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Compilation fails with Clang 13
Trying to build this project using clang 13 on OSX currently fails with the following error
+ cmake -DCMAKE_AR=/Users/runner/mambaforge/conda-bld/scine-database_1656625346687/_build_env/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=/Users/runner/mambaforge/conda-bld/scine-database_1656625346687/_build_env/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=/Users/runner/mambaforge/conda-bld/scine-database_1656625346687/_build_env/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=/Users/runner/mambaforge/conda-bld/scine-database_1656625346687/_build_env/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=/Users/runner/mambaforge/conda-bld/scine-database_1656625346687/_build_env/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=/Users/runner/mambaforge/conda-bld/scine-database_1656625346687/_build_env/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=/Users/runner/mambaforge/conda-bld/scine-database_1656625346687/_build_env/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=/Users/runner/mambaforge/conda-bld/scine-database_1656625346687/_build_env/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=/Users/runner/mambaforge/conda-bld/scine-database_1656625346687/_build_env/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=/Users/runner/mambaforge/conda-bld/scine-database_1656625346687/_build_env/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_12.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_INSTALL_PREFIX=/Users/runner/mambaforge/conda-bld/scine-database_1656625346687/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac -DCMAKE_INSTALL_LIBDIR=lib '-DCMAKE_PROGRAM_PATH=/Users/runner/mambaforge/conda-bld/scine-database_1656625346687/_build_env/bin;/Users/runner/mambaforge/conda-bld/scine-database_1656625346687/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/bin' -B _build -G Ninja -DSCINE_MARCH= -DBLA_VENDOR=Generic
-- The C compiler identification is Clang 13.0.1
-- The CXX compiler identification is Clang 13.0.1
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Scine::UtilsOS found locally at $PREFIX/lib/cmake/ScineUtilsOS
-- Could NOT find MKL (missing: MKL_INCLUDE_DIRS MKL_LIBRARIES)
-- Found LAPACKE for use with Eigen3
-- Found GTest locally at: GTest::gtest
-- Doxygen not found - Documentation for Database will not be built.
-- Configuring done
-- Generating done
-- Build files have been written to: $SRC_DIR/_build
+ cmake --build _build
[1/39] Building CXX object src/Database/CMakeFiles/Database.dir/Database/Objects/BoolProperty.cpp.o
FAILED: src/Database/CMakeFiles/Database.dir/Database/Objects/BoolProperty.cpp.o
$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DDatabase_EXPORTS -DEIGEN_USE_BLAS -I$SRC_DIR/src/Database -isystem $PREFIX/include/Scine -isystem $PREFIX/include/eigen3 -isystem $PREFIX/include/mongocxx/v_noabi -isystem $PREFIX/include/bsoncxx/v_noabi -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/scine-database-1.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Wpedantic -O3 -DNDEBUG -isysroot /Applications/Xcode_12.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -fPIC -std=gnu++17 -MD -MT src/Database/CMakeFiles/Database.dir/Database/Objects/BoolProperty.cpp.o -MF src/Database/CMakeFiles/Database.dir/Database/Objects/BoolProperty.cpp.o.d -o src/Database/CMakeFiles/Database.dir/Database/Objects/BoolProperty.cpp.o -c $SRC_DIR/src/Database/Database/Objects/BoolProperty.cpp
In file included from $SRC_DIR/src/Database/Database/Objects/BoolProperty.cpp:8:
$SRC_DIR/src/Database/Database/Collection.h:103:77: error: reference to incomplete type 'const std::string' (aka 'const basic_string<char, char_traits<char>, allocator<char>>') could not bind to an lvalue of type 'const char [1]'
ObjectClass getAndUpdateOne(const std::string& filter, const std::string& update = "", const std::string& sort = "");
^ ~~
$SRC_DIR/src/Database/Database/Collection.h:103:77: note: passing argument to parameter 'update' here
$SRC_DIR/src/Database/Database/Collection.h:103:109: error: reference to incomplete type 'const std::string' (aka 'const basic_string<char, char_traits<char>, allocator<char>>') could not bind to an lvalue of type 'const char [1]'
ObjectClass getAndUpdateOne(const std::string& filter, const std::string& update = "", const std::string& sort = "");
^ ~~
$SRC_DIR/src/Database/Database/Collection.h:103:109: note: passing argument to parameter 'sort' here
$SRC_DIR/src/Database/Database/Collection.h:116:68: error: reference to incomplete type 'const std::string' (aka 'const basic_string<char, char_traits<char>, allocator<char>>') could not bind to an lvalue of type 'const char [1]'
ObjectClass getOne(const std::string& filter, const std::string& sort = "");
^ ~~
$SRC_DIR/src/Database/Database/Collection.h:116:68: note: passing argument to parameter 'sort' here
3 errors generated.
[2/39] Building CXX object src/Database/CMakeFiles/Database.dir/Database/Objects/DenseMatrixProperty.cpp.o
FAILED: src/Database/CMakeFiles/Database.dir/Database/Objects/DenseMatrixProperty.cpp.o
$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DDatabase_EXPORTS -DEIGEN_USE_BLAS -I$SRC_DIR/src/Database -isystem $PREFIX/include/Scine -isystem $PREFIX/include/eigen3 -isystem $PREFIX/include/mongocxx/v_noabi -isystem $PREFIX/include/bsoncxx/v_noabi -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/scine-database-1.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Wpedantic -O3 -DNDEBUG -isysroot /Applications/Xcode_12.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -fPIC -std=gnu++17 -MD -MT src/Database/CMakeFiles/Database.dir/Database/Objects/DenseMatrixProperty.cpp.o -MF src/Database/CMakeFiles/Database.dir/Database/Objects/DenseMatrixProperty.cpp.o.d -o src/Database/CMakeFiles/Database.dir/Database/Objects/DenseMatrixProperty.cpp.o -c $SRC_DIR/src/Database/Database/Objects/DenseMatrixProperty.cpp
In file included from $SRC_DIR/src/Database/Database/Objects/DenseMatrixProperty.cpp:9:
In file included from $SRC_DIR/src/Database/Database/Objects/Impl/DerivedProperty.h:11:
$SRC_DIR/src/Database/Database/Collection.h:103:77: error: reference to incomplete type 'const std::string' (aka 'const basic_string<char, char_traits<char>, allocator<char>>') could not bind to an lvalue of type 'const char [1]'
ObjectClass getAndUpdateOne(const std::string& filter, const std::string& update = "", const std::string& sort = "");
^ ~~
$SRC_DIR/src/Database/Database/Collection.h:103:77: note: passing argument to parameter 'update' here
$SRC_DIR/src/Database/Database/Collection.h:103:109: error: reference to incomplete type 'const std::string' (aka 'const basic_string<char, char_traits<char>, allocator<char>>') could not bind to an lvalue of type 'const char [1]'
ObjectClass getAndUpdateOne(const std::string& filter, const std::string& update = "", const std::string& sort = "");
^ ~~
$SRC_DIR/src/Database/Database/Collection.h:103:109: note: passing argument to parameter 'sort' here
$SRC_DIR/src/Database/Database/Collection.h:116:68: error: reference to incomplete type 'const std::string' (aka 'const basic_string<char, char_traits<char>, allocator<char>>') could not bind to an lvalue of type 'const char [1]'
ObjectClass getOne(const std::string& filter, const std::string& sort = "");
^ ~~
$SRC_DIR/src/Database/Database/Collection.h:116:68: note: passing argument to parameter 'sort' here
3 errors generated.
System information
+ conda info
active environment : base
active env location : /Users/runner/mambaforge
shell level : 1
user config file : /Users/runner/.condarc
populated config files : /Users/runner/mambaforge/.condarc
conda version : 4.12.0
conda-build version : 3.21.9
python version : 3.9.13.final.0
virtual packages : __osx=10.15.7=0
__unix=0=0
__archspec=1=x86_64
base environment : /Users/runner/mambaforge (writable)
conda av data dir : /Users/runner/mambaforge/etc/conda
conda av metadata url : None
channel URLs : https://conda.anaconda.org/conda-forge/osx-64
https://conda.anaconda.org/conda-forge/noarch
package cache : /Users/runner/mambaforge/pkgs
/Users/runner/.conda/pkgs
envs directories : /Users/runner/mambaforge/envs
/Users/runner/.conda/envs
platform : osx-64
user-agent : conda/4.12.0 requests/2.27.1 CPython/3.9.13 Darwin/19.6.0 OSX/10.15.7
UID:GID : 501:20
netrc file : None
offline mode : False
Test failures due to missing database connection
I'm trying to build chemoton for a colleague, but I cannot get the database testsuite to pass. I noticed test failures while packaging for conda-forge and therefore started a local build. Most tests currently fail with
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in the test body.
build log
❯ cmake -B _build -G Ninja -DSCINE_MARCH="" -DCMAKE_INSTALL_PREFIX=$CONDA_PREFIX
-- The C compiler identification is GNU 11.2.0
-- The CXX compiler identification is GNU 11.2.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /home/abt-grimme/opt/conda/envs/gcc/bin/x86_64-conda-linux-gnu-cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /home/abt-grimme/opt/conda/envs/gcc/bin/x86_64-conda-linux-gnu-c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Setting build type to default 'RelWithDebInfo'
-- Scine::UtilsOS found locally at /home/abt-grimme/opt/conda/envs/scine/lib/cmake/ScineUtilsOS
-- Found MKL: /software/intel/parallel_studio_xe_2019/compilers_and_libraries_2019.6.324/linux/mkl/include
-- Found Intel MKL libraries:
-- /software/intel/parallel_studio_xe_2019/compilers_and_libraries_2019.6.324/linux/mkl/include
-- /software/intel/parallel_studio_xe_2019/compilers_and_libraries_2019.6.324/linux/mkl/lib/intel64/libmkl_avx2.so
-- /software/intel/parallel_studio_xe_2019/compilers_and_libraries_2019.6.324/linux/mkl/lib/intel64/libmkl_vml_avx2.so
-- /home/abt-grimme/opt/conda/envs/scine/lib/libmkl_core.so
-- /home/abt-grimme/opt/conda/envs/scine/lib/libmkl_intel_lp64.so
-- /home/abt-grimme/opt/conda/envs/scine/lib/libmkl_gnu_thread.so
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Found MKL for use with Eigen3
CMake Warning at /home/abt-grimme/opt/conda/envs/scine/lib/cmake/libmongocxx-3.6.7/libmongocxx-config.cmake:15 (message):
This CMake target is deprecated. Use 'mongo::mongocxx_shared' instead.
Consult the example projects for further details.
Call Stack (most recent call first):
dev/cmake/ImportMongoCxx.cmake:9 (find_package)
src/Database/CMakeLists.txt:10 (import_mongocxx)
CMake Warning at /home/abt-grimme/opt/conda/envs/scine/lib/cmake/libbsoncxx-3.6.7/libbsoncxx-config.cmake:15 (message):
This CMake target is deprecated. Use 'mongo::bsoncxx_shared' instead.
Consult the example projects for further details.
Call Stack (most recent call first):
/home/abt-grimme/opt/conda/envs/scine/lib/cmake/libmongocxx-3.6.7/libmongocxx-config.cmake:22 (find_package)
dev/cmake/ImportMongoCxx.cmake:9 (find_package)
src/Database/CMakeLists.txt:10 (import_mongocxx)
-- GTest and GMock were not found in your PATH, they are being downloaded.
CMake Deprecation Warning at _build/googletest-src/CMakeLists.txt:4 (cmake_minimum_required):
Compatibility with CMake < 2.8.12 will be removed from a future version of
CMake.
Update the VERSION argument <min> value or use a ...<max> suffix to tell
CMake that the project does not need compatibility with older versions.
CMake Deprecation Warning at _build/googletest-src/googlemock/CMakeLists.txt:45 (cmake_minimum_required):
Compatibility with CMake < 2.8.12 will be removed from a future version of
CMake.
Update the VERSION argument <min> value or use a ...<max> suffix to tell
CMake that the project does not need compatibility with older versions.
CMake Deprecation Warning at _build/googletest-src/googletest/CMakeLists.txt:56 (cmake_minimum_required):
Compatibility with CMake < 2.8.12 will be removed from a future version of
CMake.
Update the VERSION argument <min> value or use a ...<max> suffix to tell
CMake that the project does not need compatibility with older versions.
-- Found PythonInterp: /home/abt-grimme/opt/conda/envs/gcc/bin/python (found version "3.10.4")
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- GTest and GMock sources were downloaded.
-- Configuring done
-- Generating done
-- Build files have been written to: /tmp1/ehlert/scine/database/_build
❯ ninja -C _build/
ninja: Entering directory `_build/'
[47/47] Linking CXX executable src/Database/Database_tests
❯ ctest --test-dir _build --output-on-failure
Internal ctest changing into directory: /tmp1/ehlert/scine/database/_build
Test project /tmp1/ehlert/scine/database/_build
Start 1: Database
1/1 Test #1: Database .........................***Failed 0.63 sec
Running main() from /tmp1/ehlert/scine/database/_build/googletest-src/googletest/src/gtest_main.cc
[==========] Running 215 tests from 19 test suites.
[----------] Global test environment set-up.
[----------] 4 tests from BoolPropertyTest
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in SetUpTestSuite().
[ RUN ] BoolPropertyTest.Create1
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in the test body.
[ FAILED ] BoolPropertyTest.Create1 (0 ms)
[ RUN ] BoolPropertyTest.Create2
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in the test body.
[ FAILED ] BoolPropertyTest.Create2 (0 ms)
[ RUN ] BoolPropertyTest.Data
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in the test body.
[ FAILED ] BoolPropertyTest.Data (0 ms)
[ RUN ] BoolPropertyTest.DataFails
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in the test body.
[ FAILED ] BoolPropertyTest.DataFails (0 ms)
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in TearDownTestSuite().
[----------] 4 tests from BoolPropertyTest (0 ms total)
[----------] 11 tests from CollectionTest
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in SetUpTestSuite().
[ RUN ] CollectionTest.QueryID
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in the test body.
[ FAILED ] CollectionTest.QueryID (0 ms)
[ RUN ] CollectionTest.ReturnObjectByID
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in the test body.
[ FAILED ] CollectionTest.ReturnObjectByID (0 ms)
[ RUN ] CollectionTest.ReturnObjectByIDFails
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in the test body.
[ FAILED ] CollectionTest.ReturnObjectByIDFails (0 ms)
[ RUN ] CollectionTest.QueryByJSON
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in the test body.
[ FAILED ] CollectionTest.QueryByJSON (0 ms)
[ RUN ] CollectionTest.GetOne
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in the test body.
[ FAILED ] CollectionTest.GetOne (0 ms)
[ RUN ] CollectionTest.GetOneWithSort
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in the test body.
[ FAILED ] CollectionTest.GetOneWithSort (0 ms)
[ RUN ] CollectionTest.GetOneAndModify
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in the test body.
[ FAILED ] CollectionTest.GetOneAndModify (0 ms)
[ RUN ] CollectionTest.GetOneAndModifyWithSort
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in the test body.
[ FAILED ] CollectionTest.GetOneAndModifyWithSort (0 ms)
[ RUN ] CollectionTest.RandomSelect
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in the test body.
[ FAILED ] CollectionTest.RandomSelect (0 ms)
[ RUN ] CollectionTest.CountByJSON
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in the test body.
[ FAILED ] CollectionTest.CountByJSON (1 ms)
[ RUN ] CollectionTest.TestLoop
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in the test body.
[ FAILED ] CollectionTest.TestLoop (0 ms)
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in TearDownTestSuite().
[----------] 11 tests from CollectionTest (1 ms total)
[----------] 4 tests from DenseMatrixPropertyTest
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in SetUpTestSuite().
[ RUN ] DenseMatrixPropertyTest.Create1
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in the test body.
[ FAILED ] DenseMatrixPropertyTest.Create1 (0 ms)
[ RUN ] DenseMatrixPropertyTest.Create2
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in the test body.
[ FAILED ] DenseMatrixPropertyTest.Create2 (0 ms)
[ RUN ] DenseMatrixPropertyTest.Data
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in the test body.
[ FAILED ] DenseMatrixPropertyTest.Data (0 ms)
[ RUN ] DenseMatrixPropertyTest.DataFails
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in the test body.
[ FAILED ] DenseMatrixPropertyTest.DataFails (0 ms)
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in TearDownTestSuite().
[----------] 4 tests from DenseMatrixPropertyTest (0 ms total)
[----------] 18 tests from ElementaryStepTest
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in SetUpTestSuite().
[ RUN ] ElementaryStepTest.Create
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in the test body.
[ FAILED ] ElementaryStepTest.Create (0 ms)
[ RUN ] ElementaryStepTest.ReactantLHS
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in the test body.
[ FAILED ] ElementaryStepTest.ReactantLHS (0 ms)
[ RUN ] ElementaryStepTest.ReactantRHS
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in the test body.
[ FAILED ] ElementaryStepTest.ReactantRHS (0 ms)
[ RUN ] ElementaryStepTest.ReactantBOTH
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in the test body.
[ FAILED ] ElementaryStepTest.ReactantBOTH (0 ms)
[ RUN ] ElementaryStepTest.ReactantFails1
[ OK ] ElementaryStepTest.ReactantFails1 (0 ms)
[ RUN ] ElementaryStepTest.ReactantFails2
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in the test body.
[ FAILED ] ElementaryStepTest.ReactantFails2 (0 ms)
[ RUN ] ElementaryStepTest.Type
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in the test body.
[ FAILED ] ElementaryStepTest.Type (0 ms)
[ RUN ] ElementaryStepTest.TypeFails1
[ OK ] ElementaryStepTest.TypeFails1 (1 ms)
[ RUN ] ElementaryStepTest.TypeFails2
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in the test body.
[ FAILED ] ElementaryStepTest.TypeFails2 (0 ms)
[ RUN ] ElementaryStepTest.TransitionState
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in the test body.
[ FAILED ] ElementaryStepTest.TransitionState (0 ms)
[ RUN ] ElementaryStepTest.TransitionStateFails1
[ OK ] ElementaryStepTest.TransitionStateFails1 (0 ms)
[ RUN ] ElementaryStepTest.TransitionStateFails2
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in the test body.
[ FAILED ] ElementaryStepTest.TransitionStateFails2 (0 ms)
[ RUN ] ElementaryStepTest.Reaction
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in the test body.
[ FAILED ] ElementaryStepTest.Reaction (0 ms)
[ RUN ] ElementaryStepTest.ReactionFails1
[ OK ] ElementaryStepTest.ReactionFails1 (0 ms)
[ RUN ] ElementaryStepTest.ReactionFails2
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in the test body.
[ FAILED ] ElementaryStepTest.ReactionFails2 (0 ms)
[ RUN ] ElementaryStepTest.Spline
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in the test body.
[ FAILED ] ElementaryStepTest.Spline (0 ms)
[ RUN ] ElementaryStepTest.SplineFails1
[ OK ] ElementaryStepTest.SplineFails1 (0 ms)
[ RUN ] ElementaryStepTest.SplineFails2
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in the test body.
[ FAILED ] ElementaryStepTest.SplineFails2 (0 ms)
[----------] 18 tests from ElementaryStepTest (1 ms total)
[----------] 13 tests from ExceptionsTest
[ RUN ] ExceptionsTest.DuplicateIDException_HasWhat
[ OK ] ExceptionsTest.DuplicateIDException_HasWhat (0 ms)
[ RUN ] ExceptionsTest.MissingTimestampException_HasWhat
[ OK ] ExceptionsTest.MissingTimestampException_HasWhat (0 ms)
[ RUN ] ExceptionsTest.MissingCredentialsException_HasWhat
[ OK ] ExceptionsTest.MissingCredentialsException_HasWhat (0 ms)
[ RUN ] ExceptionsTest.MissingLinkedCollectionException_HasWhat
[ OK ] ExceptionsTest.MissingLinkedCollectionException_HasWhat (0 ms)
[ RUN ] ExceptionsTest.DatabaseDisconnectedException_HasWhat
[ OK ] ExceptionsTest.DatabaseDisconnectedException_HasWhat (0 ms)
[ RUN ] ExceptionsTest.MissingCollectionException_HasWhat
[ OK ] ExceptionsTest.MissingCollectionException_HasWhat (0 ms)
[ RUN ] ExceptionsTest.MissingIDException_HasWhat
[ OK ] ExceptionsTest.MissingIDException_HasWhat (0 ms)
[ RUN ] ExceptionsTest.IDNotFoundException_HasWhat
[ OK ] ExceptionsTest.IDNotFoundException_HasWhat (0 ms)
[ RUN ] ExceptionsTest.UnpopulatedObjectException_HasWhat
[ OK ] ExceptionsTest.UnpopulatedObjectException_HasWhat (0 ms)
[ RUN ] ExceptionsTest.ObjectTypeMismatchException_HasWhat
[ OK ] ExceptionsTest.ObjectTypeMismatchException_HasWhat (0 ms)
[ RUN ] ExceptionsTest.MissingIdOrField_HasWhat
[ OK ] ExceptionsTest.MissingIdOrField_HasWhat (0 ms)
[ RUN ] ExceptionsTest.FieldException_HasWhat
[ OK ] ExceptionsTest.FieldException_HasWhat (0 ms)
[ RUN ] ExceptionsTest.VersionMismatch_HasWhat
[ OK ] ExceptionsTest.VersionMismatch_HasWhat (0 ms)
[----------] 13 tests from ExceptionsTest (1 ms total)
[----------] 4 tests from NumberPropertyTest
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in SetUpTestSuite().
[ RUN ] NumberPropertyTest.Create1
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in the test body.
[ FAILED ] NumberPropertyTest.Create1 (0 ms)
[ RUN ] NumberPropertyTest.Create2
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in the test body.
[ FAILED ] NumberPropertyTest.Create2 (0 ms)
[ RUN ] NumberPropertyTest.Data
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in the test body.
[ FAILED ] NumberPropertyTest.Data (0 ms)
[ RUN ] NumberPropertyTest.DataFails
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in the test body.
[ FAILED ] NumberPropertyTest.DataFails (0 ms)
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in TearDownTestSuite().
[----------] 4 tests from NumberPropertyTest (1 ms total)
[----------] 15 tests from ManagerTest
[ RUN ] ManagerTest.ConnectionRefused_WrongCredentials
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in SetUp().
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in TearDown().
[ FAILED ] ManagerTest.ConnectionRefused_WrongCredentials (0 ms)
[ RUN ] ManagerTest.CredentialGetter_Working
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in SetUp().
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in TearDown().
[ FAILED ] ManagerTest.CredentialGetter_Working (1 ms)
[ RUN ] ManagerTest.DatabaseName_Working
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in SetUp().
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in TearDown().
[ FAILED ] ManagerTest.DatabaseName_Working (0 ms)
[ RUN ] ManagerTest.ConnectionCredentialsInitAndWipe
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in SetUp().
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in TearDown().
[ FAILED ] ManagerTest.ConnectionCredentialsInitAndWipe (0 ms)
[ RUN ] ManagerTest.RemoteWipe
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in SetUp().
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in TearDown().
[ FAILED ] ManagerTest.RemoteWipe (1 ms)
[ RUN ] ManagerTest.ServerTime
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in SetUp().
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in TearDown().
[ FAILED ] ManagerTest.ServerTime (0 ms)
[ RUN ] ManagerTest.Reconnect
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in SetUp().
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in TearDown().
[ FAILED ] ManagerTest.Reconnect (1 ms)
[ RUN ] ManagerTest.GetCollection
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in SetUp().
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in TearDown().
[ FAILED ] ManagerTest.GetCollection (0 ms)
[ RUN ] ManagerTest.CheckVersion
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in SetUp().
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in TearDown().
[ FAILED ] ManagerTest.CheckVersion (0 ms)
[ RUN ] ManagerTest.GetVersion
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in SetUp().
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in TearDown().
[ FAILED ] ManagerTest.GetVersion (1 ms)
[ RUN ] ManagerTest.GetCollectionFails
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in SetUp().
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in TearDown().
[ FAILED ] ManagerTest.GetCollectionFails (0 ms)
[ RUN ] ManagerTest.ExpectedDBFails
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in SetUp().
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in TearDown().
[ FAILED ] ManagerTest.ExpectedDBFails (1 ms)
[ RUN ] ManagerTest.HasCollectionFails
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in SetUp().
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in TearDown().
[ FAILED ] ManagerTest.HasCollectionFails (0 ms)
[ RUN ] ManagerTest.WipeFails
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in SetUp().
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in TearDown().
[ FAILED ] ManagerTest.WipeFails (1 ms)
[ RUN ] ManagerTest.InitFails
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in SetUp().
unknown file: Failure
C++ exception with description "No connection to a database available." thrown in TearDown().
[ FAILED ] ManagerTest.InitFails (0 ms)
[----------] 15 tests from ManagerTest (6 ms total)
...
and more of this
mamba list
❯ mamba list -n gcc
# packages in environment at /home/abt-grimme/opt/conda/envs/gcc:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 1_gnu conda-forge
binutils 2.36.1 hdd6e379_2 conda-forge
binutils_impl_linux-64 2.36.1 h193b22a_2 conda-forge
binutils_linux-64 2.36 hf3e587d_4 conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
c-ares 1.18.1 h7f98852_0 conda-forge
ca-certificates 2022.6.15 ha878542_0 conda-forge
clang 13.0.1 ha770c72_0 conda-forge
clang-13 13.0.1 default_hc23dcda_0 conda-forge
clangxx 13.0.1 default_ha53f305_0 conda-forge
cmake 3.23.2 h5432695_0 conda-forge
expat 2.4.8 h27087fc_0 conda-forge
gcc 11.2.0 h702ea55_2 conda-forge
gcc_impl_linux-64 11.2.0 h82a94d6_11 conda-forge
gcc_linux-64 11.2.0 h39a9532_4 conda-forge
gdb 11.1 py310hba97a52_3 conda-forge
gfortran 11.2.0 h8811e0c_2 conda-forge
gfortran_impl_linux-64 11.2.0 h7a446d4_11 conda-forge
gfortran_linux-64 11.2.0 h777b47f_4 conda-forge
gmp 6.2.1 h58526e2_0 conda-forge
gxx 11.2.0 h702ea55_2 conda-forge
gxx_impl_linux-64 11.2.0 h82a94d6_11 conda-forge
gxx_linux-64 11.2.0 hacbe6df_4 conda-forge
kernel-headers_linux-64 2.6.32 he073ed8_15 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
krb5 1.19.3 h08a2579_0 conda-forge
ld_impl_linux-64 2.36.1 hea4e1c9_2 conda-forge
libclang-cpp13 13.0.1 default_hc23dcda_0 conda-forge
libcurl 7.83.1 h2283fc2_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 h516909a_1 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc-devel_linux-64 11.2.0 h0952999_11 conda-forge
libgcc-ng 12.1.0 h8d9b700_16 conda-forge
libgfortran-ng 11.2.0 h69a702a_11 conda-forge
libgfortran5 11.2.0 h5c6108e_11 conda-forge
libgomp 12.1.0 h8d9b700_16 conda-forge
libllvm13 13.0.1 hf817b99_2 conda-forge
libnghttp2 1.47.0 he49606f_0 conda-forge
libnsl 2.0.0 h7f98852_0 conda-forge
libsanitizer 11.2.0 he4da1e4_11 conda-forge
libssh2 1.10.0 ha35d2d1_2 conda-forge
libstdcxx-devel_linux-64 11.2.0 h0952999_11 conda-forge
libstdcxx-ng 12.1.0 ha89aaad_16 conda-forge
libuuid 2.32.1 h7f98852_1000 conda-forge
libuv 1.43.0 h7f98852_0 conda-forge
libzlib 1.2.11 h36c2ea0_1013 conda-forge
lz4-c 1.9.3 h9c3ff4c_1 conda-forge
mpi 1.0 openmpi conda-forge
ncurses 6.3 h27087fc_1 conda-forge
ninja 1.11.0 h924138e_0 conda-forge
openmpi 4.1.1 hbfc84c5_0 conda-forge
openssl 3.0.4 h166bdaf_2 conda-forge
pip 22.0.4 pyhd8ed1ab_0 conda-forge
pkg-config 0.29.2 h36c2ea0_1008 conda-forge
pygments 2.11.2 pyhd8ed1ab_0 conda-forge
python 3.10.4 h2660328_0_cpython conda-forge
python_abi 3.10 2_cp310 conda-forge
readline 8.1 h46c0cb4_0 conda-forge
rhash 1.4.3 h166bdaf_0 conda-forge
setuptools 62.1.0 py310hff52083_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
sqlite 3.38.2 h4ff8645_0 conda-forge
sysroot_linux-64 2.12 he073ed8_15 conda-forge
tk 8.6.12 h27826a3_0 conda-forge
tzdata 2022a h191b570_0 conda-forge
wheel 0.37.1 pyhd8ed1ab_0 conda-forge
xz 5.2.5 h516909a_1 conda-forge
zlib 1.2.11 h36c2ea0_1013 conda-forge
zstd 1.5.2 h8a70e8d_1 conda-forge
❯ mamba list -n scine
# packages in environment at /home/abt-grimme/opt/conda/envs/scine:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_kmp_llvm conda-forge
boost-cpp 1.74.0 h75c5d50_8 conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
ca-certificates 2022.6.15 ha878542_0 conda-forge
cyrus-sasl 2.1.27 h7604b24_5 conda-forge
eigen 3.4.0 h4bd325d_0 conda-forge
icu 70.1 h27087fc_0 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
krb5 1.19.3 h08a2579_0 conda-forge
libblas 3.9.0 15_linux64_openblas conda-forge
libbson 1.21.2 h27087fc_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libgcc-ng 12.1.0 h8d9b700_16 conda-forge
libgfortran-ng 12.1.0 h69a702a_16 conda-forge
libgfortran5 12.1.0 hdcd56e2_16 conda-forge
libgomp 12.1.0 h8d9b700_16 conda-forge
liblapack 3.9.0 15_linux64_openblas conda-forge
libmongoc 1.21.2 h0506597_0 conda-forge
libmongocxx 3.6.7 h6e2fe03_0 conda-forge
libntlm 1.4 h7f98852_1002 conda-forge
libopenblas 0.3.20 pthreads_h78a6416_0 conda-forge
libstdcxx-ng 12.1.0 ha89aaad_16 conda-forge
libzlib 1.2.12 h166bdaf_1 conda-forge
llvm-openmp 14.0.4 he0ac6c6_0 conda-forge
lz4-c 1.9.3 h9c3ff4c_1 conda-forge
mctc-lib 0.3.0 hc3ea6d6_0 conda-forge
mkl 2022.1.0 h84fe81f_915 conda-forge
nauty 2.7.2 h7f98852_0 conda-forge
ncurses 6.3 h27087fc_1 conda-forge
openssl 3.0.4 h166bdaf_2 conda-forge
scine-core 4.0.1 h6e2fe03_0 conda-forge
scine-readuct 4.0.0 he3004b7_0 conda-forge
scine-sparrow 3.0.1 he3004b7_1 conda-forge
scine-utilsos 5.0.0 h99171d1_0 conda-forge
scine-xtb 1.0.1 h886c582_1 conda-forge
snappy 1.1.9 hbd366e4_1 conda-forge
tbb 2021.5.0 h924138e_1 conda-forge
xtb 6.5.0 h9d67668_0 conda-forge
xz 5.2.5 h516909a_1 conda-forge
yaml-cpp 0.7.0 h27087fc_1 conda-forge
zstd 1.5.2 h8a70e8d_2 conda-forge
mamba info
active environment : scine
active env location : /home/abt-grimme/opt/conda/envs/scine
shell level : 3
user config file : /home/ehlert/.condarc
populated config files : /home/abt-grimme/opt/conda/.condarc
/home/ehlert/.condarc
conda version : 4.12.0
conda-build version : not installed
python version : 3.9.10.final.0
virtual packages : __linux=4.12.14=0
__glibc=2.26=0
__unix=0=0
__archspec=1=x86_64
base environment : /home/abt-grimme/opt/conda (writable)
conda av data dir : /home/abt-grimme/opt/conda/etc/conda
conda av metadata url : None
channel URLs : https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/noarch
package cache : /home/abt-grimme/opt/conda/pkgs
/home/ehlert/.conda/pkgs
envs directories : /home/abt-grimme/opt/conda/envs
/home/ehlert/.conda/envs
platform : linux-64
user-agent : conda/4.12.0 requests/2.27.1 CPython/3.9.10 Linux/4.12.14-lp151.28.13-default opensuse-leap/15.1 glibc/2.26
UID:GID : 1748:1001
netrc file : None
offline mode : False
Deprecated CMake target used for mongo-cxx-driver
Using mongo-cxx-driver 3.6.7 the following warning is raised in the configure step
CMake Warning at /home/conda/staged-recipes/build_artifacts/scine-database_1656618507957/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/cmake/libmongocxx-3.6.7/libmongocxx-config.cmake:15 (message):
This CMake target is deprecated. Use 'mongo::mongocxx_shared' instead.
Consult the example projects for further details.
Call Stack (most recent call first):
dev/cmake/ImportMongoCxx.cmake:9 (find_package)
src/Database/CMakeLists.txt:10 (import_mongocxx)
CMake Warning at /home/conda/staged-recipes/build_artifacts/scine-database_1656618507957/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/cmake/libbsoncxx-3.6.7/libbsoncxx-config.cmake:15 (message):
This CMake target is deprecated. Use 'mongo::bsoncxx_shared' instead.
Consult the example projects for further details.
Call Stack (most recent call first):
/home/conda/staged-recipes/build_artifacts/scine-database_1656618507957/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/cmake/libmongocxx-3.6.7/libmongocxx-config.cmake:22 (find_package)
dev/cmake/ImportMongoCxx.cmake:9 (find_package)
src/Database/CMakeLists.txt:10 (import_mongocxx)
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