Log file: /var/tmp/sci-libs:chemkit-0.1-r2:20191102-085206.log

chemkit-0.1-r2.log (text/plain), 277.14 KB, created by Luis Ferreira on 2019-11-02 09:12:39 UTC

[32;01m * [39;49;00mPackage:    sci-libs/chemkit-0.1-r2
[32;01m * [39;49;00mRepository: gentoo
[32;01m * [39;49;00mMaintainer: [e-mail]
[32;01m * [39;49;00mUSE:        abi_x86_64 amd64 elibc_glibc kernel_linux python python_targets_python2_7 userland_GNU
[32;01m * [39;49;00mFEATURES:   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/inchicmp.h'
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removed 'src/3rdparty/inchi/ichicomn.h'
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removed 'src/3rdparty/inchi/ichirvr5.c'
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removed 'src/3rdparty/inchi/inchi_dll_main.h'
removed 'src/3rdparty/inchi/ichirvr3.c'
removed 'src/3rdparty/inchi/incomdef.h'
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removed 'src/3rdparty/lemon/lemon/quad_heap.h'
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removed 'src/3rdparty/lemon/lemon/binomial_heap.h'
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removed 'src/3rdparty/lemon/lemon/lp_base.cc'
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removed 'src/3rdparty/lemon/lemon/tolerance.h'
removed 'src/3rdparty/lemon/lemon/glpk.cc'
removed 'src/3rdparty/lemon/lemon/soplex.h'
removed 'src/3rdparty/lemon/lemon/core.h'
removed 'src/3rdparty/lemon/lemon/connectivity.h'
removed 'src/3rdparty/lemon/lemon/fractional_matching.h'
removed 'src/3rdparty/lemon/lemon/fib_heap.h'
removed 'src/3rdparty/lemon/lemon/howard_mmc.h'
removed 'src/3rdparty/lemon/lemon/network_simplex.h'
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removed directory 'src/3rdparty/lemon/lemon/bits'
removed 'src/3rdparty/lemon/lemon/lp_skeleton.h'
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removed 'src/3rdparty/lemon/lemon/radix_heap.h'
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removed 'src/3rdparty/lemon/lemon/CMakeLists.txt'
removed 'src/3rdparty/lemon/lemon/bin_heap.h'
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removed 'src/3rdparty/lemon/lemon/list_graph.h'
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removed 'src/3rdparty/lemon/lemon/hao_orlin.h'
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 [32;01m*[0m Applying chemkit-0.1-multilib.patch ...
[A[263C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Applying chemkit-0.1-unbundle.patch ...
[A[263C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Hardcoded definition(s) removed in CMakeLists.txt:
 [32;01m*[0m    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 8.3.0
-- The CXX compiler identification is GNU 8.3.0
-- 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") 
-- Boost version: 1.71.0
CMake Warning at /usr/share/cmake/Modules/FindBoost.cmake:905 (message):
  New Boost version may have incorrect or missing dependencies and imported
  targets
Call Stack (most recent call first):
  /usr/share/cmake/Modules/FindBoost.cmake:1027 (_Boost_COMPONENT_DEPENDENCIES)
  /usr/share/cmake/Modules/FindBoost.cmake:1727 (_Boost_MISSING_DEPENDENCIES)
  src/chemkit/CMakeLists.txt:7 (find_package)


CMake Warning at /usr/share/cmake/Modules/FindBoost.cmake:905 (message):
  New Boost version may have incorrect or missing dependencies and imported
  targets
Call Stack (most recent call first):
  /usr/share/cmake/Modules/FindBoost.cmake:1027 (_Boost_COMPONENT_DEPENDENCIES)
  /usr/share/cmake/Modules/FindBoost.cmake:1727 (_Boost_MISSING_DEPENDENCIES)
  src/chemkit/CMakeLists.txt:7 (find_package)


CMake Warning at /usr/share/cmake/Modules/FindBoost.cmake:905 (message):
  New Boost version may have incorrect or missing dependencies and imported
  targets
Call Stack (most recent call first):
  /usr/share/cmake/Modules/FindBoost.cmake:1027 (_Boost_COMPONENT_DEPENDENCIES)
  /usr/share/cmake/Modules/FindBoost.cmake:1727 (_Boost_MISSING_DEPENDENCIES)
  src/chemkit/CMakeLists.txt:7 (find_package)


CMake Warning at /usr/share/cmake/Modules/FindBoost.cmake:905 (message):
  New Boost version may have incorrect or missing dependencies and imported
  targets
Call Stack (most recent call first):
  /usr/share/cmake/Modules/FindBoost.cmake:1027 (_Boost_COMPONENT_DEPENDENCIES)
  /usr/share/cmake/Modules/FindBoost.cmake:1727 (_Boost_MISSING_DEPENDENCIES)
  src/chemkit/CMakeLists.txt:7 (find_package)


CMake Warning at /usr/share/cmake/Modules/FindBoost.cmake:905 (message):
  New Boost version may have incorrect or missing dependencies and imported
  targets
Call Stack (most recent call first):
  /usr/share/cmake/Modules/FindBoost.cmake:1027 (_Boost_COMPONENT_DEPENDENCIES)
  /usr/share/cmake/Modules/FindBoost.cmake:1727 (_Boost_MISSING_DEPENDENCIES)
  src/chemkit/CMakeLists.txt:7 (find_package)


CMake Warning at /usr/share/cmake/Modules/FindBoost.cmake:905 (message):
  New Boost version may have incorrect or missing dependencies and imported
  targets
Call Stack (most recent call first):
  /usr/share/cmake/Modules/FindBoost.cmake:1027 (_Boost_COMPONENT_DEPENDENCIES)
  /usr/share/cmake/Modules/FindBoost.cmake:1727 (_Boost_MISSING_DEPENDENCIES)
  src/chemkit/CMakeLists.txt:7 (find_package)


-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- 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  
-- Boost version: 1.71.0
-- Found the following Boost libraries:
--   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.

CMake Warning at /usr/share/cmake/Modules/FindBoost.cmake:905 (message):
  New Boost version may have incorrect or missing dependencies and imported
  targets
Call Stack (most recent call first):
  /usr/share/cmake/Modules/FindBoost.cmake:1027 (_Boost_COMPONENT_DEPENDENCIES)
  /usr/share/cmake/Modules/FindBoost.cmake:1727 (_Boost_MISSING_DEPENDENCIES)
  src/io/CMakeLists.txt:4 (find_package)


CMake Warning at /usr/share/cmake/Modules/FindBoost.cmake:905 (message):
  New Boost version may have incorrect or missing dependencies and imported
  targets
Call Stack (most recent call first):
  /usr/share/cmake/Modules/FindBoost.cmake:1027 (_Boost_COMPONENT_DEPENDENCIES)
  /usr/share/cmake/Modules/FindBoost.cmake:1727 (_Boost_MISSING_DEPENDENCIES)
  src/io/CMakeLists.txt:4 (find_package)


-- Boost version: 1.71.0
-- Found the following Boost libraries:
--   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/lib/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               -march=corei7 -O2 -pipe
C++             -march=corei7 -O2 -pipe -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 -j9 -l8 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 --color=
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".
[35m[1mScanning dependencies of target chemkit[0m
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
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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 -march=corei7 -O2 -pipe -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
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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 -march=corei7 -O2 -pipe -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
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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 -march=corei7 -O2 -pipe -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%] [32mBuilding CXX object src/chemkit/CMakeFiles/chemkit.dir/polymer.cpp.o[0m
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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 -march=corei7 -O2 -pipe -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
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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 -march=corei7 -O2 -pipe -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
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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 -march=corei7 -O2 -pipe -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
[ 27%] [32mBuilding CXX object src/plugins/graphdescriptors/CMakeFiles/graphdescriptors.dir/graphdescriptorsplugin.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[ 27%] [32m[1mLinking CXX shared library gasteiger.so[0m
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 -march=corei7 -O2 -pipe -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
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make -f src/plugins/hydrogenbonds/CMakeFiles/hydrogenbonds.dir/build.make src/plugins/hydrogenbonds/CMakeFiles/hydrogenbonds.dir/depend
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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 --color=
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[35m[1mScanning dependencies of target hydrogenbonds[0m
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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'
[ 27%] [32mBuilding CXX object src/plugins/hydrogenbonds/CMakeFiles/hydrogenbonds.dir/hydrogenbondacceptorsdescriptor.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[ 27%] [32mBuilding CXX object src/md/CMakeFiles/chemkit-md.dir/forcefield.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[ 27%] [32m[1mLinking CXX shared library countdescriptors.so[0m
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 -march=corei7 -O2 -pipe -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
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make -f src/plugins/mannhold/CMakeFiles/mannhold.dir/build.make src/plugins/mannhold/CMakeFiles/mannhold.dir/depend
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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 --color=
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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 -march=corei7 -O2 -pipe -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
[ 28%] [32mBuilding CXX object src/plugins/formula/CMakeFiles/formula.dir/htmlformulalineformat.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[ 28%] [32m[1mLinking CXX shared library apol.so[0m
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 -march=corei7 -O2 -pipe -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
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[ 28%] Built target apol
make -f src/plugins/massdescriptors/CMakeFiles/massdescriptors.dir/build.make src/plugins/massdescriptors/CMakeFiles/massdescriptors.dir/depend
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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 --color=
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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".
[35m[1mScanning dependencies of target massdescriptors[0m
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make -f src/plugins/massdescriptors/CMakeFiles/massdescriptors.dir/build.make src/plugins/massdescriptors/CMakeFiles/massdescriptors.dir/build
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 -march=corei7 -O2 -pipe -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 
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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 -march=corei7 -O2 -pipe -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
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
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make -f src/plugins/mcdl/CMakeFiles/mcdl.dir/build.make src/plugins/mcdl/CMakeFiles/mcdl.dir/depend
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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 --color=
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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 -march=corei7 -O2 -pipe -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
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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 -march=corei7 -O2 -pipe -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'
[ 30%] Built target fp2
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 --color=
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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".
[35m[1mScanning dependencies of target moriguchi[0m
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'
[ 31%] [32mBuilding CXX object src/plugins/moriguchi/CMakeFiles/moriguchi.dir/moriguchilogpdescriptor.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[ 32%] [32mBuilding CXX object src/plugins/hydrogenbonds/CMakeFiles/hydrogenbonds.dir/hydrogenbonddonorsdescriptor.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[ 32%] [32mBuilding CXX object src/plugins/mannhold/CMakeFiles/mannhold.dir/mannholdplugin.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[ 33%] [32mBuilding CXX object src/plugins/formula/CMakeFiles/formula.dir/spacedformulalineformat.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[ 34%] [32mBuilding CXX object src/plugins/massdescriptors/CMakeFiles/massdescriptors.dir/massdescriptorsplugin.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[ 34%] [32mBuilding CXX object src/io/CMakeFiles/chemkit-io.dir/moleculefileformat.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[ 34%] [32mBuilding CXX object src/plugins/mcdl/CMakeFiles/mcdl.dir/mcdlplugin.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[ 35%] [32m[1mLinking CXX shared library mannhold.so[0m
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
[ 36%] [32mBuilding CXX object src/md/CMakeFiles/chemkit-md.dir/integrator.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
/usr/bin/x86_64-pc-linux-gnu-g++ -fPIC -march=corei7 -O2 -pipe -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 
[ 37%] [32mBuilding CXX object src/plugins/elementtypers/CMakeFiles/elementtypers.dir/elementtypersplugin.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
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
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[ 37%] [32m[1mLinking CXX shared library massdescriptors.so[0m
[ 37%] Built target mannhold
make -f src/plugins/pubchem/CMakeFiles/pubchem.dir/build.make src/plugins/pubchem/CMakeFiles/pubchem.dir/depend
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 -march=corei7 -O2 -pipe -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 
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 --color=
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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".
[35m[1mScanning dependencies of target pubchem[0m
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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'
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'
[ 37%] Built target massdescriptors
make -f src/plugins/randicindex/CMakeFiles/randicindex.dir/build.make src/plugins/randicindex/CMakeFiles/randicindex.dir/depend
[ 37%] [32mBuilding CXX object src/plugins/pubchem/CMakeFiles/pubchem.dir/pubchemfingerprint.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
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 --color=
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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".
[35m[1mScanning dependencies of target randicindex[0m
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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'
[ 38%] [32mBuilding CXX object src/plugins/randicindex/CMakeFiles/randicindex.dir/randicindexdescriptor.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[ 38%] [32mBuilding CXX object src/plugins/hydrogenbonds/CMakeFiles/hydrogenbonds.dir/hydrogenbondsplugin.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[ 39%] [32mBuilding CXX object src/plugins/mcdl/CMakeFiles/mcdl.dir/mcdlreader.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[ 39%] [32mBuilding CXX object src/plugins/moriguchi/CMakeFiles/moriguchi.dir/moriguchiplugin.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[ 39%] [32m[1mLinking CXX shared library elementtypers.so[0m
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 -march=corei7 -O2 -pipe -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'
[ 39%] Built target elementtypers
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 --color=
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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".
[35m[1mScanning dependencies of target rof5[0m
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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'
[ 39%] [32mBuilding CXX object src/plugins/rof5/CMakeFiles/rof5.dir/rof5plugin.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[ 39%] [32m[1mLinking CXX shared library formula.so[0m
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 -march=corei7 -O2 -pipe -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'
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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 --color=
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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".
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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'
[ 40%] [32mBuilding CXX object src/plugins/rotatablebonds/CMakeFiles/rotatablebonds.dir/rotatablebondsdescriptor.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[ 41%] [32mBuilding CXX object src/io/CMakeFiles/chemkit-io.dir/polymerfile.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[ 42%] [32m[1mLinking CXX shared library hydrogenbonds.so[0m
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 -march=corei7 -O2 -pipe -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'
[ 42%] Built target hydrogenbonds
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 --color=
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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".
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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'
[ 42%] [32mBuilding CXX object src/plugins/surfacedescriptors/CMakeFiles/surfacedescriptors.dir/surfacedescriptors.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[ 43%] [32m[1mLinking CXX shared library moriguchi.so[0m
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 -march=corei7 -O2 -pipe -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'
[ 43%] Built target moriguchi
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 --color=
[ 44%] [32mBuilding CXX object src/plugins/rof5/CMakeFiles/rof5.dir/ruleoffivedescriptor.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
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".
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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'
[ 44%] [32mBuilding CXX object src/plugins/tpsa/CMakeFiles/tpsa.dir/tpsadescriptor.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[ 45%] [32mBuilding CXX object src/plugins/pubchem/CMakeFiles/pubchem.dir/pubchemplugin.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[ 45%] [32mBuilding CXX object src/plugins/randicindex/CMakeFiles/randicindex.dir/randicindexplugin.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[ 45%] [32m[1mLinking CXX shared library mcdl.so[0m
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 -march=corei7 -O2 -pipe -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'
[ 45%] Built target mcdl
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 --color=
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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".
[35m[1mScanning dependencies of target vabc[0m
[ 45%] [32mBuilding CXX object src/md/CMakeFiles/chemkit-md.dir/md.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
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'
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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 -march=corei7 -O2 -pipe -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
[ 47%] [32mBuilding CXX object src/md/CMakeFiles/chemkit-md.dir/moleculegeometryoptimizer.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[01m[K/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/rotatablebonds/rotatablebondsdescriptor.cpp:[m[K In member function ‘[01m[Kvirtual chemkit::Variant RotatableBondsDescriptor::value(const chemkit::Molecule*) const[m[K’:
[01m[K/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/rotatablebonds/rotatablebondsdescriptor.cpp:58:27:[m[K [01;35m[Kwarning: [m[Klogical not is only applied to the left hand side of comparison [[01;35m[K-Wlogical-not-parentheses[m[K]
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            [01;36m[K^~~~~~~~~~~~~~[m[K
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/usr/bin/x86_64-pc-linux-gnu-g++ -fPIC -march=corei7 -O2 -pipe -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
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[ 47%] [32mBuilding CXX object src/md/CMakeFiles/chemkit-md.dir/potential.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[ 47%] [32mBuilding CXX object src/plugins/rotatablebonds/CMakeFiles/rotatablebonds.dir/rotatablebondsplugin.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[ 47%] [32mBuilding CXX object src/plugins/rof5/CMakeFiles/rof5.dir/ruleoffiveviolationsdescriptor.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[ 48%] [32mBuilding CXX object src/plugins/tpsa/CMakeFiles/tpsa.dir/tpsaplugin.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[ 49%] [32m[1mLinking CXX shared library randicindex.so[0m
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 -march=corei7 -O2 -pipe -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'
[ 49%] Built target randicindex
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 --color=
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".
[35m[1mScanning dependencies of target wienerindex[0m
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make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build'
[ 49%] [32mBuilding CXX object src/plugins/wienerindex/CMakeFiles/wienerindex.dir/wienerindexdescriptor.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
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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 -march=corei7 -O2 -pipe -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
[ 50%] [32mBuilding CXX object src/plugins/vabc/CMakeFiles/vabc.dir/vabcplugin.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[ 50%] [32mBuilding CXX object src/io/CMakeFiles/chemkit-io.dir/polymerfileformat.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[ 51%] [32m[1mLinking CXX shared library rotatablebonds.so[0m
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 -march=corei7 -O2 -pipe -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
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[ 52%] [32mBuilding CXX object src/plugins/wienerindex/CMakeFiles/wienerindex.dir/wienerindexplugin.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[ 52%] [32m[1mLinking CXX shared library surfacedescriptors.so[0m
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 -march=corei7 -O2 -pipe -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'
[ 52%] Built target surfacedescriptors
[ 53%] [32mBuilding CXX object src/md/CMakeFiles/chemkit-md.dir/topology.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[ 53%] [32m[1mLinking CXX shared library rof5.so[0m
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 -march=corei7 -O2 -pipe -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 
[ 53%] [32m[1mLinking CXX shared library tpsa.so[0m
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 -march=corei7 -O2 -pipe -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/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'
[ 53%] Built target rof5
[ 53%] [32mBuilding CXX object src/md/CMakeFiles/chemkit-md.dir/topologybuilder.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
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'
[ 53%] Built target tpsa
[ 54%] [32mBuilding CXX object src/md/CMakeFiles/chemkit-md.dir/trajectory.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
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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 -march=corei7 -O2 -pipe -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
[ 55%] [32m[1mLinking CXX shared library libchemkit-io.so[0m
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 -march=corei7 -O2 -pipe -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'
[ 55%] Built target chemkit-io
make -f src/plugins/chemjson/CMakeFiles/chemjson.dir/build.make src/plugins/chemjson/CMakeFiles/chemjson.dir/depend
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/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 --color=
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 --color=
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[35m[1mScanning dependencies of target chemjson[0m
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make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build'
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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'
[ 56%] [32mBuilding CXX object src/plugins/cml/CMakeFiles/cml.dir/cmlfileformat.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[ 57%] [32mBuilding CXX object src/plugins/chemjson/CMakeFiles/chemjson.dir/chemjsonfileformat.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[ 57%] [32mBuilding CXX object src/plugins/chemjson/CMakeFiles/chemjson.dir/chemjsonplugin.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[ 58%] [32m[1mLinking CXX shared library vabc.so[0m
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 -march=corei7 -O2 -pipe -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 
[ 58%] [32mBuilding CXX object src/plugins/chemjson/CMakeFiles/chemjson.dir/__/__/3rdparty/jsoncpp/jsoncpp.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
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'
[ 58%] Built target vabc
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 --color=
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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".
[35m[1mScanning dependencies of target fhz[0m
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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'
[ 59%] [32mBuilding CXX object src/plugins/fhz/CMakeFiles/fhz.dir/fhzfileformat.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[ 59%] [32mBuilding CXX object src/plugins/fhz/CMakeFiles/fhz.dir/fhzplugin.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
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 --color=
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/usr/bin/x86_64-pc-linux-gnu-g++ -fPIC -march=corei7 -O2 -pipe -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/gaussian/CMakeFiles/gaussian.dir/build.make src/plugins/gaussian/CMakeFiles/gaussian.dir/depend
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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 --color=
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make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build'
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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 -march=corei7 -O2 -pipe -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
[ 61%] [32mBuilding CXX object src/plugins/gaussian/CMakeFiles/gaussian.dir/gaussianplugin.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[ 61%] [32mBuilding CXX object src/plugins/fps/CMakeFiles/fps.dir/fpsplugin.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
make -f src/plugins/inchi/CMakeFiles/inchi.dir/build.make src/plugins/inchi/CMakeFiles/inchi.dir/depend
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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 --color=
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make -f src/plugins/inchi/CMakeFiles/inchi.dir/build.make src/plugins/inchi/CMakeFiles/inchi.dir/build
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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 -march=corei7 -O2 -pipe -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
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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 -march=corei7 -O2 -pipe -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
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make -f src/plugins/mdl/CMakeFiles/mdl.dir/build.make src/plugins/mdl/CMakeFiles/mdl.dir/depend
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make -f src/plugins/mdl/CMakeFiles/mdl.dir/build.make src/plugins/mdl/CMakeFiles/mdl.dir/build
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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 -march=corei7 -O2 -pipe -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
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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 -march=corei7 -O2 -pipe -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
[01m[K/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/fhz/fhzfileformat.cpp:[m[K In member function ‘[01m[Kvirtual bool FhzFileFormat::read(std::istream&, chemkit::MoleculeFile*)[m[K’:
[01m[K/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/fhz/fhzfileformat.cpp:94:57:[m[K [01;35m[Kwarning: [m[Kthis statement may fall through [[01;35m[K-Wimplicit-fallthrough=[m[K]
                 phi = [01;35m[Kboost::lexical_cast<chemkit::Real>(tokens[6])[m[K;
                       [01;35m[K~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~[m[K
[01m[K/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/fhz/fhzfileformat.cpp:95:13:[m[K [01;36m[Knote: [m[Khere
             [01;36m[Kcase[m[K 2:
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                         [01;35m[K~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~[m[K
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/usr/bin/x86_64-pc-linux-gnu-g++ -fPIC -march=corei7 -O2 -pipe -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
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[ 65%] [32mBuilding CXX object src/plugins/mmff/CMakeFiles/mmff.dir/mmffaromaticitymodel.cpp.o[0m
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[ 65%] [32mBuilding CXX object src/plugins/mmff/CMakeFiles/mmff.dir/mmffatomtyper.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[ 66%] [32m[1mLinking CXX shared library fhz.so[0m
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 -march=corei7 -O2 -pipe -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'
[ 66%] Built target fhz
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 --color=
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".
[35m[1mScanning dependencies of target mopac[0m
[ 67%] [32m[1mLinking CXX shared library fps.so[0m
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 -march=corei7 -O2 -pipe -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 
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'
[ 67%] [32mBuilding CXX object src/plugins/mopac/CMakeFiles/mopac.dir/mopacplugin.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
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'
[ 67%] Built target fps
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 --color=
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".
[35m[1mScanning dependencies of target opls[0m
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'
[ 67%] [32mBuilding CXX object src/plugins/opls/CMakeFiles/opls.dir/oplsatomtyper.cpp.o[0m
[ 68%] [32m[1mLinking CXX shared library gaussian.so[0m
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 -march=corei7 -O2 -pipe -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
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 -march=corei7 -O2 -pipe -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'
[ 68%] Built target gaussian
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 --color=
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".
[35m[1mScanning dependencies of target pdb[0m
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'
[ 68%] [32mBuilding CXX object src/plugins/pdb/CMakeFiles/pdb.dir/pdbfileformat.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[ 69%] [32mBuilding CXX object src/plugins/inchi/CMakeFiles/inchi.dir/inchilineformat.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[ 70%] [32m[1mLinking CXX shared library cml.so[0m
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 -march=corei7 -O2 -pipe -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'
[ 70%] Built target cml
[01m[K/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/mdl/mdlfileformat.cpp:[m[K In member function ‘[01m[Kvoid MdlFileFormat::writeBondBlock(const chemkit::Molecule*, std::ostream&)[m[K’:
[01m[K/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/mdl/mdlfileformat.cpp:337:23:[m[K [01;35m[Kwarning: [m[K‘[01m[K%3d[m[K’ directive writing 3 bytes into a region of size between 1 and 17 [[01;35m[K-Wformat-overflow=[m[K]
         sprintf(line, [01;35m[K"%3d%3d%3d  0  0  0  0\n"[m[K, static_cast<int>(bond->atom1()->index()) + 1,
                       [01;35m[K^~~~~~~~~~~~~~~~~~~~~~~~~[m[K
[ 70%] [32mBuilding CXX object src/plugins/inchi/CMakeFiles/inchi.dir/inchiplugin.cpp.o[0m
[01m[K/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/mdl/mdlfileformat.cpp:337:23:[m[K [01;36m[Knote: [m[Kdirective argument in the range [0, 255]
In file included from [01m[K/usr/include/stdio.h:867[m[K,
                 from [01m[K/usr/lib/gcc/x86_64-pc-linux-gnu/8.3.0/include/g++-v8/cstdio:42[m[K,
                 from [01m[K/usr/lib/gcc/x86_64-pc-linux-gnu/8.3.0/include/g++-v8/ext/string_conversions.h:43[m[K,
                 from [01m[K/usr/lib/gcc/x86_64-pc-linux-gnu/8.3.0/include/g++-v8/bits/basic_string.h:6400[m[K,
                 from [01m[K/usr/lib/gcc/x86_64-pc-linux-gnu/8.3.0/include/g++-v8/string:52[m[K,
                 from [01m[K/usr/lib/gcc/x86_64-pc-linux-gnu/8.3.0/include/g++-v8/stdexcept:39[m[K,
                 from [01m[K/usr/lib/gcc/x86_64-pc-linux-gnu/8.3.0/include/g++-v8/array:39[m[K,
                 from [01m[K/usr/lib/gcc/x86_64-pc-linux-gnu/8.3.0/include/g++-v8/tuple:39[m[K,
                 from [01m[K/usr/lib/gcc/x86_64-pc-linux-gnu/8.3.0/include/g++-v8/bits/stl_map.h:63[m[K,
                 from [01m[K/usr/lib/gcc/x86_64-pc-linux-gnu/8.3.0/include/g++-v8/map:61[m[K,
                 from [01m[K/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include/chemkit/../../src/chemkit/molecule.h:41[m[K,
                 from [01m[K/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/include/chemkit/molecule.h:1[m[K,
                 from [01m[K/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/mdl/mdlfileformat.h:39[m[K,
                 from [01m[K/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/mdl/mdlfileformat.cpp:41[m[K:
[01m[K/usr/include/bits/stdio2.h:36:34:[m[K [01;36m[Knote: [m[K‘[01m[K__builtin___sprintf_chk[m[K’ output between 23 and 39 bytes into a destination of size 23
   return [01;36m[K__builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,[m[K
          [01;36m[K~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~[m[K
 [01;36m[K      __bos (__s), __fmt, __va_arg_pack ())[m[K;
       [01;36m[K~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~[m[K
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 -march=corei7 -O2 -pipe -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
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 --color=
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".
[35m[1mScanning dependencies of target pqr[0m
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'
[ 71%] [32mBuilding CXX object src/plugins/pqr/CMakeFiles/pqr.dir/pqrfileformat.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[ 71%] [32m[1mLinking CXX shared library mdl.so[0m
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 -march=corei7 -O2 -pipe -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'
[ 71%] Built target mdl
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 --color=
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".
[35m[1mScanning dependencies of target smiles[0m
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'
[ 71%] [32mBuilding CXX object src/plugins/smiles/CMakeFiles/smiles.dir/daylightaromaticitymodel.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[ 72%] [32mBuilding CXX object src/plugins/mopac/CMakeFiles/mopac.dir/mopcrtfileformat.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[ 73%] [32mBuilding CXX object src/plugins/mmff/CMakeFiles/mmff.dir/mmffcalculation.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[ 74%] [32mBuilding CXX object src/plugins/opls/CMakeFiles/opls.dir/oplscalculation.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[ 74%] [32mBuilding CXX object src/plugins/mmff/CMakeFiles/mmff.dir/mmffforcefield.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[01m[K/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/pdb/pdbfileformat.cpp:328:1:[m[K [01;35m[Kwarning: [m[K‘[01m[K{anonymous}::PdbLigand::~PdbLigand()[m[K’ defined but not used [[01;35m[K-Wunused-function[m[K]
 [01;35m[KPdbLigand[m[K::~PdbLigand()
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[01m[K/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/pdb/pdbfileformat.cpp:196:13:[m[K [01;35m[Kwarning: [m[K‘[01m[Kstd::__cxx11::string {anonymous}::PdbChain::name() const[m[K’ defined but not used [[01;35m[K-Wunused-function[m[K]
 std::string [01;35m[KPdbChain[m[K::name() const
             [01;35m[K^~~~~~~~[m[K
[ 75%] [32mBuilding CXX object src/plugins/smiles/CMakeFiles/smiles.dir/kekulizer.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[ 75%] [32mBuilding CXX object src/plugins/smiles/CMakeFiles/smiles.dir/smilesgraph.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[01m[K/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/pdb/pdbfileformat.cpp:[m[K In member function ‘[01m[Kvoid {anonymous}::PdbFile::writePolymerFile(chemkit::PolymerFile*)[m[K’:
[01m[K/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/pdb/pdbfileformat.cpp:571:22:[m[K [01;35m[Kwarning: [m[K‘[01m[Ksymbol[m[K’ may be used uninitialized in this function [[01;35m[K-Wmaybe-uninitialized[m[K]
                 else [01;35m[Kif[m[K(symbol == 'U'){
                      [01;35m[K^~[m[K
[ 75%] [32mBuilding CXX object src/plugins/pqr/CMakeFiles/pqr.dir/pqrplugin.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[ 75%] [32mBuilding CXX object src/plugins/opls/CMakeFiles/opls.dir/oplsforcefield.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[ 75%] [32mBuilding CXX object src/plugins/mopac/CMakeFiles/mopac.dir/mopinfileformat.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[ 76%] [32mBuilding CXX object src/plugins/pdb/CMakeFiles/pdb.dir/pdbmlfileformat.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[ 76%] [32m[1mLinking CXX shared library inchi.so[0m
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
[ 77%] [32m[1mLinking CXX shared library pqr.so[0m
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 -march=corei7 -O2 -pipe -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 
/usr/bin/x86_64-pc-linux-gnu-g++ -fPIC -march=corei7 -O2 -pipe -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/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'
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
[ 77%] Built target inchi
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 --color=
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/txyz/CMakeFiles/txyz.dir/build.make src/plugins/txyz/CMakeFiles/txyz.dir/depend
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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".
[35m[1mScanning dependencies of target sybyl[0m
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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 --color=
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".
[35m[1mScanning dependencies of target txyz[0m
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'
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'
[ 78%] [32mBuilding CXX object src/plugins/txyz/CMakeFiles/txyz.dir/txyzfileformat.cpp.o[0m
[ 78%] [32mBuilding CXX object src/plugins/sybyl/CMakeFiles/sybyl.dir/sybylatomtyper.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
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 -march=corei7 -O2 -pipe -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
[ 79%] [32mBuilding CXX object src/plugins/mmff/CMakeFiles/mmff.dir/mmffparameters.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[ 79%] [32mBuilding CXX object src/plugins/mmff/CMakeFiles/mmff.dir/mmffparametersdata.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[ 80%] [32mBuilding CXX object src/plugins/smiles/CMakeFiles/smiles.dir/smileslineformat.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[ 81%] [32mBuilding CXX object src/plugins/mmff/CMakeFiles/mmff.dir/mmffpartialchargemodel.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[ 82%] [32mBuilding CXX object src/plugins/sybyl/CMakeFiles/sybyl.dir/sybylplugin.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[ 83%] [32mBuilding CXX object src/plugins/opls/CMakeFiles/opls.dir/oplsparameters.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[ 83%] [32m[1mLinking CXX shared library mopac.so[0m
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 -march=corei7 -O2 -pipe -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 
[ 83%] [32mBuilding CXX object src/plugins/pdb/CMakeFiles/pdb.dir/pdbplugin.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
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'
[ 83%] Built target mopac
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 --color=
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".
[35m[1mScanning dependencies of target uff[0m
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'
[ 83%] [32mBuilding CXX object src/plugins/uff/CMakeFiles/uff.dir/uffatomtyper.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[ 83%] [32mBuilding CXX object src/plugins/sybyl/CMakeFiles/sybyl.dir/mol2fileformat.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[01m[K/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit/src/plugins/smiles/smileslineformat.cpp:163:5:[m[K [01;35m[Kwarning: [m[K‘[01m[Kint {anonymous}::readCharge(const char**)[m[K’ defined but not used [[01;35m[K-Wunused-function[m[K]
 int [01;35m[KreadCharge[m[K(const char **p)
     [01;35m[K^~~~~~~~~~[m[K
[ 83%] [32mBuilding CXX object src/plugins/txyz/CMakeFiles/txyz.dir/txyzplugin.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[ 83%] [32mBuilding CXX object src/plugins/mmff/CMakeFiles/mmff.dir/mmffplugin.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[ 83%] [32mBuilding CXX object src/plugins/opls/CMakeFiles/opls.dir/oplsplugin.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[ 84%] [32mBuilding CXX object src/plugins/uff/CMakeFiles/uff.dir/uffplugin.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[ 84%] [32mBuilding CXX object src/plugins/smiles/CMakeFiles/smiles.dir/smilesplugin.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[ 85%] [32m[1mLinking CXX shared library txyz.so[0m
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 -march=corei7 -O2 -pipe -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'
[ 85%] Built target txyz
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 --color=
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".
[35m[1mScanning dependencies of target xyz[0m
make[2]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build'
make -f src/plugins/xyz/CMakeFiles/xyz.dir/build.make src/plugins/xyz/CMakeFiles/xyz.dir/build
make[2]: Entering directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build'
[ 86%] [32mBuilding CXX object src/plugins/xyz/CMakeFiles/xyz.dir/xyzfileformat.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[ 86%] [32mBuilding CXX object src/plugins/uff/CMakeFiles/uff.dir/uffcalculation.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[ 86%] [32mBuilding CXX object src/plugins/uff/CMakeFiles/uff.dir/uffforcefield.cpp.o[0m
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 -march=corei7 -O2 -pipe -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
[ 87%] [32m[1mLinking CXX shared library sybyl.so[0m
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
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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
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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
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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 -march=corei7 -O2 -pipe -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
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/usr/lib64/python2.7/site-packages/Cython/Compiler/Main.py:367: 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 5156, in analyse_expressions: SingleAssignmentNode(atom.pxi:253:13,
    first = True)
File 'Nodes.py', line 5298, 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 5298, 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/Makefile2:2841: bindings/python/CMakeFiles/chemkit-python.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
[ 94%] [32m[1mLinking CXX shared library libchemkit-md-io.so[0m
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 -march=corei7 -O2 -pipe -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'
[ 94%] Built target chemkit-md-io
make[1]: Leaving directory '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build'
make: *** [Makefile:141: all] Error 2
 [31;01m*[0m ERROR: sci-libs/chemkit-0.1-r2::gentoo failed (compile phase):
 [31;01m*[0m   emake failed
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 [31;01m*[0m If you need support, post the output of `emerge --info '=sci-libs/chemkit-0.1-r2::gentoo'`,
 [31;01m*[0m the complete build log and the output of `emerge -pqv '=sci-libs/chemkit-0.1-r2::gentoo'`.
 [31;01m*[0m The complete build log is located at '/var/tmp/sci-libs:chemkit-0.1-r2:20191102-085206.log'.
 [31;01m*[0m For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-libs/chemkit-0.1-r2/temp/build.log'.
 [31;01m*[0m The ebuild environment file is located at '/var/tmp/portage/sci-libs/chemkit-0.1-r2/temp/environment'.
 [31;01m*[0m Working directory: '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit-0.1_build'
 [31;01m*[0m S: '/var/tmp/portage/sci-libs/chemkit-0.1-r2/work/chemkit'