; Lhs = Eigen::Transpose<Eigen::Matrix<double, -1, -1> >; Rhs = Eigen::Matrix<double, -1, -1>; int Options = 0; Scalar = double; Eigen::internal::Assignment<DstXprType, Eigen::Product<Lhs, Rhs, Options>, Eigen::internal::assign_op<Scalar, Scalar>, Eigen::internal::Dense2Dense, typename Eigen::internal::enable_if<((Options == Eigen::DefaultProduct) || (Options == Eigen::AliasFreeProduct))>::type>::SrcXprType = Eigen::Product<Eigen::Transpose<Eigen::Matrix<double, -1, -1> >, Eigen::Matrix<double, -1, -1>, 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<double, 3, 3>; Src = Eigen::Product<Eigen::Transpose<Eigen::Matrix<double, -1, -1> >, Eigen::Matrix<double, -1, -1>, 0>; Func = Eigen::internal::assign_op<double, double>]’
/usr/include/eigen3/Eigen/src/Core/PlainObjectBase.h:732:41:   required from ‘Derived& Eigen::PlainObjectBase<Derived>::_set_noalias(const Eigen::DenseBase<OtherDerived>&) [with OtherDerived = Eigen::Product<Eigen::Transpose<Eigen::Matrix<double, -1, -1> >, Eigen::Matrix<double, -1, -1>, 0>; Derived = Eigen::Matrix<double, 3, 3>]’
/usr/include/eigen3/Eigen/src/Core/PlainObjectBase.h:537:7:   required from ‘Eigen::PlainObjectBase<Derived>::PlainObjectBase(const Eigen::DenseBase<OtherDerived>&) [with OtherDerived = Eigen::Product<Eigen::Transpose<Eigen::Matrix<double, -1, -1> >, Eigen::Matrix<double, -1, -1>, 0>; Derived = Eigen::Matrix<double, 3, 3>]’
/usr/include/eigen3/Eigen/src/Core/Matrix.h:377:29:   required from ‘Eigen::Matrix<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>::Matrix(const Eigen::EigenBase<OtherDerived>&) [with OtherDerived = Eigen::Product<Eigen::Transpose<Eigen::Matrix<double, -1, -1> >, Eigen::Matrix<double, -1, -1>, 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<Eigen::Matrix<double, -1, -1> >::Transpose(const Eigen::Transpose<Eigen::Matrix<double, -1, -1> >&)’ 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<Eigen::Matrix<double, -1, -1> >’ has user-provided ‘Derived& Eigen::MatrixBase<Derived>::operator=(const Eigen::MatrixBase<Derived>&) [with Derived = Eigen::Transpose<Eigen::Matrix<double, -1, -1> >]’
   55 | EIGEN_STRONG_INLINE Derived& MatrixBase<Derived>::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<Eigen::Product<Lhs, Rhs, 1>, ProductTag, Eigen::DenseShape, Eigen::DenseShape>::product_evaluator(const XprType&) [with Lhs = Eigen::Transpose<Eigen::Matrix<double, -1, -1> >; Rhs = Eigen::Matrix<double, -1, -1>; int ProductTag = 8; typename Eigen::internal::traits<typename Eigen::Product<Lhs, Rhs, 1>::Rhs>::Scalar = double; typename Eigen::internal::traits<typename Eigen::Product<Lhs, Rhs, 1>::Lhs>::Scalar = double; Eigen::internal::product_evaluator<Eigen::Product<Lhs, Rhs, 1>, ProductTag, Eigen::DenseShape, Eigen::DenseShape>::XprType = Eigen::Product<Eigen::Transpose<Eigen::Matrix<double, -1, -1> >, Eigen::Matrix<double, -1, -1>, 1>]’:
/usr/include/eigen3/Eigen/src/Core/ProductEvaluators.h:35:90:   required from ‘Eigen::internal::evaluator<Eigen::Product<Lhs, Rhs, Option> >::evaluator(const XprType&) [with Lhs = Eigen::Transpose<Eigen::Matrix<double, -1, -1> >; Rhs = Eigen::Matrix<double, -1, -1>; int Options = 1; Eigen::internal::evaluator<Eigen::Product<Lhs, Rhs, Option> >::XprType = Eigen::Product<Eigen::Transpose<Eigen::Matrix<double, -1, -1> >, Eigen::Matrix<double, -1, -1>, 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<double, 3, 3>; SrcXprType = Eigen::Product<Eigen::Transpose<Eigen::Matrix<double, -1, -1> >, Eigen::Matrix<double, -1, -1>, 1>; Functor = Eigen::internal::assign_op<double, double>]’
/usr/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:31:   required from ‘static void Eigen::internal::Assignment<DstXprType, SrcXprType, Functor, Eigen::internal::Dense2Dense, Weak>::run(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen::Matrix<double, 3, 3>; SrcXprType = Eigen::Product<Eigen::Transpose<Eigen::Matrix<double, -1, -1> >, Eigen::Matrix<double, -1, -1>, 1>; Functor = Eigen::internal::assign_op<double, double>; 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<double, 3, 3>; Src = Eigen::Product<Eigen::Transpose<Eigen::Matrix<double, -1, -1> >, Eigen::Matrix<double, -1, -1>, 1>; Func = Eigen::internal::assign_op<double, double>]’
/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<DstXprType, Eigen::Product<Lhs, Rhs, Options>, Eigen::internal::assign_op<Scalar, Scalar>, Eigen::internal::Dense2Dense, typename Eigen::internal::enable_if<((Options == Eigen::DefaultProduct) || (Options == Eigen::AliasFreeProduct))>::type>::run(DstXprType&, const SrcXprType&, const Eigen::internal::assign_op<Scalar, Scalar>&) [with DstXprType = Eigen::Matrix<double, 3, 3>; Lhs = Eigen::Transpose<Eigen::Matrix<double, -1, -1> >; Rhs = Eigen::Matrix<double, -1, -1>; int Options = 0; Scalar = double; Eigen::internal::Assignment<DstXprType, Eigen::Product<Lhs, Rhs, Options>, Eigen::internal::assign_op<Scalar, Scalar>, Eigen::internal::Dense2Dense, typename Eigen::internal::enable_if<((Options == Eigen::DefaultProduct) || (Options == Eigen::AliasFreeProduct))>::type>::SrcXprType = Eigen::Product<Eigen::Transpose<Eigen::Matrix<double, -1, -1> >, Eigen::Matrix<double, -1, -1>, 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<double, 3, 3>; Src = Eigen::Product<Eigen::Transpose<Eigen::Matrix<double, -1, -1> >, Eigen::Matrix<double, -1, -1>, 0>; Func = Eigen::internal::assign_op<double, double>]’
/usr/include/eigen3/Eigen/src/Core/PlainObjectBase.h:732:41:   required from ‘Derived& Eigen::PlainObjectBase<Derived>::_set_noalias(const Eigen::DenseBase<OtherDerived>&) [with OtherDerived = Eigen::Product<Eigen::Transpose<Eigen::Matrix<double, -1, -1> >, Eigen::Matrix<double, -1, -1>, 0>; Derived = Eigen::Matrix<double, 3, 3>]’
/usr/include/eigen3/Eigen/src/Core/PlainObjectBase.h:537:7:   required from ‘Eigen::PlainObjectBase<Derived>::PlainObjectBase(const Eigen::DenseBase<OtherDerived>&) [with OtherDerived = Eigen::Product<Eigen::Transpose<Eigen::Matrix<double, -1, -1> >, Eigen::Matrix<double, -1, -1>, 0>; Derived = Eigen::Matrix<double, 3, 3>]’
/usr/include/eigen3/Eigen/src/Core/Matrix.h:377:29:   required from ‘Eigen::Matrix<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>::Matrix(const Eigen::EigenBase<OtherDerived>&) [with OtherDerived = Eigen::Product<Eigen::Transpose<Eigen::Matrix<double, -1, -1> >, Eigen::Matrix<double, -1, -1>, 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<Eigen::Matrix<double, -1, -1> >::Transpose(const Eigen::Transpose<Eigen::Matrix<double, -1, -1> >&)’ 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<Eigen::Matrix<double, -1, -1> >’ has user-provided ‘Derived& Eigen::MatrixBase<Derived>::operator=(const Eigen::MatrixBase<Derived>&) [with Derived = Eigen::Transpose<Eigen::Matrix<double, -1, -1> >]’
   55 | EIGEN_STRONG_INLINE Derived& MatrixBase<Derived>::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<MatrixType>::Transpose(MatrixType&) [with MatrixType = const Eigen::Block<const Eigen::Transpose<Eigen::Matrix<double, -1, -1> >, 1, -1, true>]’:
/usr/include/eigen3/Eigen/src/Core/Transpose.h:186:10:   required from ‘Eigen::DenseBase<Derived>::ConstTransposeReturnType Eigen::DenseBase<Derived>::transpose() const [with Derived = Eigen::Block<const Eigen::Transpose<Eigen::Matrix<double, -1, -1> >, 1, -1, true>; Eigen::DenseBase<Derived>::ConstTransposeReturnType = const Eigen::Transpose<const Eigen::Block<const Eigen::Transpose<Eigen::Matrix<double, -1, -1> >, 1, -1, true> >]’
/usr/include/eigen3/Eigen/src/Core/ProductEvaluators.h:552:40:   required from ‘const CoeffReturnType Eigen::internal::product_evaluator<Eigen::Product<Lhs, Rhs, 1>, ProductTag, Eigen::DenseShape, Eigen::DenseShape>::coeff(Eigen::Index, Eigen::Index) const [with Lhs = Eigen::Transpose<Eigen::Matrix<double, -1, -1> >; Rhs = Eigen::Matrix<double, -1, -1>; int ProductTag = 8; typename Eigen::internal::traits<typename Eigen::Product<Lhs, Rhs, 1>::Rhs>::Scalar = double; typename Eigen::internal::traits<typename Eigen::Product<Lhs, Rhs, 1>::Lhs>::Scalar = double; Eigen::internal::product_evaluator<Eigen::Product<Lhs, Rhs, 1>, 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<DstEvaluatorTypeT, SrcEvaluatorTypeT, Functor, Version>::assignCoeff(Eigen::Index, Eigen::Index) [with DstEvaluatorTypeT = Eigen::internal::evaluator<Eigen::Matrix<double, 3, 3> >; SrcEvaluatorTypeT = Eigen::internal::evaluator<Eigen::Product<Eigen::Transpose<Eigen::Matrix<double, -1, -1> >, Eigen::Matrix<double, -1, -1>, 1> >; Functor = Eigen::internal::assign_op<double, double>; 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<DstEvaluatorTypeT, SrcEvaluatorTypeT, Functor, Version>::assignCoeffByOuterInner(Eigen::Index, Eigen::Index) [with DstEvaluatorTypeT = Eigen::internal::evaluator<Eigen::Matrix<double, 3, 3> >; SrcEvaluatorTypeT = Eigen::internal::evaluator<Eigen::Product<Eigen::Transpose<Eigen::Matrix<double, -1, -1> >, Eigen::Matrix<double, -1, -1>, 1> >; Functor = Eigen::internal::assign_op<double, double>; 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<Kernel, 0, 0>::run(Kernel&) [with Kernel = Eigen::internal::generic_dense_assignment_kernel<Eigen::internal::evaluator<Eigen::Matrix<double, 3, 3> >, Eigen::internal::evaluator<Eigen::Product<Eigen::Transpose<Eigen::Matrix<double, -1, -1> >, Eigen::Matrix<double, -1, -1>, 1> >, Eigen::internal::assign_op<double, double>, 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<DstXprType, Eigen::Product<Lhs, Rhs, Options>, Eigen::internal::assign_op<Scalar, Scalar>, Eigen::internal::Dense2Dense, typename Eigen::internal::enable_if<((Options == Eigen::DefaultProduct) || (Options == Eigen::AliasFreeProduct))>::type>::run(DstXprType&, const SrcXprType&, const Eigen::internal::assign_op<Scalar, Scalar>&) [with DstXprType = Eigen::Matrix<double, 3, 3>; Lhs = Eigen::Transpose<Eigen::Matrix<double, -1, -1> >; Rhs = Eigen::Matrix<double, -1, -1>; int Options = 0; Scalar = double; Eigen::internal::Assignment<DstXprType, Eigen::Product<Lhs, Rhs, Options>, Eigen::internal::assign_op<Scalar, Scalar>, Eigen::internal::Dense2Dense, typename Eigen::internal::enable_if<((Options == Eigen::DefaultProduct) || (Options == Eigen::AliasFreeProduct))>::type>::SrcXprType = Eigen::Product<Eigen::Transpose<Eigen::Matrix<double, -1, -1> >, Eigen::Matrix<double, -1, -1>, 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<double, 3, 3>; Src = Eigen::Product<Eigen::Transpose<Eigen::Matrix<double, -1, -1> >, Eigen::Matrix<double, -1, -1>, 0>; Func = Eigen::internal::assign_op<double, double>]’
/usr/include/eigen3/Eigen/src/Core/PlainObjectBase.h:732:41:   required from ‘Derived& Eigen::PlainObjectBase<Derived>::_set_noalias(const Eigen::DenseBase<OtherDerived>&) [with OtherDerived = Eigen::Product<Eigen::Transpose<Eigen::Matrix<double, -1, -1> >, Eigen::Matrix<double, -1, -1>, 0>; Derived = Eigen::Matrix<double, 3, 3>]’
/usr/include/eigen3/Eigen/src/Core/PlainObjectBase.h:537:7:   required from ‘Eigen::PlainObjectBase<Derived>::PlainObjectBase(const Eigen::DenseBase<OtherDerived>&) [with OtherDerived = Eigen::Product<Eigen::Transpose<Eigen::Matrix<double, -1, -1> >, Eigen::Matrix<double, -1, -1>, 0>; Derived = Eigen::Matrix<double, 3, 3>]’
/usr/include/eigen3/Eigen/src/Core/Matrix.h:377:29:   required from ‘Eigen::Matrix<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>::Matrix(const Eigen::EigenBase<OtherDerived>&) [with OtherDerived = Eigen::Product<Eigen::Transpose<Eigen::Matrix<double, -1, -1> >, Eigen::Matrix<double, -1, -1>, 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<const Eigen::Transpose<Eigen::Matrix<double, -1, -1> >, 1, -1, true>::Block(const Eigen::Block<const Eigen::Transpose<Eigen::Matrix<double, -1, -1> >, 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<const Eigen::Transpose<Eigen::Matrix<double, -1, -1> >, 1, -1, true>’ has user-provided ‘Eigen::BlockImpl<XprType, BlockRows, BlockCols, InnerPanel, Eigen::Dense>& Eigen::BlockImpl<XprType, BlockRows, BlockCols, InnerPanel, Eigen::Dense>::operator=(const Eigen::BlockImpl<XprType, BlockRows, BlockCols, InnerPanel, Eigen::Dense>&) [with XprType = const Eigen::Transpose<Eigen::Matrix<double, -1, -1> >; 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<BinaryOp, Lhs, Rhs>::CwiseBinaryOp(const Lhs&, const Rhs&, const BinaryOp&) [with BinaryOp = Eigen::internal::scalar_product_op<double, double>; LhsType = const Eigen::Transpose<const Eigen::Block<const Eigen::Transpose<Eigen::Matrix<double, -1, -1> >, 1, -1, true> >; RhsType = const Eigen::Block<const Eigen::Matrix<double, -1, -1>, -1, 1, true>; Eigen::CwiseBinaryOp<BinaryOp, Lhs, Rhs>::Lhs = Eigen::Transpose<const Eigen::Block<const Eigen::Transpose<Eigen::Matrix<double, -1, -1> >, 1, -1, true> >; Eigen::CwiseBinaryOp<BinaryOp, Lhs, Rhs>::Rhs = Eigen::Block<const Eigen::Matrix<double, -1, -1>, -1, 1, true>]’:
/usr/include/eigen3/Eigen/src/Core/../plugins/MatrixCwiseBinaryOps.h:25:10:   required from ‘const Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<typename Eigen::internal::traits<T>::Scalar, typename Eigen::internal::traits<OtherDerived>::Scalar>, const Derived, const OtherDerived> Eigen::MatrixBase<Derived>::cwiseProduct(const Eigen::MatrixBase<OtherDerived>&) const [with OtherDerived = Eigen::Block<const Eigen::Matrix<double, -1, -1>, -1, 1, true>; Derived = Eigen::Transpose<const Eigen::Block<const Eigen::Transpose<Eigen::Matrix<double, -1, -1> >, 1, -1, true> >; typename Eigen::internal::traits<OtherDerived>::Scalar = double; typename Eigen::internal::traits<T>::Scalar = double]’
/usr/include/eigen3/Eigen/src/Core/ProductEvaluators.h:552:72:   required from ‘const CoeffReturnType Eigen::internal::product_evaluator<Eigen::Product<Lhs, Rhs, 1>, ProductTag, Eigen::DenseShape, Eigen::DenseShape>::coeff(Eigen::Index, Eigen::Index) const [with Lhs = Eigen::Transpose<Eigen::Matrix<double, -1, -1> >; Rhs = Eigen::Matrix<double, -1, -1>; int ProductTag = 8; typename Eigen::internal::traits<typename Eigen::Product<Lhs, Rhs, 1>::Rhs>::Scalar = double; typename Eigen::internal::traits<typename Eigen::Product<Lhs, Rhs, 1>::Lhs>::Scalar = double; Eigen::internal::product_evaluator<Eigen::Product<Lhs, Rhs, 1>, 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<DstEvaluatorTypeT, SrcEvaluatorTypeT, Functor, Version>::assignCoeff(Eigen::Index, Eigen::Index) [with DstEvaluatorTypeT = Eigen::internal::evaluator<Eigen::Matrix<double, 3, 3> >; SrcEvaluatorTypeT = Eigen::internal::evaluator<Eigen::Product<Eigen::Transpose<Eigen::Matrix<double, -1, -1> >, Eigen::Matrix<double, -1, -1>, 1> >; Functor = Eigen::internal::assign_op<double, double>; 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<DstEvaluatorTypeT, SrcEvaluatorTypeT, Functor, Version>::assignCoeffByOuterInner(Eigen::Index, Eigen::Index) [with DstEvaluatorTypeT = Eigen::internal::evaluator<Eigen::Matrix<double, 3, 3> >; SrcEvaluatorTypeT = Eigen::internal::evaluator<Eigen::Product<Eigen::Transpose<Eigen::Matrix<double, -1, -1> >, Eigen::Matrix<double, -1, -1>, 1> >; Functor = Eigen::internal::assign_op<double, double>; 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<Kernel, 0, 0>::run(Kernel&) [with Kernel = Eigen::internal::generic_dense_assignment_kernel<Eigen::internal::evaluator<Eigen::Matrix<double, 3, 3> >, Eigen::internal::evaluator<Eigen::Product<Eigen::Transpose<Eigen::Matrix<double, -1, -1> >, Eigen::Matrix<double, -1, -1>, 1> >, Eigen::internal::assign_op<double, double>, 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<DstXprType, Eigen::Product<Lhs, Rhs, Options>, Eigen::internal::assign_op<Scalar, Scalar>, Eigen::internal::Dense2Dense, typename Eigen::internal::enable_if<((Options == Eigen::DefaultProduct) || (Options == Eigen::AliasFreeProduct))>::type>::run(DstXprType&, const SrcXprType&, const Eigen::internal::assign_op<Scalar, Scalar>&) [with DstXprType = Eigen::Matrix<double, 3, 3>; Lhs = Eigen::Transpose<Eigen::Matrix<double, -1, -1> >; Rhs = Eigen::Matrix<double, -1, -1>; int Options = 0; Scalar = double; Eigen::internal::Assignment<DstXprType, Eigen::Product<Lhs, Rhs, Options>, Eigen::internal::assign_op<Scalar, Scalar>, Eigen::internal::Dense2Dense, typename Eigen::internal::enable_if<((Options == Eigen::DefaultProduct) || (Options == Eigen::AliasFreeProduct))>::type>::SrcXprType = Eigen::Product<Eigen::Transpose<Eigen::Matrix<double, -1, -1> >, Eigen::Matrix<double, -1, -1>, 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<double, 3, 3>; Src = Eigen::Product<Eigen::Transpose<Eigen::Matrix<double, -1, -1> >, Eigen::Matrix<double, -1, -1>, 0>; Func = Eigen::internal::assign_op<double, double>]’
/usr/include/eigen3/Eigen/src/Core/PlainObjectBase.h:732:41:   required from ‘Derived& Eigen::PlainObjectBase<Derived>::_set_noalias(const Eigen::DenseBase<OtherDerived>&) [with OtherDerived = Eigen::Product<Eigen::Transpose<Eigen::Matrix<double, -1, -1> >, Eigen::Matrix<double, -1, -1>, 0>; Derived = Eigen::Matrix<double, 3, 3>]’
/usr/include/eigen3/Eigen/src/Core/PlainObjectBase.h:537:7:   required from ‘Eigen::PlainObjectBase<Derived>::PlainObjectBase(const Eigen::DenseBase<OtherDerived>&) [with OtherDerived = Eigen::Product<Eigen::Transpose<Eigen::Matrix<double, -1, -1> >, Eigen::Matrix<double, -1, -1>, 0>; Derived = Eigen::Matrix<double, 3, 3>]’
/usr/include/eigen3/Eigen/src/Core/Matrix.h:377:29:   required from ‘Eigen::Matrix<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>::Matrix(const Eigen::EigenBase<OtherDerived>&) [with OtherDerived = Eigen::Product<Eigen::Transpose<Eigen::Matrix<double, -1, -1> >, Eigen::Matrix<double, -1, -1>, 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<const Eigen::Block<const Eigen::Transpose<Eigen::Matrix<double, -1, -1> >, 1, -1, true> >::Transpose(const Eigen::Transpose<const Eigen::Block<const Eigen::Transpose<Eigen::Matrix<double, -1, -1> >, 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<const Eigen::Block<const Eigen::Transpose<Eigen::Matrix<double, -1, -1> >, 1, -1, true> >’ has user-provided ‘Derived& Eigen::MatrixBase<Derived>::operator=(const Eigen::MatrixBase<Derived>&) [with Derived = Eigen::Transpose<const Eigen::Block<const Eigen::Transpose<Eigen::Matrix<double, -1, -1> >, 1, -1, true> >]’
   55 | EIGEN_STRONG_INLINE Derived& MatrixBase<Derived>::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<const Eigen::Matrix<double, -1, -1>, -1, 1, true>::Block(const Eigen::Block<const Eigen::Matrix<double, -1, -1>, -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<const Eigen::Matrix<double, -1, -1>, -1, 1, true>’ has user-provided ‘Eigen::BlockImpl<XprType, BlockRows, BlockCols, InnerPanel, Eigen::Dense>& Eigen::BlockImpl<XprType, BlockRows, BlockCols, InnerPanel, Eigen::Dense>::operator=(const Eigen::BlockImpl<XprType, BlockRows, BlockCols, InnerPanel, Eigen::Dense>&) [with XprType = const Eigen::Matrix<double, -1, -1>; 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<XprType, BlockRows, BlockCols, InnerPanel, true>::BlockImpl_dense(XprType&, Eigen::Index) [with XprType = const Eigen::Transpose<Eigen::Matrix<double, -1, -1> >; 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<XprType, BlockRows, BlockCols, InnerPanel, Eigen::Dense>::BlockImpl(XprType&, Eigen::Index) [with XprType = const Eigen::Transpose<Eigen::Matrix<double, -1, -1> >; 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<XprType, BlockRows, BlockCols, InnerPanel>::Block(XprType&, Eigen::Index) [with XprType = const Eigen::Transpose<Eigen::Matrix<double, -1, -1> >; 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<Derived>::ConstRowXpr Eigen::DenseBase<Derived>::row(Eigen::Index) const [with Derived = Eigen::Transpose<Eigen::Matrix<double, -1, -1> >; Eigen::DenseBase<Derived>::ConstRowXpr = const Eigen::Block<const Eigen::Transpose<Eigen::Matrix<double, -1, -1> >, 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<Eigen::Product<Lhs, Rhs, 1>, ProductTag, Eigen::DenseShape, Eigen::DenseShape>::coeff(Eigen::Index, Eigen::Index) const [with Lhs = Eigen::Transpose<Eigen::Matrix<double, -1, -1> >; Rhs = Eigen::Matrix<double, -1, -1>; int ProductTag = 8; typename Eigen::internal::traits<typename Eigen::Product<Lhs, Rhs, 1>::Rhs>::Scalar = double; typename Eigen::internal::traits<typename Eigen::Product<Lhs, Rhs, 1>::Lhs>::Scalar = double; Eigen::internal::product_evaluator<Eigen::Product<Lhs, Rhs, 1>, 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<DstEvaluatorTypeT, SrcEvaluatorTypeT, Functor, Version>::assignCoeff(Eigen::Index, Eigen::Index) [with DstEvaluatorTypeT = Eigen::internal::evaluator<Eigen::Matrix<double, 3, 3> >; SrcEvaluatorTypeT = Eigen::internal::evaluator<Eigen::Product<Eigen::Transpose<Eigen::Matrix<double, -1, -1> >, Eigen::Matrix<double, -1, -1>, 1> >; Functor = Eigen::internal::assign_op<double, double>; 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<DstXprType, Eigen::Product<Lhs, Rhs, Options>, Eigen::internal::assign_op<Scalar, Scalar>, Eigen::internal::Dense2Dense, typename Eigen::internal::enable_if<((Options == Eigen::DefaultProduct) || (Options == Eigen::AliasFreeProduct))>::type>::run(DstXprType&, const SrcXprType&, const Eigen::internal::assign_op<Scalar, Scalar>&) [with DstXprType = Eigen::Matrix<double, 3, 3>; Lhs = Eigen::Transpose<Eigen::Matrix<double, -1, -1> >; Rhs = Eigen::Matrix<double, -1, -1>; int Options = 0; Scalar = double; Eigen::internal::Assignment<DstXprType, Eigen::Product<Lhs, Rhs, Options>, Eigen::internal::assign_op<Scalar, Scalar>, Eigen::internal::Dense2Dense, typename Eigen::internal::enable_if<((Options == Eigen::DefaultProduct) || (Options == Eigen::AliasFreeProduct))>::type>::SrcXprType = Eigen::Product<Eigen::Transpose<Eigen::Matrix<double, -1, -1> >, Eigen::Matrix<double, -1, -1>, 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<double, 3, 3>; Src = Eigen::Product<Eigen::Transpose<Eigen::Matrix<double, -1, -1> >, Eigen::Matrix<double, -1, -1>, 0>; Func = Eigen::internal::assign_op<double, double>]’
/usr/include/eigen3/Eigen/src/Core/PlainObjectBase.h:732:41:   required from ‘Derived& Eigen::PlainObjectBase<Derived>::_set_noalias(const Eigen::DenseBase<OtherDerived>&) [with OtherDerived = Eigen::Product<Eigen::Transpose<Eigen::Matrix<double, -1, -1> >, Eigen::Matrix<double, -1, -1>, 0>; Derived = Eigen::Matrix<double, 3, 3>]’
/usr/include/eigen3/Eigen/src/Core/PlainObjectBase.h:537:7:   required from ‘Eigen::PlainObjectBase<Derived>::PlainObjectBase(const Eigen::DenseBase<OtherDerived>&) [with OtherDerived = Eigen::Product<Eigen::Transpose<Eigen::Matrix<double, -1, -1> >, Eigen::Matrix<double, -1, -1>, 0>; Derived = Eigen::Matrix<double, 3, 3>]’
/usr/include/eigen3/Eigen/src/Core/Matrix.h:377:29:   required from ‘Eigen::Matrix<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>::Matrix(const Eigen::EigenBase<OtherDerived>&) [with OtherDerived = Eigen::Product<Eigen::Transpose<Eigen::Matrix<double, -1, -1> >, Eigen::Matrix<double, -1, -1>, 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<Eigen::Matrix<double, -1, -1> >::Transpose(const Eigen::Transpose<Eigen::Matrix<double, -1, -1> >&)’ 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<Eigen::Matrix<double, -1, -1> >’ has user-provided ‘Derived& Eigen::MatrixBase<Derived>::operator=(const Eigen::MatrixBase<Derived>&) [with Derived = Eigen::Transpose<Eigen::Matrix<double, -1, -1> >]’
   55 | EIGEN_STRONG_INLINE Derived& MatrixBase<Derived>::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<Derived>::normalized() const [with Derived = Eigen::CwiseBinaryOp<Eigen::internal::scalar_difference_op<double, double>, const Eigen::Matrix<double, 3, 1>, const Eigen::Matrix<double, 3, 1> >; Eigen::MatrixBase<Derived>::PlainObject = Eigen::Matrix<double, 3, 1>]’:
/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<Eigen::internal::scalar_difference_op<double, double>, const Eigen::Matrix<double, 3, 1>, const Eigen::Matrix<double, 3, 1> >::CwiseBinaryOp(const Eigen::CwiseBinaryOp<Eigen::internal::scalar_difference_op<double, double>, const Eigen::Matrix<double, 3, 1>, const Eigen::Matrix<double, 3, 1> >&)’ 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<MatrixType>::Transpose(MatrixType&) [with MatrixType = const Eigen::Block<const Eigen::Matrix<double, 3, 3>, 1, 3, false>]’:
/usr/include/eigen3/Eigen/src/Core/Transpose.h:186:10:   required from ‘Eigen::DenseBase<Derived>::ConstTransposeReturnType Eigen::DenseBase<Derived>::transpose() const [with Derived = Eigen::Block<const Eigen::Matrix<double, 3, 3>, 1, 3, false>; Eigen::DenseBase<Derived>::ConstTransposeReturnType = const Eigen::Transpose<const Eigen::Block<const Eigen::Matrix<double, 3, 3>, 1, 3, false> >]’
/usr/include/eigen3/Eigen/src/Core/ProductEvaluators.h:552:40:   required from ‘const CoeffReturnType Eigen::internal::product_evaluator<Eigen::Product<Lhs, Rhs, 1>, ProductTag, Eigen::DenseShape, Eigen::DenseShape>::coeff(Eigen::Index, Eigen::Index) const [with Lhs = Eigen::Matrix<double, 3, 3>; Rhs = Eigen::Matrix<double, 3, 1>; int ProductTag = 3; typename Eigen::internal::traits<typename Eigen::Product<Lhs, Rhs, 1>::Rhs>::Scalar = double; typename Eigen::internal::traits<typename Eigen::Product<Lhs, Rhs, 1>::Lhs>::Scalar = double; Eigen::internal::product_evaluator<Eigen::Product<Lhs, Rhs, 1>, 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<DstEvaluatorTypeT, SrcEvaluatorTypeT, Functor, Version>::assignCoeff(Eigen::Index, Eigen::Index) [with DstEvaluatorTypeT = Eigen::internal::evaluator<Eigen::Matrix<double, 3, 1> >; SrcEvaluatorTypeT = Eigen::internal::evaluator<Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 1>, 1> >; Functor = Eigen::internal::assign_op<double, double>; 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<DstEvaluatorTypeT, SrcEvaluatorTypeT, Functor, Version>::assignCoeffByOuterInner(Eigen::Index, Eigen::Index) [with DstEvaluatorTypeT = Eigen::internal::evaluator<Eigen::Matrix<double, 3, 1> >; SrcEvaluatorTypeT = Eigen::internal::evaluator<Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 1>, 1> >; Functor = Eigen::internal::assign_op<double, double>; 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<Kernel, Index, Stop>::run(Kernel&) [with Kernel = Eigen::internal::generic_dense_assignment_kernel<Eigen::internal::evaluator<Eigen::Matrix<double, 3, 1> >, Eigen::internal::evaluator<Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 1>, 1> >, Eigen::internal::assign_op<double, double>, 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<DstXprType, SrcXprType, Functor, Eigen::internal::Dense2Dense, Weak>::run(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen::Matrix<double, 3, 1>; SrcXprType = Eigen::CwiseBinaryOp<Eigen::internal::scalar_sum_op<double, double>, const Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 1>, 0>, const Eigen::Matrix<double, 3, 1> >; Functor = Eigen::internal::assign_op<double, double>; 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<double, 3, 1>; Src = Eigen::CwiseBinaryOp<Eigen::internal::scalar_sum_op<double, double>, const Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 1>, 0>, const Eigen::Matrix<double, 3, 1> >; Func = Eigen::internal::assign_op<double, double>]’
/usr/include/eigen3/Eigen/src/Core/PlainObjectBase.h:732:41:   required from ‘Derived& Eigen::PlainObjectBase<Derived>::_set_noalias(const Eigen::DenseBase<OtherDerived>&) [with OtherDerived = Eigen::CwiseBinaryOp<Eigen::internal::scalar_sum_op<double, double>, const Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 1>, 0>, const Eigen::Matrix<double, 3, 1> >; Derived = Eigen::Matrix<double, 3, 1>]’
/usr/include/eigen3/Eigen/src/Core/PlainObjectBase.h:537:7:   required from ‘Eigen::PlainObjectBase<Derived>::PlainObjectBase(const Eigen::DenseBase<OtherDerived>&) [with OtherDerived = Eigen::CwiseBinaryOp<Eigen::internal::scalar_sum_op<double, double>, const Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 1>, 0>, const Eigen::Matrix<double, 3, 1> >; Derived = Eigen::Matrix<double, 3, 1>]’
/usr/include/eigen3/Eigen/src/Core/Matrix.h:377:29:   required from ‘Eigen::Matrix<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>::Matrix(const Eigen::EigenBase<OtherDerived>&) [with OtherDerived = Eigen::CwiseBinaryOp<Eigen::internal::scalar_sum_op<double, double>, const Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 1>, 0>, const Eigen::Matrix<double, 3, 1> >; _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<const Eigen::Matrix<double, 3, 3>, 1, 3, false>::Block(const Eigen::Block<const Eigen::Matrix<double, 3, 3>, 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<const Eigen::Matrix<double, 3, 3>, 1, 3, false>’ has user-provided ‘Eigen::BlockImpl<XprType, BlockRows, BlockCols, InnerPanel, Eigen::Dense>& Eigen::BlockImpl<XprType, BlockRows, BlockCols, InnerPanel, Eigen::Dense>::operator=(const Eigen::BlockImpl<XprType, BlockRows, BlockCols, InnerPanel, Eigen::Dense>&) [with XprType = const Eigen::Matrix<double, 3, 3>; 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<BinaryOp, Lhs, Rhs>::CwiseBinaryOp(const Lhs&, const Rhs&, const BinaryOp&) [with BinaryOp = Eigen::internal::scalar_product_op<double, double>; LhsType = const Eigen::Transpose<const Eigen::Block<const Eigen::Matrix<double, 3, 3>, 1, 3, false> >; RhsType = const Eigen::Block<const Eigen::Matrix<double, 3, 1>, 3, 1, true>; Eigen::CwiseBinaryOp<BinaryOp, Lhs, Rhs>::Lhs = Eigen::Transpose<const Eigen::Block<const Eigen::Matrix<double, 3, 3>, 1, 3, false> >; Eigen::CwiseBinaryOp<BinaryOp, Lhs, Rhs>::Rhs = Eigen::Block<const Eigen::Matrix<double, 3, 1>, 3, 1, true>]’:
/usr/include/eigen3/Eigen/src/Core/../plugins/MatrixCwiseBinaryOps.h:25:10:   required from ‘const Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<typename Eigen::internal::traits<T>::Scalar, typename Eigen::internal::traits<OtherDerived>::Scalar>, const Derived, const OtherDerived> Eigen::MatrixBase<Derived>::cwiseProduct(const Eigen::MatrixBase<OtherDerived>&) const [with OtherDerived = Eigen::Block<const Eigen::Matrix<double, 3, 1>, 3, 1, true>; Derived = Eigen::Transpose<const Eigen::Block<const Eigen::Matrix<double, 3, 3>, 1, 3, false> >; typename Eigen::internal::traits<OtherDerived>::Scalar = double; typename Eigen::internal::traits<T>::Scalar = double]’
/usr/include/eigen3/Eigen/src/Core/ProductEvaluators.h:552:72:   required from ‘const CoeffReturnType Eigen::internal::product_evaluator<Eigen::Product<Lhs, Rhs, 1>, ProductTag, Eigen::DenseShape, Eigen::DenseShape>::coeff(Eigen::Index, Eigen::Index) const [with Lhs = Eigen::Matrix<double, 3, 3>; Rhs = Eigen::Matrix<double, 3, 1>; int ProductTag = 3; typename Eigen::internal::traits<typename Eigen::Product<Lhs, Rhs, 1>::Rhs>::Scalar = double; typename Eigen::internal::traits<typename Eigen::Product<Lhs, Rhs, 1>::Lhs>::Scalar = double; Eigen::internal::product_evaluator<Eigen::Product<Lhs, Rhs, 1>, 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<DstEvaluatorTypeT, SrcEvaluatorTypeT, Functor, Version>::assignCoeff(Eigen::Index, Eigen::Index) [with DstEvaluatorTypeT = Eigen::internal::evaluator<Eigen::Matrix<double, 3, 1> >; SrcEvaluatorTypeT = Eigen::internal::evaluator<Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 1>, 1> >; Functor = Eigen::internal::assign_op<double, double>; 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<DstEvaluatorTypeT, SrcEvaluatorTypeT, Functor, Version>::assignCoeffByOuterInner(Eigen::Index, Eigen::Index) [with DstEvaluatorTypeT = Eigen::internal::evaluator<Eigen::Matrix<double, 3, 1> >; SrcEvaluatorTypeT = Eigen::internal::evaluator<Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 1>, 1> >; Functor = Eigen::internal::assign_op<double, double>; 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<Kernel, Index, Stop>::run(Kernel&) [with Kernel = Eigen::internal::generic_dense_assignment_kernel<Eigen::internal::evaluator<Eigen::Matrix<double, 3, 1> >, Eigen::internal::evaluator<Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 1>, 1> >, Eigen::internal::assign_op<double, double>, 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<DstXprType, SrcXprType, Functor, Eigen::internal::Dense2Dense, Weak>::run(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen::Matrix<double, 3, 1>; SrcXprType = Eigen::CwiseBinaryOp<Eigen::internal::scalar_sum_op<double, double>, const Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 1>, 0>, const Eigen::Matrix<double, 3, 1> >; Functor = Eigen::internal::assign_op<double, double>; 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<double, 3, 1>; Src = Eigen::CwiseBinaryOp<Eigen::internal::scalar_sum_op<double, double>, const Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 1>, 0>, const Eigen::Matrix<double, 3, 1> >; Func = Eigen::internal::assign_op<double, double>]’
/usr/include/eigen3/Eigen/src/Core/PlainObjectBase.h:732:41:   required from ‘Derived& Eigen::PlainObjectBase<Derived>::_set_noalias(const Eigen::DenseBase<OtherDerived>&) [with OtherDerived = Eigen::CwiseBinaryOp<Eigen::internal::scalar_sum_op<double, double>, const Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 1>, 0>, const Eigen::Matrix<double, 3, 1> >; Derived = Eigen::Matrix<double, 3, 1>]’
/usr/include/eigen3/Eigen/src/Core/PlainObjectBase.h:537:7:   required from ‘Eigen::PlainObjectBase<Derived>::PlainObjectBase(const Eigen::DenseBase<OtherDerived>&) [with OtherDerived = Eigen::CwiseBinaryOp<Eigen::internal::scalar_sum_op<double, double>, const Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 1>, 0>, const Eigen::Matrix<double, 3, 1> >; Derived = Eigen::Matrix<double, 3, 1>]’
/usr/include/eigen3/Eigen/src/Core/Matrix.h:377:29:   required from ‘Eigen::Matrix<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>::Matrix(const Eigen::EigenBase<OtherDerived>&) [with OtherDerived = Eigen::CwiseBinaryOp<Eigen::internal::scalar_sum_op<double, double>, const Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 1>, 0>, const Eigen::Matrix<double, 3, 1> >; _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<const Eigen::Block<const Eigen::Matrix<double, 3, 3>, 1, 3, false> >::Transpose(const Eigen::Transpose<const Eigen::Block<const Eigen::Matrix<double, 3, 3>, 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<const Eigen::Block<const Eigen::Matrix<double, 3, 3>, 1, 3, false> >’ has user-provided ‘Derived& Eigen::MatrixBase<Derived>::operator=(const Eigen::MatrixBase<Derived>&) [with Derived = Eigen::Transpose<const Eigen::Block<const Eigen::Matrix<double, 3, 3>, 1, 3, false> >]’
   55 | EIGEN_STRONG_INLINE Derived& MatrixBase<Derived>::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<const Eigen::Matrix<double, 3, 1>, 3, 1, true>::Block(const Eigen::Block<const Eigen::Matrix<double, 3, 1>, 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<const Eigen::Matrix<double, 3, 1>, 3, 1, true>’ has user-provided ‘Eigen::BlockImpl<XprType, BlockRows, BlockCols, InnerPanel, Eigen::Dense>& Eigen::BlockImpl<XprType, BlockRows, BlockCols, InnerPanel, Eigen::Dense>::operator=(const Eigen::BlockImpl<XprType, BlockRows, BlockCols, InnerPanel, Eigen::Dense>&) [with XprType = const Eigen::Matrix<double, 3, 1>; 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<Lhs, Rhs, Option>::Product(const Lhs&, const Rhs&) [with _Lhs = Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 3>, 0>; _Rhs = Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >; int Option = 0; Eigen::Product<Lhs, Rhs, Option>::Lhs = Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 3>, 0>; Eigen::Product<Lhs, Rhs, Option>::Rhs = Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >]’:
/usr/include/eigen3/Eigen/src/Core/GeneralProduct.h:415:10:   required from ‘const Eigen::Product<Derived, OtherDerived> Eigen::MatrixBase<Derived>::operator*(const Eigen::MatrixBase<OtherDerived>&) const [with OtherDerived = Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >; Derived = Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 3>, 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<const Eigen::Matrix<double, 3, 3> >::Transpose(const Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >&)’ 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<const Eigen::Matrix<double, 3, 3> >’ has user-provided ‘Derived& Eigen::MatrixBase<Derived>::operator=(const Eigen::MatrixBase<Derived>&) [with Derived = Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >]’
   55 | EIGEN_STRONG_INLINE Derived& MatrixBase<Derived>::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<BinaryOp, Lhs, Rhs>::CwiseBinaryOp(const Lhs&, const Rhs&, const BinaryOp&) [with BinaryOp = Eigen::internal::scalar_quotient_op<double, double>; LhsType = const Eigen::Block<const Eigen::Matrix<double, 3, 3>, -1, -1, false>; RhsType = const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Matrix<double, -1, -1, 0, 3, 3> >; Eigen::CwiseBinaryOp<BinaryOp, Lhs, Rhs>::Lhs = Eigen::Block<const Eigen::Matrix<double, 3, 3>, -1, -1, false>; Eigen::CwiseBinaryOp<BinaryOp, Lhs, Rhs>::Rhs = Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Matrix<double, -1, -1, 0, 3, 3> >]’:
/usr/include/eigen3/Eigen/src/Core/../plugins/CommonCwiseBinaryOps.h:69:1:   required from ‘typename Eigen::internal::enable_if<true, const Eigen::CwiseBinaryOp<Eigen::internal::scalar_quotient_op<typename Eigen::internal::traits<T>::Scalar, typename Eigen::internal::promote_scalar_arg<typename Eigen::internal::traits<T>::Scalar, T, Eigen::internal::has_ReturnType<Eigen::ScalarBinaryOpTraits<typename Eigen::internal::traits<T>::Scalar, T, Eigen::internal::scalar_quotient_op<typename Eigen::internal::traits<T>::Scalar, T> > >::value>::type>, const Derived, const typename Eigen::internal::plain_constant_type<Derived, typename Eigen::internal::promote_scalar_arg<typename Eigen::internal::traits<T>::Scalar, T, Eigen::internal::has_ReturnType<Eigen::ScalarBinaryOpTraits<typename Eigen::internal::traits<T>::Scalar, T, Eigen::internal::scalar_quotient_op<typename Eigen::internal::traits<T>::Scalar, T> > >::value>::type>::type> >::type Eigen::MatrixBase<Derived>::operator/(const T&) const [with T = double; Derived = Eigen::Block<const Eigen::Matrix<double, 3, 3>, -1, -1, false>; typename Eigen::internal::enable_if<true, const Eigen::CwiseBinaryOp<Eigen::internal::scalar_quotient_op<typename Eigen::internal::traits<T>::Scalar, typename Eigen::internal::promote_scalar_arg<typename Eigen::internal::traits<T>::Scalar, T, Eigen::internal::has_ReturnType<Eigen::ScalarBinaryOpTraits<typename Eigen::internal::traits<T>::Scalar, T, Eigen::internal::scalar_quotient_op<typename Eigen::internal::traits<T>::Scalar, T> > >::value>::type>, const Derived, const typename Eigen::internal::plain_constant_type<Derived, typename Eigen::internal::promote_scalar_arg<typename Eigen::internal::traits<T>::Scalar, T, Eigen::internal::has_ReturnType<Eigen::ScalarBinaryOpTraits<typename Eigen::internal::traits<T>::Scalar, T, Eigen::internal::scalar_quotient_op<typename Eigen::internal::traits<T>::Scalar, T> > >::value>::type>::type> >::type = const Eigen::CwiseBinaryOp<Eigen::internal::scalar_quotient_op<double, double>, const Eigen::Block<const Eigen::Matrix<double, 3, 3>, -1, -1, false>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Matrix<double, -1, -1, 0, 3, 3> > >]’
/usr/include/eigen3/Eigen/src/SVD/JacobiSVD.h:689:60:   required from ‘Eigen::JacobiSVD<MatrixType, QRPreconditioner>& Eigen::JacobiSVD<MatrixType, QRPreconditioner>::compute(const MatrixType&, unsigned int) [with _MatrixType = Eigen::Matrix<double, 3, 3>; int QRPreconditioner = 2; Eigen::JacobiSVD<MatrixType, QRPreconditioner>::MatrixType = Eigen::Matrix<double, 3, 3>]’
/usr/include/eigen3/Eigen/src/SVD/JacobiSVD.h:548:7:   required from ‘Eigen::JacobiSVD<MatrixType, QRPreconditioner>::JacobiSVD(const MatrixType&, unsigned int) [with _MatrixType = Eigen::Matrix<double, 3, 3>; int QRPreconditioner = 2; Eigen::JacobiSVD<MatrixType, QRPreconditioner>::MatrixType = Eigen::Matrix<double, 3, 3>]’
/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<const Eigen::Matrix<double, 3, 3>, -1, -1, false>::Block(const Eigen::Block<const Eigen::Matrix<double, 3, 3>, -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<const Eigen::Matrix<double, 3, 3>, -1, -1, false>’ has user-provided ‘Eigen::BlockImpl<XprType, BlockRows, BlockCols, InnerPanel, Eigen::Dense>& Eigen::BlockImpl<XprType, BlockRows, BlockCols, InnerPanel, Eigen::Dense>::operator=(const Eigen::BlockImpl<XprType, BlockRows, BlockCols, InnerPanel, Eigen::Dense>&) [with XprType = const Eigen::Matrix<double, 3, 3>; 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<UnaryOp, MatrixType>::CwiseUnaryOp(const XprType&, const UnaryOp&) [with UnaryOp = Eigen::internal::scalar_opposite_op<double>; XprType = const Eigen::Block<Eigen::Matrix<double, 3, 3>, 3, 1, true>]’:
/usr/include/eigen3/Eigen/src/Core/../plugins/CommonCwiseUnaryOps.h:45:28:   required from ‘const NegativeReturnType Eigen::MatrixBase<Derived>::operator-() const [with Derived = Eigen::Block<Eigen::Matrix<double, 3, 3>, 3, 1, true>; Eigen::MatrixBase<Derived>::NegativeReturnType = Eigen::CwiseUnaryOp<Eigen::internal::scalar_opposite_op<double>, const Eigen::Block<Eigen::Matrix<double, 3, 3>, 3, 1, true> >; typename Eigen::internal::traits<T>::Scalar = double]’
/usr/include/eigen3/Eigen/src/SVD/JacobiSVD.h:757:62:   required from ‘Eigen::JacobiSVD<MatrixType, QRPreconditioner>& Eigen::JacobiSVD<MatrixType, QRPreconditioner>::compute(const MatrixType&, unsigned int) [with _MatrixType = Eigen::Matrix<double, 3, 3>; int QRPreconditioner = 2; Eigen::JacobiSVD<MatrixType, QRPreconditioner>::MatrixType = Eigen::Matrix<double, 3, 3>]’
/usr/include/eigen3/Eigen/src/SVD/JacobiSVD.h:548:7:   required from ‘Eigen::JacobiSVD<MatrixType, QRPreconditioner>::JacobiSVD(const MatrixType&, unsigned int) [with _MatrixType = Eigen::Matrix<double, 3, 3>; int QRPreconditioner = 2; Eigen::JacobiSVD<MatrixType, QRPreconditioner>::MatrixType = Eigen::Matrix<double, 3, 3>]’
/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<Eigen::Matrix<double, 3, 3>, 3, 1, true>::Block(const Eigen::Block<Eigen::Matrix<double, 3, 3>, 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<Eigen::Matrix<double, 3, 3>, 3, 1, true>’ has user-provided ‘Eigen::BlockImpl<XprType, BlockRows, BlockCols, InnerPanel, Eigen::Dense>& Eigen::BlockImpl<XprType, BlockRows, BlockCols, InnerPanel, Eigen::Dense>::operator=(const Eigen::BlockImpl<XprType, BlockRows, BlockCols, InnerPanel, Eigen::Dense>&) [with XprType = Eigen::Matrix<double, 3, 3>; 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<Lhs, Rhs, Option>::Product(const Lhs&, const Rhs&) [with _Lhs = Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 3>, 0>; _Rhs = Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >; int Option = 1; Eigen::Product<Lhs, Rhs, Option>::Lhs = Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 3>, 0>; Eigen::Product<Lhs, Rhs, Option>::Rhs = Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >]’:
/usr/include/eigen3/Eigen/src/Core/GeneralProduct.h:450:10:   required from ‘const Eigen::Product<Derived, OtherDerived, 1> Eigen::MatrixBase<Derived>::lazyProduct(const Eigen::MatrixBase<OtherDerived>&) const [with OtherDerived = Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >; Derived = Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 3>, 0>]’
/usr/include/eigen3/Eigen/src/Core/ProductEvaluators.h:397:29:   required from ‘static void Eigen::internal::generic_product_impl<Lhs, Rhs, Eigen::DenseShape, Eigen::DenseShape, 3>::evalTo(Dst&, const Lhs&, const Rhs&) [with Dst = Eigen::Matrix<double, 3, 3, 1, 3, 3>; Lhs = Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 3>, 0>; Rhs = Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >]’
/usr/include/eigen3/Eigen/src/Core/ProductEvaluators.h:148:43:   required from ‘static void Eigen::internal::Assignment<DstXprType, Eigen::Product<Lhs, Rhs, Options>, Eigen::internal::assign_op<Scalar, Scalar>, Eigen::internal::Dense2Dense, typename Eigen::internal::enable_if<((Options == Eigen::DefaultProduct) || (Options == Eigen::AliasFreeProduct))>::type>::run(DstXprType&, const SrcXprType&, const Eigen::internal::assign_op<Scalar, Scalar>&) [with DstXprType = Eigen::Matrix<double, 3, 3, 1, 3, 3>; Lhs = Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 3>, 0>; Rhs = Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >; int Options = 0; Scalar = double; Eigen::internal::Assignment<DstXprType, Eigen::Product<Lhs, Rhs, Options>, Eigen::internal::assign_op<Scalar, Scalar>, Eigen::internal::Dense2Dense, typename Eigen::internal::enable_if<((Options == Eigen::DefaultProduct) || (Options == Eigen::AliasFreeProduct))>::type>::SrcXprType = Eigen::Product<Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 3>, 0>, Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >, 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<double, 3, 3, 1, 3, 3>; Src = Eigen::Product<Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 3>, 0>, Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >, 0>; Func = Eigen::internal::assign_op<double, double>]’
/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::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 3>, 0>, Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >, 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<Eigen::internal::evaluator_assume_aliasing<Src>::value, void*>::type) [with Dst = Eigen::Matrix<double, 3, 3>; Src = Eigen::Product<Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 3>, 0>, Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >, 0>; Func = Eigen::internal::assign_op<double, double>; typename Eigen::internal::enable_if<Eigen::internal::evaluator_assume_aliasing<Src>::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<double, 3, 3>; Src = Eigen::Product<Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 3>, 0>, Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >, 0>]’
/usr/include/eigen3/Eigen/src/Core/PlainObjectBase.h:714:32:   required from ‘Derived& Eigen::PlainObjectBase<Derived>::_set(const Eigen::DenseBase<OtherDerived>&) [with OtherDerived = Eigen::Product<Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 3>, 0>, Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >, 0>; Derived = Eigen::Matrix<double, 3, 3>]’
/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<OtherDerived>&) [with OtherDerived = Eigen::Product<Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 3>, 0>, Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >, 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<const Eigen::Matrix<double, 3, 3> >::Transpose(const Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >&)’ 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<const Eigen::Matrix<double, 3, 3> >’ has user-provided ‘Derived& Eigen::MatrixBase<Derived>::operator=(const Eigen::MatrixBase<Derived>&) [with Derived = Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >]’
   55 | EIGEN_STRONG_INLINE Derived& MatrixBase<Derived>::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<Eigen::Product<Lhs, Rhs, 1>, ProductTag, Eigen::DenseShape, Eigen::DenseShape>::product_evaluator(const XprType&) [with Lhs = Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 3>, 0>; Rhs = Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >; int ProductTag = 3; typename Eigen::internal::traits<typename Eigen::Product<Lhs, Rhs, 1>::Rhs>::Scalar = double; typename Eigen::internal::traits<typename Eigen::Product<Lhs, Rhs, 1>::Lhs>::Scalar = double; Eigen::internal::product_evaluator<Eigen::Product<Lhs, Rhs, 1>, ProductTag, Eigen::DenseShape, Eigen::DenseShape>::XprType = Eigen::Product<Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 3>, 0>, Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >, 1>]’:
/usr/include/eigen3/Eigen/src/Core/ProductEvaluators.h:35:90:   required from ‘Eigen::internal::evaluator<Eigen::Product<Lhs, Rhs, Option> >::evaluator(const XprType&) [with Lhs = Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 3>, 0>; Rhs = Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >; int Options = 1; Eigen::internal::evaluator<Eigen::Product<Lhs, Rhs, Option> >::XprType = Eigen::Product<Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 3>, 0>, Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >, 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<double, 3, 3, 1, 3, 3>; SrcXprType = Eigen::Product<Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 3>, 0>, Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >, 1>; Functor = Eigen::internal::assign_op<double, double>]’
/usr/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:31:   required from ‘static void Eigen::internal::Assignment<DstXprType, SrcXprType, Functor, Eigen::internal::Dense2Dense, Weak>::run(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen::Matrix<double, 3, 3, 1, 3, 3>; SrcXprType = Eigen::Product<Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 3>, 0>, Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >, 1>; Functor = Eigen::internal::assign_op<double, double>; 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<double, 3, 3, 1, 3, 3>; Src = Eigen::Product<Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 3>, 0>, Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >, 1>; Func = Eigen::internal::assign_op<double, double>]’
/usr/include/eigen3/Eigen/src/Core/ProductEvaluators.h:397:29:   required from ‘static void Eigen::internal::generic_product_impl<Lhs, Rhs, Eigen::DenseShape, Eigen::DenseShape, 3>::evalTo(Dst&, const Lhs&, const Rhs&) [with Dst = Eigen::Matrix<double, 3, 3, 1, 3, 3>; Lhs = Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 3>, 0>; Rhs = Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >]’
/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::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 3>, 0>, Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >, 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<Eigen::internal::evaluator_assume_aliasing<Src>::value, void*>::type) [with Dst = Eigen::Matrix<double, 3, 3>; Src = Eigen::Product<Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 3>, 0>, Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >, 0>; Func = Eigen::internal::assign_op<double, double>; typename Eigen::internal::enable_if<Eigen::internal::evaluator_assume_aliasing<Src>::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<double, 3, 3>; Src = Eigen::Product<Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 3>, 0>, Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >, 0>]’
/usr/include/eigen3/Eigen/src/Core/PlainObjectBase.h:714:32:   required from ‘Derived& Eigen::PlainObjectBase<Derived>::_set(const Eigen::DenseBase<OtherDerived>&) [with OtherDerived = Eigen::Product<Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 3>, 0>, Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >, 0>; Derived = Eigen::Matrix<double, 3, 3>]’
/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<OtherDerived>&) [with OtherDerived = Eigen::Product<Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 3>, 0>, Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >, 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<const Eigen::Matrix<double, 3, 3> >::Transpose(const Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >&)’ 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<const Eigen::Matrix<double, 3, 3> >’ has user-provided ‘Derived& Eigen::MatrixBase<Derived>::operator=(const Eigen::MatrixBase<Derived>&) [with Derived = Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >]’
   55 | EIGEN_STRONG_INLINE Derived& MatrixBase<Derived>::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<MatrixType>::Transpose(MatrixType&) [with MatrixType = const Eigen::Block<const Eigen::Matrix<double, 3, 3>, 1, 3, false>]’:
/usr/include/eigen3/Eigen/src/Core/Transpose.h:186:10:   required from ‘Eigen::DenseBase<Derived>::ConstTransposeReturnType Eigen::DenseBase<Derived>::transpose() const [with Derived = Eigen::Block<const Eigen::Matrix<double, 3, 3>, 1, 3, false>; Eigen::DenseBase<Derived>::ConstTransposeReturnType = const Eigen::Transpose<const Eigen::Block<const Eigen::Matrix<double, 3, 3>, 1, 3, false> >]’
/usr/include/eigen3/Eigen/src/Core/ProductEvaluators.h:552:40:   required from ‘const CoeffReturnType Eigen::internal::product_evaluator<Eigen::Product<Lhs, Rhs, 1>, ProductTag, Eigen::DenseShape, Eigen::DenseShape>::coeff(Eigen::Index, Eigen::Index) const [with Lhs = Eigen::Matrix<double, 3, 3>; Rhs = Eigen::Matrix<double, 3, 1>; int ProductTag = 3; typename Eigen::internal::traits<typename Eigen::Product<Lhs, Rhs, 1>::Rhs>::Scalar = double; typename Eigen::internal::traits<typename Eigen::Product<Lhs, Rhs, 1>::Lhs>::Scalar = double; Eigen::internal::product_evaluator<Eigen::Product<Lhs, Rhs, 1>, 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<DstEvaluatorTypeT, SrcEvaluatorTypeT, Functor, Version>::assignCoeff(Eigen::Index, Eigen::Index) [with DstEvaluatorTypeT = Eigen::internal::evaluator<Eigen::Matrix<double, 3, 1> >; SrcEvaluatorTypeT = Eigen::internal::evaluator<Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 1>, 1> >; Functor = Eigen::internal::assign_op<double, double>; 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<DstEvaluatorTypeT, SrcEvaluatorTypeT, Functor, Version>::assignCoeffByOuterInner(Eigen::Index, Eigen::Index) [with DstEvaluatorTypeT = Eigen::internal::evaluator<Eigen::Matrix<double, 3, 1> >; SrcEvaluatorTypeT = Eigen::internal::evaluator<Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 1>, 1> >; Functor = Eigen::internal::assign_op<double, double>; 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<Kernel, Index, Stop>::run(Kernel&) [with Kernel = Eigen::internal::generic_dense_assignment_kernel<Eigen::internal::evaluator<Eigen::Matrix<double, 3, 1> >, Eigen::internal::evaluator<Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 1>, 1> >, Eigen::internal::assign_op<double, double>, 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<DstXprType, Eigen::Product<Lhs, Rhs, Options>, Eigen::internal::assign_op<Scalar, Scalar>, Eigen::internal::Dense2Dense, typename Eigen::internal::enable_if<((Options == Eigen::DefaultProduct) || (Options == Eigen::AliasFreeProduct))>::type>::run(DstXprType&, const SrcXprType&, const Eigen::internal::assign_op<Scalar, Scalar>&) [with DstXprType = Eigen::Matrix<double, 3, 1>; Lhs = Eigen::Matrix<double, 3, 3>; Rhs = Eigen::Matrix<double, 3, 1>; int Options = 0; Scalar = double; Eigen::internal::Assignment<DstXprType, Eigen::Product<Lhs, Rhs, Options>, Eigen::internal::assign_op<Scalar, Scalar>, Eigen::internal::Dense2Dense, typename Eigen::internal::enable_if<((Options == Eigen::DefaultProduct) || (Options == Eigen::AliasFreeProduct))>::type>::SrcXprType = Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 1>, 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<double, 3, 1>; Src = Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 1>, 0>; Func = Eigen::internal::assign_op<double, double>]’
/usr/include/eigen3/Eigen/src/Core/PlainObjectBase.h:732:41:   required from ‘Derived& Eigen::PlainObjectBase<Derived>::_set_noalias(const Eigen::DenseBase<OtherDerived>&) [with OtherDerived = Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 1>, 0>; Derived = Eigen::Matrix<double, 3, 1>]’
/usr/include/eigen3/Eigen/src/Core/PlainObjectBase.h:537:7:   required from ‘Eigen::PlainObjectBase<Derived>::PlainObjectBase(const Eigen::DenseBase<OtherDerived>&) [with OtherDerived = Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 1>, 0>; Derived = Eigen::Matrix<double, 3, 1>]’
/usr/include/eigen3/Eigen/src/Core/Matrix.h:377:29:   required from ‘Eigen::Matrix<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>::Matrix(const Eigen::EigenBase<OtherDerived>&) [with OtherDerived = Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 1>, 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<const Eigen::Matrix<double, 3, 3>, 1, 3, false>::Block(const Eigen::Block<const Eigen::Matrix<double, 3, 3>, 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<const Eigen::Matrix<double, 3, 3>, 1, 3, false>’ has user-provided ‘Eigen::BlockImpl<XprType, BlockRows, BlockCols, InnerPanel, Eigen::Dense>& Eigen::BlockImpl<XprType, BlockRows, BlockCols, InnerPanel, Eigen::Dense>::operator=(const Eigen::BlockImpl<XprType, BlockRows, BlockCols, InnerPanel, Eigen::Dense>&) [with XprType = const Eigen::Matrix<double, 3, 3>; 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<BinaryOp, Lhs, Rhs>::CwiseBinaryOp(const Lhs&, const Rhs&, const BinaryOp&) [with BinaryOp = Eigen::internal::scalar_product_op<double, double>; LhsType = const Eigen::Transpose<const Eigen::Block<const Eigen::Matrix<double, 3, 3>, 1, 3, false> >; RhsType = const Eigen::Block<const Eigen::Matrix<double, 3, 1>, 3, 1, true>; Eigen::CwiseBinaryOp<BinaryOp, Lhs, Rhs>::Lhs = Eigen::Transpose<const Eigen::Block<const Eigen::Matrix<double, 3, 3>, 1, 3, false> >; Eigen::CwiseBinaryOp<BinaryOp, Lhs, Rhs>::Rhs = Eigen::Block<const Eigen::Matrix<double, 3, 1>, 3, 1, true>]’:
/usr/include/eigen3/Eigen/src/Core/../plugins/MatrixCwiseBinaryOps.h:25:10:   required from ‘const Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<typename Eigen::internal::traits<T>::Scalar, typename Eigen::internal::traits<OtherDerived>::Scalar>, const Derived, const OtherDerived> Eigen::MatrixBase<Derived>::cwiseProduct(const Eigen::MatrixBase<OtherDerived>&) const [with OtherDerived = Eigen::Block<const Eigen::Matrix<double, 3, 1>, 3, 1, true>; Derived = Eigen::Transpose<const Eigen::Block<const Eigen::Matrix<double, 3, 3>, 1, 3, false> >; typename Eigen::internal::traits<OtherDerived>::Scalar = double; typename Eigen::internal::traits<T>::Scalar = double]’
/usr/include/eigen3/Eigen/src/Core/ProductEvaluators.h:552:72:   required from ‘const CoeffReturnType Eigen::internal::product_evaluator<Eigen::Product<Lhs, Rhs, 1>, ProductTag, Eigen::DenseShape, Eigen::DenseShape>::coeff(Eigen::Index, Eigen::Index) const [with Lhs = Eigen::Matrix<double, 3, 3>; Rhs = Eigen::Matrix<double, 3, 1>; int ProductTag = 3; typename Eigen::internal::traits<typename Eigen::Product<Lhs, Rhs, 1>::Rhs>::Scalar = double; typename Eigen::internal::traits<typename Eigen::Product<Lhs, Rhs, 1>::Lhs>::Scalar = double; Eigen::internal::product_evaluator<Eigen::Product<Lhs, Rhs, 1>, 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<DstEvaluatorTypeT, SrcEvaluatorTypeT, Functor, Version>::assignCoeff(Eigen::Index, Eigen::Index) [with DstEvaluatorTypeT = Eigen::internal::evaluator<Eigen::Matrix<double, 3, 1> >; SrcEvaluatorTypeT = Eigen::internal::evaluator<Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 1>, 1> >; Functor = Eigen::internal::assign_op<double, double>; 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<DstEvaluatorTypeT, SrcEvaluatorTypeT, Functor, Version>::assignCoeffByOuterInner(Eigen::Index, Eigen::Index) [with DstEvaluatorTypeT = Eigen::internal::evaluator<Eigen::Matrix<double, 3, 1> >; SrcEvaluatorTypeT = Eigen::internal::evaluator<Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 1>, 1> >; Functor = Eigen::internal::assign_op<double, double>; 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<Kernel, Index, Stop>::run(Kernel&) [with Kernel = Eigen::internal::generic_dense_assignment_kernel<Eigen::internal::evaluator<Eigen::Matrix<double, 3, 1> >, Eigen::internal::evaluator<Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 1>, 1> >, Eigen::internal::assign_op<double, double>, 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<DstXprType, Eigen::Product<Lhs, Rhs, Options>, Eigen::internal::assign_op<Scalar, Scalar>, Eigen::internal::Dense2Dense, typename Eigen::internal::enable_if<((Options == Eigen::DefaultProduct) || (Options == Eigen::AliasFreeProduct))>::type>::run(DstXprType&, const SrcXprType&, const Eigen::internal::assign_op<Scalar, Scalar>&) [with DstXprType = Eigen::Matrix<double, 3, 1>; Lhs = Eigen::Matrix<double, 3, 3>; Rhs = Eigen::Matrix<double, 3, 1>; int Options = 0; Scalar = double; Eigen::internal::Assignment<DstXprType, Eigen::Product<Lhs, Rhs, Options>, Eigen::internal::assign_op<Scalar, Scalar>, Eigen::internal::Dense2Dense, typename Eigen::internal::enable_if<((Options == Eigen::DefaultProduct) || (Options == Eigen::AliasFreeProduct))>::type>::SrcXprType = Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 1>, 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<double, 3, 1>; Src = Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 1>, 0>; Func = Eigen::internal::assign_op<double, double>]’
/usr/include/eigen3/Eigen/src/Core/PlainObjectBase.h:732:41:   required from ‘Derived& Eigen::PlainObjectBase<Derived>::_set_noalias(const Eigen::DenseBase<OtherDerived>&) [with OtherDerived = Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 1>, 0>; Derived = Eigen::Matrix<double, 3, 1>]’
/usr/include/eigen3/Eigen/src/Core/PlainObjectBase.h:537:7:   required from ‘Eigen::PlainObjectBase<Derived>::PlainObjectBase(const Eigen::DenseBase<OtherDerived>&) [with OtherDerived = Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 1>, 0>; Derived = Eigen::Matrix<double, 3, 1>]’
/usr/include/eigen3/Eigen/src/Core/Matrix.h:377:29:   required from ‘Eigen::Matrix<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>::Matrix(const Eigen::EigenBase<OtherDerived>&) [with OtherDerived = Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 1>, 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<const Eigen::Block<const Eigen::Matrix<double, 3, 3>, 1, 3, false> >::Transpose(const Eigen::Transpose<const Eigen::Block<const Eigen::Matrix<double, 3, 3>, 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<const Eigen::Block<const Eigen::Matrix<double, 3, 3>, 1, 3, false> >’ has user-provided ‘Derived& Eigen::MatrixBase<Derived>::operator=(const Eigen::MatrixBase<Derived>&) [with Derived = Eigen::Transpose<const Eigen::Block<const Eigen::Matrix<double, 3, 3>, 1, 3, false> >]’
   55 | EIGEN_STRONG_INLINE Derived& MatrixBase<Derived>::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<const Eigen::Matrix<double, 3, 1>, 3, 1, true>::Block(const Eigen::Block<const Eigen::Matrix<double, 3, 1>, 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<const Eigen::Matrix<double, 3, 1>, 3, 1, true>’ has user-provided ‘Eigen::BlockImpl<XprType, BlockRows, BlockCols, InnerPanel, Eigen::Dense>& Eigen::BlockImpl<XprType, BlockRows, BlockCols, InnerPanel, Eigen::Dense>::operator=(const Eigen::BlockImpl<XprType, BlockRows, BlockCols, InnerPanel, Eigen::Dense>&) [with XprType = const Eigen::Matrix<double, 3, 1>; 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<BinaryOp, Lhs, Rhs>::CwiseBinaryOp(const Lhs&, const Rhs&, const BinaryOp&) [with BinaryOp = Eigen::internal::scalar_product_op<double, double>; LhsType = const Eigen::Transpose<const Eigen::Block<const Eigen::Matrix<double, 3, 3>, 1, 3, false> >; RhsType = const Eigen::Block<const Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >, 3, 1, false>; Eigen::CwiseBinaryOp<BinaryOp, Lhs, Rhs>::Lhs = Eigen::Transpose<const Eigen::Block<const Eigen::Matrix<double, 3, 3>, 1, 3, false> >; Eigen::CwiseBinaryOp<BinaryOp, Lhs, Rhs>::Rhs = Eigen::Block<const Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >, 3, 1, false>]’:
/usr/include/eigen3/Eigen/src/Core/../plugins/MatrixCwiseBinaryOps.h:25:10:   required from ‘const Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<typename Eigen::internal::traits<T>::Scalar, typename Eigen::internal::traits<OtherDerived>::Scalar>, const Derived, const OtherDerived> Eigen::MatrixBase<Derived>::cwiseProduct(const Eigen::MatrixBase<OtherDerived>&) const [with OtherDerived = Eigen::Block<const Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >, 3, 1, false>; Derived = Eigen::Transpose<const Eigen::Block<const Eigen::Matrix<double, 3, 3>, 1, 3, false> >; typename Eigen::internal::traits<OtherDerived>::Scalar = double; typename Eigen::internal::traits<T>::Scalar = double]’
/usr/include/eigen3/Eigen/src/Core/ProductEvaluators.h:552:72:   required from ‘const CoeffReturnType Eigen::internal::product_evaluator<Eigen::Product<Lhs, Rhs, 1>, ProductTag, Eigen::DenseShape, Eigen::DenseShape>::coeff(Eigen::Index, Eigen::Index) const [with Lhs = Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 3>, 0>; Rhs = Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >; int ProductTag = 3; typename Eigen::internal::traits<typename Eigen::Product<Lhs, Rhs, 1>::Rhs>::Scalar = double; typename Eigen::internal::traits<typename Eigen::Product<Lhs, Rhs, 1>::Lhs>::Scalar = double; Eigen::internal::product_evaluator<Eigen::Product<Lhs, Rhs, 1>, 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<DstEvaluatorTypeT, SrcEvaluatorTypeT, Functor, Version>::assignCoeff(Eigen::Index, Eigen::Index) [with DstEvaluatorTypeT = Eigen::internal::evaluator<Eigen::Matrix<double, 3, 3, 1, 3, 3> >; SrcEvaluatorTypeT = Eigen::internal::evaluator<Eigen::Product<Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 3>, 0>, Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >, 1> >; Functor = Eigen::internal::assign_op<double, double>; 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<DstEvaluatorTypeT, SrcEvaluatorTypeT, Functor, Version>::assignCoeffByOuterInner(Eigen::Index, Eigen::Index) [with DstEvaluatorTypeT = Eigen::internal::evaluator<Eigen::Matrix<double, 3, 3, 1, 3, 3> >; SrcEvaluatorTypeT = Eigen::internal::evaluator<Eigen::Product<Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 3>, 0>, Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >, 1> >; Functor = Eigen::internal::assign_op<double, double>; 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<Kernel, Index_, Stop>::run(Kernel&, Eigen::Index) [with Kernel = Eigen::internal::generic_dense_assignment_kernel<Eigen::internal::evaluator<Eigen::Matrix<double, 3, 3, 1, 3, 3> >, Eigen::internal::evaluator<Eigen::Product<Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 3>, 0>, Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >, 1> >, Eigen::internal::assign_op<double, double>, 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::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 3>, 0>, Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >, 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<Eigen::internal::evaluator_assume_aliasing<Src>::value, void*>::type) [with Dst = Eigen::Matrix<double, 3, 3>; Src = Eigen::Product<Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 3>, 0>, Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >, 0>; Func = Eigen::internal::assign_op<double, double>; typename Eigen::internal::enable_if<Eigen::internal::evaluator_assume_aliasing<Src>::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<double, 3, 3>; Src = Eigen::Product<Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 3>, 0>, Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >, 0>]’
/usr/include/eigen3/Eigen/src/Core/PlainObjectBase.h:714:32:   required from ‘Derived& Eigen::PlainObjectBase<Derived>::_set(const Eigen::DenseBase<OtherDerived>&) [with OtherDerived = Eigen::Product<Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 3>, 0>, Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >, 0>; Derived = Eigen::Matrix<double, 3, 3>]’
/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<OtherDerived>&) [with OtherDerived = Eigen::Product<Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 3>, 0>, Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >, 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<const Eigen::Block<const Eigen::Matrix<double, 3, 3>, 1, 3, false> >::Transpose(const Eigen::Transpose<const Eigen::Block<const Eigen::Matrix<double, 3, 3>, 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<const Eigen::Block<const Eigen::Matrix<double, 3, 3>, 1, 3, false> >’ has user-provided ‘Derived& Eigen::MatrixBase<Derived>::operator=(const Eigen::MatrixBase<Derived>&) [with Derived = Eigen::Transpose<const Eigen::Block<const Eigen::Matrix<double, 3, 3>, 1, 3, false> >]’
   55 | EIGEN_STRONG_INLINE Derived& MatrixBase<Derived>::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<const Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >, 3, 1, false>::Block(const Eigen::Block<const Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >, 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<const Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >, 3, 1, false>’ has user-provided ‘Eigen::BlockImpl<XprType, BlockRows, BlockCols, InnerPanel, Eigen::Dense>& Eigen::BlockImpl<XprType, BlockRows, BlockCols, InnerPanel, Eigen::Dense>::operator=(const Eigen::BlockImpl<XprType, BlockRows, BlockCols, InnerPanel, Eigen::Dense>&) [with XprType = const Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >; 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<XprType, BlockRows, BlockCols, InnerPanel, true>::BlockImpl_dense(XprType&, Eigen::Index) [with XprType = const Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >; 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<XprType, BlockRows, BlockCols, InnerPanel, Eigen::Dense>::BlockImpl(XprType&, Eigen::Index) [with XprType = const Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >; 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<XprType, BlockRows, BlockCols, InnerPanel>::Block(XprType&, Eigen::Index) [with XprType = const Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >; 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<Derived>::ConstColXpr Eigen::DenseBase<Derived>::col(Eigen::Index) const [with Derived = Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >; Eigen::DenseBase<Derived>::ConstColXpr = const Eigen::Block<const Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >, 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<Eigen::Product<Lhs, Rhs, 1>, ProductTag, Eigen::DenseShape, Eigen::DenseShape>::coeff(Eigen::Index, Eigen::Index) const [with Lhs = Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 3>, 0>; Rhs = Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >; int ProductTag = 3; typename Eigen::internal::traits<typename Eigen::Product<Lhs, Rhs, 1>::Rhs>::Scalar = double; typename Eigen::internal::traits<typename Eigen::Product<Lhs, Rhs, 1>::Lhs>::Scalar = double; Eigen::internal::product_evaluator<Eigen::Product<Lhs, Rhs, 1>, 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<DstEvaluatorTypeT, SrcEvaluatorTypeT, Functor, Version>::assignCoeff(Eigen::Index, Eigen::Index) [with DstEvaluatorTypeT = Eigen::internal::evaluator<Eigen::Matrix<double, 3, 3, 1, 3, 3> >; SrcEvaluatorTypeT = Eigen::internal::evaluator<Eigen::Product<Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 3>, 0>, Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >, 1> >; Functor = Eigen::internal::assign_op<double, double>; 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::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 3>, 0>, Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >, 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<Eigen::internal::evaluator_assume_aliasing<Src>::value, void*>::type) [with Dst = Eigen::Matrix<double, 3, 3>; Src = Eigen::Product<Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 3>, 0>, Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >, 0>; Func = Eigen::internal::assign_op<double, double>; typename Eigen::internal::enable_if<Eigen::internal::evaluator_assume_aliasing<Src>::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<double, 3, 3>; Src = Eigen::Product<Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 3>, 0>, Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >, 0>]’
/usr/include/eigen3/Eigen/src/Core/PlainObjectBase.h:714:32:   required from ‘Derived& Eigen::PlainObjectBase<Derived>::_set(const Eigen::DenseBase<OtherDerived>&) [with OtherDerived = Eigen::Product<Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 3>, 0>, Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >, 0>; Derived = Eigen::Matrix<double, 3, 3>]’
/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<OtherDerived>&) [with OtherDerived = Eigen::Product<Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 3>, 0>, Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >, 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<const Eigen::Matrix<double, 3, 3> >::Transpose(const Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >&)’ 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<const Eigen::Matrix<double, 3, 3> >’ has user-provided ‘Derived& Eigen::MatrixBase<Derived>::operator=(const Eigen::MatrixBase<Derived>&) [with Derived = Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >]’
   55 | EIGEN_STRONG_INLINE Derived& MatrixBase<Derived>::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<BinaryOp, Lhs, Rhs>::CwiseBinaryOp(const Lhs&, const Rhs&, const BinaryOp&) [with BinaryOp = Eigen::internal::scalar_product_op<double, double>; LhsType = const Eigen::Transpose<const Eigen::Block<const Eigen::Matrix<double, 3, 3>, 1, 3, false> >; RhsType = const Eigen::Block<const Eigen::Matrix<double, 3, 3>, 3, 1, true>; Eigen::CwiseBinaryOp<BinaryOp, Lhs, Rhs>::Lhs = Eigen::Transpose<const Eigen::Block<const Eigen::Matrix<double, 3, 3>, 1, 3, false> >; Eigen::CwiseBinaryOp<BinaryOp, Lhs, Rhs>::Rhs = Eigen::Block<const Eigen::Matrix<double, 3, 3>, 3, 1, true>]’:
/usr/include/eigen3/Eigen/src/Core/../plugins/MatrixCwiseBinaryOps.h:25:10:   required from ‘const Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<typename Eigen::internal::traits<T>::Scalar, typename Eigen::internal::traits<OtherDerived>::Scalar>, const Derived, const OtherDerived> Eigen::MatrixBase<Derived>::cwiseProduct(const Eigen::MatrixBase<OtherDerived>&) const [with OtherDerived = Eigen::Block<const Eigen::Matrix<double, 3, 3>, 3, 1, true>; Derived = Eigen::Transpose<const Eigen::Block<const Eigen::Matrix<double, 3, 3>, 1, 3, false> >; typename Eigen::internal::traits<OtherDerived>::Scalar = double; typename Eigen::internal::traits<T>::Scalar = double]’
/usr/include/eigen3/Eigen/src/Core/ProductEvaluators.h:552:72:   required from ‘const CoeffReturnType Eigen::internal::product_evaluator<Eigen::Product<Lhs, Rhs, 1>, ProductTag, Eigen::DenseShape, Eigen::DenseShape>::coeff(Eigen::Index, Eigen::Index) const [with Lhs = Eigen::Matrix<double, 3, 3>; Rhs = Eigen::Matrix<double, 3, 3>; int ProductTag = 3; typename Eigen::internal::traits<typename Eigen::Product<Lhs, Rhs, 1>::Rhs>::Scalar = double; typename Eigen::internal::traits<typename Eigen::Product<Lhs, Rhs, 1>::Lhs>::Scalar = double; Eigen::internal::product_evaluator<Eigen::Product<Lhs, Rhs, 1>, 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<DstEvaluatorTypeT, SrcEvaluatorTypeT, Functor, Version>::assignCoeff(Eigen::Index, Eigen::Index) [with DstEvaluatorTypeT = Eigen::internal::evaluator<Eigen::Matrix<double, 3, 3> >; SrcEvaluatorTypeT = Eigen::internal::evaluator<Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 3>, 1> >; Functor = Eigen::internal::assign_op<double, double>; 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<DstEvaluatorTypeT, SrcEvaluatorTypeT, Functor, Version>::assignCoeffByOuterInner(Eigen::Index, Eigen::Index) [with DstEvaluatorTypeT = Eigen::internal::evaluator<Eigen::Matrix<double, 3, 3> >; SrcEvaluatorTypeT = Eigen::internal::evaluator<Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 3>, 1> >; Functor = Eigen::internal::assign_op<double, double>; 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<Kernel, Index_, Stop>::run(Kernel&, Eigen::Index) [with Kernel = Eigen::internal::generic_dense_assignment_kernel<Eigen::internal::evaluator<Eigen::Matrix<double, 3, 3> >, Eigen::internal::evaluator<Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 3>, 1> >, Eigen::internal::assign_op<double, double>, 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::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 3>, 0>, Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >, 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<Eigen::internal::evaluator_assume_aliasing<Src>::value, void*>::type) [with Dst = Eigen::Matrix<double, 3, 3>; Src = Eigen::Product<Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 3>, 0>, Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >, 0>; Func = Eigen::internal::assign_op<double, double>; typename Eigen::internal::enable_if<Eigen::internal::evaluator_assume_aliasing<Src>::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<double, 3, 3>; Src = Eigen::Product<Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 3>, 0>, Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >, 0>]’
/usr/include/eigen3/Eigen/src/Core/PlainObjectBase.h:714:32:   required from ‘Derived& Eigen::PlainObjectBase<Derived>::_set(const Eigen::DenseBase<OtherDerived>&) [with OtherDerived = Eigen::Product<Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 3>, 0>, Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >, 0>; Derived = Eigen::Matrix<double, 3, 3>]’
/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<OtherDerived>&) [with OtherDerived = Eigen::Product<Eigen::Product<Eigen::Matrix<double, 3, 3>, Eigen::Matrix<double, 3, 3>, 0>, Eigen::Transpose<const Eigen::Matrix<double, 3, 3> >, 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<const Eigen::Block<const Eigen::Matrix<double, 3, 3>, 1, 3, false> >::Transpose(const Eigen::Transpose<const Eigen::Block<const Eigen::Matrix<double, 3, 3>, 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<const Eigen::Block<const Eigen::Matrix<double, 3, 3>, 1, 3, false> >’ has user-provided ‘Derived& Eigen::MatrixBase<Derived>::operator=(const Eigen::MatrixBase<Derived>&) [with Derived = Eigen::Transpose<const Eigen::Block<const Eigen::Matrix<double, 3, 3>, 1, 3, false> >]’
   55 | EIGEN_STRONG_INLINE Derived& MatrixBase<Derived>::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<const Eigen::Matrix<double, 3, 3>, 3, 1, true>::Block(const Eigen::Block<const Eigen::Matrix<double, 3, 3>, 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<const Eigen::Matrix<double, 3, 3>, 3, 1, true>’ has user-provided ‘Eigen::BlockImpl<XprType, BlockRows, BlockCols, InnerPanel, Eigen::Dense>& Eigen::BlockImpl<XprType, BlockRows, BlockCols, InnerPanel, Eigen::Dense>::operator=(const Eigen::BlockImpl<XprType, BlockRows, BlockCols, InnerPanel, Eigen::Dense>&) [with XprType = const Eigen::Matrix<double, 3, 3>; 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 -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC   -o CMakeFiles/chemkit.dir/stereochemistry.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/stereochemistry.cpp
[ 18%] Building CXX object src/chemkit/CMakeFiles/chemkit.dir/structuresimilaritydescriptor.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/structuresimilaritydescriptor.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/structuresimilaritydescriptor.cpp
[ 19%] Building CXX object src/chemkit/CMakeFiles/chemkit.dir/substructurequery.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/substructurequery.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/substructurequery.cpp
[ 19%] Building CXX object src/chemkit/CMakeFiles/chemkit.dir/unitcell.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/unitcell.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/chemkit/unitcell.cpp
[ 20%] Linking CXX shared library libchemkit.so
cd /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/chemkit && /usr/bin/cmake -E cmake_link_script CMakeFiles/chemkit.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.so -o libchemkit.so CMakeFiles/chemkit.dir/alphashape.cpp.o CMakeFiles/chemkit.dir/aminoacid.cpp.o CMakeFiles/chemkit.dir/aromaticitymodel.cpp.o CMakeFiles/chemkit.dir/atom.cpp.o CMakeFiles/chemkit.dir/atomtyper.cpp.o CMakeFiles/chemkit.dir/bond.cpp.o CMakeFiles/chemkit.dir/bondpredictor.cpp.o CMakeFiles/chemkit.dir/cartesiancoordinates.cpp.o CMakeFiles/chemkit.dir/chemkit.cpp.o 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 src/io/CMakeFiles/chemkit-io.dir/build.make src/io/CMakeFiles/chemkit-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/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/io /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/io/CMakeFiles/chemkit-io.dir/DependInfo.cmake
Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/io/CMakeFiles/chemkit-io.dir/DependInfo.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/io/CMakeFiles/chemkit-io.dir/depend.internal".
Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/io/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/io/CMakeFiles/chemkit-io.dir/depend.internal".
Scanning dependencies of target chemkit-io
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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 /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/moleculefile.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/io/moleculefile.cpp
[ 21%] Building CXX object src/io/CMakeFiles/chemkit-io.dir/moleculefileformat.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/moleculefileformat.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/io/moleculefileformat.cpp
[ 22%] Building CXX object src/io/CMakeFiles/chemkit-io.dir/polymerfile.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/polymerfile.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/io/polymerfile.cpp
[ 22%] Building CXX object src/io/CMakeFiles/chemkit-io.dir/polymerfileformat.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/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 /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 /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 /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/md/CMakeFiles/chemkit-md.dir/DependInfo.cmake
Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/md/CMakeFiles/chemkit-md.dir/DependInfo.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/md/CMakeFiles/chemkit-md.dir/depend.internal".
Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/md/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/md/CMakeFiles/chemkit-md.dir/depend.internal".
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 -pedantic -Wall -Wextra -Wno-long-long -fPIC   -o CMakeFiles/chemkit-md.dir/integrator.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/md/integrator.cpp
[ 24%] Building CXX object src/md/CMakeFiles/chemkit-md.dir/md.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/md.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/md/md.cpp
[ 25%] Building CXX object src/md/CMakeFiles/chemkit-md.dir/moleculegeometryoptimizer.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/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 -fvisibility-inlines-hidden -pedantic -Wall -Wextra -Wno-long-long -fPIC   -o CMakeFiles/chemkit-md.dir/topologybuilder.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/md/topologybuilder.cpp
[ 27%] Building CXX object src/md/CMakeFiles/chemkit-md.dir/trajectory.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/trajectory.cpp.o -c /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/md/trajectory.cpp
[ 27%] Building CXX object src/md/CMakeFiles/chemkit-md.dir/trajectoryframe.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/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 /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/amber /var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/amber/CMakeFiles/amber.dir/DependInfo.cmake
Dependee "/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build/src/plugins/amber/CMakeFiles/amber.dir/DependInfo.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".
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<chemkit::Real>(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<chemkit::Real>(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<int>(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<int>(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
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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".
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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
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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'