Failing tests after building RDKit from source on Windows 11 #7105

jzhang1705 · 2024-01-29T17:08:23Z

jzhang1705
Jan 29, 2024

TLDR: I am failing 138 tests after using the Cmake command below and compiling the build using Visual Studio on Windows. Has anyone had a similar issue?

I'm not using Conda as this is not allowed for my organization. I have been able to build RDKit using this Cmake command:

PS C:\Users\jeffreyz\OneDrive - MathWorks\Desktop\rdkit-master\rdkit-master\build> cmake -G "Visual Studio 17 2022" -A x64 `
>> -DVCPKG_TARGET_TRIPLET=x64-windows `
>> -DCMAKE_TOOLCHAIN_FILE="C:\Users\jeffreyz\OneDrive - MathWorks\Desktop\vcpkg\scripts\buildsystems\vcpkg.cmake" `
>> -DBoost_NO_SYSTEM_PATHS=TRUE `
>> -DBoost_ROOT="C:\Users\jeffreyz\OneDrive - MathWorks\Desktop\boost_1_84_0" `
>> -DBOOST_LIBRARYDIR="C:\Users\jeffreyz\OneDrive - MathWorks\Desktop\boost_1_84_0\lib64-msvc-14.3" `
>> -DBoost_NO_BOOST_CMAKE=TRUE `
>> -DBOOST_INCLUDEDIR="C:\Users\jeffreyz\OneDrive - MathWorks\Desktop\boost_1_84_0" `
>> -DBoost_SYSTEM_LIBRARY_RELEASE="C:\Users\jeffreyz\OneDrive - MathWorks\Desktop\boost_1_84_0\lib64-msvc-14.3\libboost_system-vc143-mt-x64-1_84.lib" `
>> -DBoost_SYSTEM_LIBRARY_DEBUG="C:\Users\jeffreyz\OneDrive - MathWorks\Desktop\boost_1_84_0\lib64-msvc-14.3\libboost_system-vc143-mt-gd-x64-1_84.lib" `
>> -DBoost_SERIALIZATION_LIBRARY_RELEASE="C:\Users\jeffreyz\OneDrive - MathWorks\Desktop\boost_1_84_0\lib64-msvc-14.3\libboost_serialization-vc143-mt-x64-1_84.lib" `
>> -DBoost_SERIALIZATION_LIBRARY_DEBUG="C:\Users\jeffreyz\OneDrive - MathWorks\Desktop\boost_1_84_0\lib64-msvc-14.3\libboost_serialization-vc143-mt-gd-x64-1_84.lib" `
>> -DBoost_IOSTREAMS_LIBRARY_RELEASE="C:\Users\jeffreyz\OneDrive - MathWorks\Desktop\boost_1_84_0\lib64-msvc-14.3\libboost_iostreams-vc143-mt-x64-1_84.lib" `
>> -DBoost_IOSTREAMS_LIBRARY_DEBUG="C:\Users\jeffreyz\OneDrive - MathWorks\Desktop\boost_1_84_0\lib64-msvc-14.3\libboost_iostreams-vc143-mt-gd-x64-1_84.lib" `
>> -DRDK_BUILD_PYTHON_WRAPPERS=OFF `
>> -DCMAKE_CXX_STANDARD=17 `
>> -DRDK_BUILD_CAIRO_SUPPORT=ON `
>> -DCMAKE_POLICY_DEFAULT_CMP0074=NEW `
>> -DCMAKE_PREFIX_PATH="C:/Users/jeffreyz/OneDrive - MathWorks/Desktop/MSYS2/mingw64" `
>> -DCAIRO_INCLUDE_DIR="C:/Users/jeffreyz/OneDrive - MathWorks/Desktop/MSYS2/mingw64/include/cairo" `
>> -DCAIRO_LIBRARIES="C:/Users/jeffreyz\OneDrive - MathWorks/Desktop/MSYS2/mingw64/lib/libcairo.a" `
>> -DFREETYPE_INCLUDE_DIR_freetype2="C:/Users/jeffreyz/OneDrive - MathWorks/Desktop/MSYS2/mingw64/include/freetype2" `
>> -DFREETYPE_INCLUDE_DIR_ft2build="C:/Users/jeffreyz\OneDrive - MathWorks/Desktop/MSYS2/mingw64/include" `
>> -DFREETYPE_LIBRARY="C:/Users/jeffreyz\OneDrive - MathWorks/Desktop/MSYS2/mingw64/lib/libfreetype.a" `
>> -DBoost_REGEX_LIBRARY_RELEASE="C:\Users\jeffreyz\OneDrive - MathWorks\Desktop\boost_1_84_0\lib64-msvc-14.3\libboost_regex-vc143-mt-x64-1_84.lib" `
>> -DBoost_REGEX_LIBRARY_DEBUG="C:\Users\jeffreyz\OneDrive - MathWorks\Desktop\boost_1_84_0\lib64-msvc-14.3\libboost_regex-vc143-mt-gd-x64-1_84.lib" `
>> -DZLIB_LIBRARY_RELEASE="C:\Users\jeffreyz\OneDrive - MathWorks\Desktop\boost_1_84_0\lib64-msvc-14.3\libboost_zlib-vc143-mt-x64-1_84.lib" `
>> -DZLIB_LIBRARY_DEBUG="C:\Users\jeffreyz\OneDrive - MathWorks\Desktop\boost_1_84_0\lib64-msvc-14.3\libboost_zlib-vc143-mt-gd-x64-1_84.lib" ..

To which it outputs:

-- The C compiler identification is MSVC 19.37.32822.0
-- The CXX compiler identification is MSVC 19.37.32822.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: C:/Program Files/Microsoft Visual Studio/2022/Professional/VC/Tools/MSVC/14.37.32822/bin/Hostx64/x64/cl.exe - 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: C:/Program Files/Microsoft Visual Studio/2022/Professional/VC/Tools/MSVC/14.37.32822/bin/Hostx64/x64/cl.exe - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
Disabling boost::stacktrace on non-linux platform
-- Found Catch2 source in C:/Users/jeffreyz/OneDrive - MathWorks/Desktop/rdkit-master/rdkit-master/External/catch/catch
CATCH: C:/Users/jeffreyz/OneDrive - MathWorks/Desktop/rdkit-master/rdkit-master/External/catch/catch/single_include/catch2
-- Found Boost: C:/Users/jeffreyz/OneDrive - MathWorks/Desktop/boost_1_84_0 (found suitable version "1.84.0", minimum required is "1.58.0")
-- Could NOT find Eigen3 (missing: EIGEN3_INCLUDE_DIR EIGEN3_VERSION_OK) (Required is at least version "2.91.0")
-- 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 - not found
-- Found Threads: TRUE
CMake Warning at C:/Program Files/CMake/share/cmake-3.28/Modules/FindBoost.cmake:1398 (message):
  New Boost version may have incorrect or missing dependencies and imported
  targets
Call Stack (most recent call first):
  C:/Program Files/CMake/share/cmake-3.28/Modules/FindBoost.cmake:1523 (_Boost_COMPONENT_DEPENDENCIES)
  C:/Program Files/CMake/share/cmake-3.28/Modules/FindBoost.cmake:2134 (_Boost_MISSING_DEPENDENCIES)
  C:/Users/jeffreyz/OneDrive - MathWorks/Desktop/vcpkg/scripts/buildsystems/vcpkg.cmake:859 (_find_package)
  CMakeLists.txt:442 (find_package)


CMake Warning at C:/Program Files/CMake/share/cmake-3.28/Modules/FindBoost.cmake:1398 (message):
  New Boost version may have incorrect or missing dependencies and imported
  targets
Call Stack (most recent call first):
  C:/Program Files/CMake/share/cmake-3.28/Modules/FindBoost.cmake:1523 (_Boost_COMPONENT_DEPENDENCIES)
  C:/Program Files/CMake/share/cmake-3.28/Modules/FindBoost.cmake:2134 (_Boost_MISSING_DEPENDENCIES)
  C:/Users/jeffreyz/OneDrive - MathWorks/Desktop/vcpkg/scripts/buildsystems/vcpkg.cmake:859 (_find_package)
  CMakeLists.txt:442 (find_package)


CMake Warning at C:/Program Files/CMake/share/cmake-3.28/Modules/FindBoost.cmake:1398 (message):
  New Boost version may have incorrect or missing dependencies and imported
  targets
Call Stack (most recent call first):
  C:/Program Files/CMake/share/cmake-3.28/Modules/FindBoost.cmake:1523 (_Boost_COMPONENT_DEPENDENCIES)
  C:/Program Files/CMake/share/cmake-3.28/Modules/FindBoost.cmake:2134 (_Boost_MISSING_DEPENDENCIES)
  C:/Users/jeffreyz/OneDrive - MathWorks/Desktop/vcpkg/scripts/buildsystems/vcpkg.cmake:859 (_find_package)
  CMakeLists.txt:442 (find_package)


CMake Warning at C:/Program Files/CMake/share/cmake-3.28/Modules/FindBoost.cmake:1398 (message):
  New Boost version may have incorrect or missing dependencies and imported
  targets
Call Stack (most recent call first):
  C:/Program Files/CMake/share/cmake-3.28/Modules/FindBoost.cmake:1523 (_Boost_COMPONENT_DEPENDENCIES)
  C:/Program Files/CMake/share/cmake-3.28/Modules/FindBoost.cmake:2134 (_Boost_MISSING_DEPENDENCIES)
  C:/Users/jeffreyz/OneDrive - MathWorks/Desktop/vcpkg/scripts/buildsystems/vcpkg.cmake:859 (_find_package)
  CMakeLists.txt:442 (find_package)


-- Found Boost: C:/Users/jeffreyz/OneDrive - MathWorks/Desktop/boost_1_84_0 (found suitable version "1.84.0", minimum required is "1.58.0") found components: system serialization iostreams regex
== Using strict rotor definition
CMake Warning at C:/Program Files/CMake/share/cmake-3.28/Modules/FindBoost.cmake:1398 (message):
  New Boost version may have incorrect or missing dependencies and imported
  targets
Call Stack (most recent call first):
  C:/Program Files/CMake/share/cmake-3.28/Modules/FindBoost.cmake:1523 (_Boost_COMPONENT_DEPENDENCIES)
  C:/Program Files/CMake/share/cmake-3.28/Modules/FindBoost.cmake:2134 (_Boost_MISSING_DEPENDENCIES)
  C:/Users/jeffreyz/OneDrive - MathWorks/Desktop/vcpkg/scripts/buildsystems/vcpkg.cmake:859 (_find_package)
  External/CoordGen/CMakeLists.txt:9 (find_package)


CMake Warning at C:/Program Files/CMake/share/cmake-3.28/Modules/FindBoost.cmake:1398 (message):
  New Boost version may have incorrect or missing dependencies and imported
  targets
Call Stack (most recent call first):
  C:/Program Files/CMake/share/cmake-3.28/Modules/FindBoost.cmake:1523 (_Boost_COMPONENT_DEPENDENCIES)
  C:/Program Files/CMake/share/cmake-3.28/Modules/FindBoost.cmake:2134 (_Boost_MISSING_DEPENDENCIES)
  C:/Users/jeffreyz/OneDrive - MathWorks/Desktop/vcpkg/scripts/buildsystems/vcpkg.cmake:859 (_find_package)
  External/CoordGen/CMakeLists.txt:9 (find_package)


CMake Warning at C:/Program Files/CMake/share/cmake-3.28/Modules/FindBoost.cmake:1398 (message):
  New Boost version may have incorrect or missing dependencies and imported
  targets
Call Stack (most recent call first):
  C:/Program Files/CMake/share/cmake-3.28/Modules/FindBoost.cmake:1523 (_Boost_COMPONENT_DEPENDENCIES)
  C:/Program Files/CMake/share/cmake-3.28/Modules/FindBoost.cmake:2134 (_Boost_MISSING_DEPENDENCIES)
  C:/Users/jeffreyz/OneDrive - MathWorks/Desktop/vcpkg/scripts/buildsystems/vcpkg.cmake:859 (_find_package)
  External/CoordGen/CMakeLists.txt:9 (find_package)


-- Found Boost: C:/Users/jeffreyz/OneDrive - MathWorks/Desktop/boost_1_84_0 (found suitable version "1.84.0", minimum required is "1.58.0") found components: system iostreams regex
CMake Warning at C:/Program Files/CMake/share/cmake-3.28/Modules/FindBoost.cmake:1398 (message):
  New Boost version may have incorrect or missing dependencies and imported
  targets
Call Stack (most recent call first):
  C:/Program Files/CMake/share/cmake-3.28/Modules/FindBoost.cmake:1523 (_Boost_COMPONENT_DEPENDENCIES)
  C:/Program Files/CMake/share/cmake-3.28/Modules/FindBoost.cmake:2134 (_Boost_MISSING_DEPENDENCIES)
  C:/Users/jeffreyz/OneDrive - MathWorks/Desktop/vcpkg/scripts/buildsystems/vcpkg.cmake:859 (_find_package)
  External/CoordGen/CMakeLists.txt:17 (find_package)


-- Found Boost: C:/Users/jeffreyz/OneDrive - MathWorks/Desktop/boost_1_84_0 (found suitable version "1.84.0", minimum required is "1.58.0") found components: zlib
-- maeparser include dir set as 'maeparser_INCLUDE_DIRS-NOTFOUND'
-- maeparser libraries set as 'maeparser_LIBRARIES-NOTFOUND'
-- Could NOT find maeparser (missing: maeparser_INCLUDE_DIRS maeparser_LIBRARIES)
-- Found MAEParser source in C:/Users/jeffreyz/OneDrive - MathWorks/Desktop/rdkit-master/rdkit-master/External/CoordGen/maeparser
-- coordgen include dir set as coordgen_INCLUDE_DIRS-NOTFOUND
-- coordgen libraries set as 'coordgen_LIBRARIES-NOTFOUND'
-- Could NOT find coordgen (missing: coordgen_INCLUDE_DIRS coordgen_LIBRARIES)
-- Found coordgenlibs source in C:/Users/jeffreyz/OneDrive - MathWorks/Desktop/rdkit-master/rdkit-master/External/CoordGen/coordgen
-- Found RingDecomposerLib source in C:/Users/jeffreyz/OneDrive - MathWorks/Desktop/rdkit-master/rdkit-master/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib
CMake Warning at C:/Program Files/CMake/share/cmake-3.28/Modules/FindBoost.cmake:1398 (message):
  New Boost version may have incorrect or missing dependencies and imported
  targets
Call Stack (most recent call first):
  C:/Program Files/CMake/share/cmake-3.28/Modules/FindBoost.cmake:1523 (_Boost_COMPONENT_DEPENDENCIES)
  C:/Program Files/CMake/share/cmake-3.28/Modules/FindBoost.cmake:2134 (_Boost_MISSING_DEPENDENCIES)
  C:/Users/jeffreyz/OneDrive - MathWorks/Desktop/vcpkg/scripts/buildsystems/vcpkg.cmake:859 (_find_package)
  Code/RDStreams/CMakeLists.txt:4 (find_package)


CMake Warning at C:/Program Files/CMake/share/cmake-3.28/Modules/FindBoost.cmake:1398 (message):
  New Boost version may have incorrect or missing dependencies and imported
  targets
Call Stack (most recent call first):
  C:/Program Files/CMake/share/cmake-3.28/Modules/FindBoost.cmake:1523 (_Boost_COMPONENT_DEPENDENCIES)
  C:/Program Files/CMake/share/cmake-3.28/Modules/FindBoost.cmake:2134 (_Boost_MISSING_DEPENDENCIES)
  C:/Users/jeffreyz/OneDrive - MathWorks/Desktop/vcpkg/scripts/buildsystems/vcpkg.cmake:859 (_find_package)
  Code/RDStreams/CMakeLists.txt:4 (find_package)


-- Found Boost: C:/Users/jeffreyz/OneDrive - MathWorks/Desktop/boost_1_84_0 (found suitable version "1.84.0", minimum required is "1.58.0") found components: iostreams regex
CMake Warning at C:/Program Files/CMake/share/cmake-3.28/Modules/FindBoost.cmake:1398 (message):
  New Boost version may have incorrect or missing dependencies and imported
  targets
Call Stack (most recent call first):
  C:/Program Files/CMake/share/cmake-3.28/Modules/FindBoost.cmake:1523 (_Boost_COMPONENT_DEPENDENCIES)
  C:/Program Files/CMake/share/cmake-3.28/Modules/FindBoost.cmake:2134 (_Boost_MISSING_DEPENDENCIES)
  C:/Users/jeffreyz/OneDrive - MathWorks/Desktop/vcpkg/scripts/buildsystems/vcpkg.cmake:859 (_find_package)
  Code/RDStreams/CMakeLists.txt:10 (find_package)


-- Found Boost: C:/Users/jeffreyz/OneDrive - MathWorks/Desktop/boost_1_84_0 (found suitable version "1.84.0", minimum required is "1.58.0") found components: zlib
CMake Warning at C:/Program Files/CMake/share/cmake-3.28/Modules/FindBoost.cmake:1398 (message):
  New Boost version may have incorrect or missing dependencies and imported
  targets
Call Stack (most recent call first):
  C:/Program Files/CMake/share/cmake-3.28/Modules/FindBoost.cmake:1523 (_Boost_COMPONENT_DEPENDENCIES)
  C:/Program Files/CMake/share/cmake-3.28/Modules/FindBoost.cmake:2134 (_Boost_MISSING_DEPENDENCIES)
  C:/Users/jeffreyz/OneDrive - MathWorks/Desktop/vcpkg/scripts/buildsystems/vcpkg.cmake:859 (_find_package)
  Code/GraphMol/FileParsers/CMakeLists.txt:5 (find_package)


CMake Warning at C:/Program Files/CMake/share/cmake-3.28/Modules/FindBoost.cmake:1398 (message):
  New Boost version may have incorrect or missing dependencies and imported
  targets
Call Stack (most recent call first):
  C:/Program Files/CMake/share/cmake-3.28/Modules/FindBoost.cmake:1523 (_Boost_COMPONENT_DEPENDENCIES)
  C:/Program Files/CMake/share/cmake-3.28/Modules/FindBoost.cmake:2134 (_Boost_MISSING_DEPENDENCIES)
  C:/Users/jeffreyz/OneDrive - MathWorks/Desktop/vcpkg/scripts/buildsystems/vcpkg.cmake:859 (_find_package)
  Code/GraphMol/FileParsers/CMakeLists.txt:5 (find_package)


CMake Warning at C:/Program Files/CMake/share/cmake-3.28/Modules/FindBoost.cmake:1398 (message):
  New Boost version may have incorrect or missing dependencies and imported
  targets
Call Stack (most recent call first):
  C:/Program Files/CMake/share/cmake-3.28/Modules/FindBoost.cmake:1523 (_Boost_COMPONENT_DEPENDENCIES)
  C:/Program Files/CMake/share/cmake-3.28/Modules/FindBoost.cmake:2134 (_Boost_MISSING_DEPENDENCIES)
  C:/Users/jeffreyz/OneDrive - MathWorks/Desktop/vcpkg/scripts/buildsystems/vcpkg.cmake:859 (_find_package)
  Code/GraphMol/FileParsers/CMakeLists.txt:5 (find_package)


-- Found Boost: C:/Users/jeffreyz/OneDrive - MathWorks/Desktop/boost_1_84_0 (found suitable version "1.84.0", minimum required is "1.58.0") found components: system iostreams regex
-- Found ZLIB: optimized;C:/Users/jeffreyz/OneDrive - MathWorks/Desktop/boost_1_84_0/lib64-msvc-14.3/libboost_zlib-vc143-mt-x64-1_84.lib;debug;C:/Users/jeffreyz/OneDrive - MathWorks/Desktop/boost_1_84_0/lib64-msvc-14.3/libboost_zlib-vc143-mt-gd-x64-1_84.lib (found version "1.3")
CMake Warning at C:/Program Files/CMake/share/cmake-3.28/Modules/FindBoost.cmake:1398 (message):
  New Boost version may have incorrect or missing dependencies and imported
  targets
Call Stack (most recent call first):
  C:/Program Files/CMake/share/cmake-3.28/Modules/FindBoost.cmake:1523 (_Boost_COMPONENT_DEPENDENCIES)
  C:/Program Files/CMake/share/cmake-3.28/Modules/FindBoost.cmake:2134 (_Boost_MISSING_DEPENDENCIES)
  C:/Users/jeffreyz/OneDrive - MathWorks/Desktop/vcpkg/scripts/buildsystems/vcpkg.cmake:859 (_find_package)
  Code/GraphMol/FileParsers/CMakeLists.txt:12 (find_package)


-- Found Boost: C:/Users/jeffreyz/OneDrive - MathWorks/Desktop/boost_1_84_0 (found suitable version "1.84.0", minimum required is "1.58.0") found components: zlib
CMake Warning (dev) at C:/Users/jeffreyz/OneDrive - MathWorks/Desktop/vcpkg/scripts/buildsystems/vcpkg.cmake:859 (_find_package):
  Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules
  are removed.  Run "cmake --help-policy CMP0148" for policy details.  Use
  the cmake_policy command to set the policy and suppress this warning.

Call Stack (most recent call first):
  Code/GraphMol/FilterCatalog/CMakeLists.txt:8 (find_package)
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Found PythonInterp: C:/Users/jeffreyz/OneDrive - MathWorks/Desktop/MSYS2/mingw64/bin/python.exe (found version "3.11.7")
C:/Users/jeffreyz/OneDrive - MathWorks/Desktop/rdkit-master/rdkit-master/Data/Fonts/ComicNeue-Regular.ttf already there, skipping the download
-- Found PkgConfig: C:/Users/jeffreyz/OneDrive - MathWorks/Desktop/vcpkg/installed/x64-windows/tools/pkgconf/pkgconf.exe (found version "2.1.0")
-- Found Cairo: C:/Users/jeffreyz/OneDrive - MathWorks/Desktop/MSYS2/mingw64/include/cairo
CMake Warning at C:/Program Files/CMake/share/cmake-3.28/Modules/FindBoost.cmake:1398 (message):
  New Boost version may have incorrect or missing dependencies and imported
  targets
Call Stack (most recent call first):
  C:/Program Files/CMake/share/cmake-3.28/Modules/FindBoost.cmake:1523 (_Boost_COMPONENT_DEPENDENCIES)
  C:/Program Files/CMake/share/cmake-3.28/Modules/FindBoost.cmake:2134 (_Boost_MISSING_DEPENDENCIES)
  C:/Users/jeffreyz/OneDrive - MathWorks/Desktop/vcpkg/scripts/buildsystems/vcpkg.cmake:859 (_find_package)
  Code/GraphMol/RGroupDecomposition/CMakeLists.txt:26 (find_package)


-- Found Boost: C:/Users/jeffreyz/OneDrive - MathWorks/Desktop/boost_1_84_0 (found suitable version "1.84.0", minimum required is "1.58.0") found components: program_options
-- Found RapidJSON source in C:/Users/jeffreyz/OneDrive - MathWorks/Desktop/rdkit-master/rdkit-master/External
-- Configuring done (12.6s)
-- Generating done (3.8s)
CMake Warning:
  Manually-specified variables were not used by the project:

    FREETYPE_INCLUDE_DIR_ft2build
    FREETYPE_LIBRARY


-- Build files have been written to: C:/Users/jeffreyz/OneDrive - MathWorks/Desktop/rdkit-master/rdkit-master/build`

The directory then looks like this:

Directory: C:\Users\jeffreyz\OneDrive - MathWorks\Desktop\rdkit-master\rdkit-master\build


Mode                 LastWriteTime         Length Name
----                 -------------         ------ ----
d-----         1/27/2024   1:20 PM                CMakeFiles
d-----         1/27/2024   1:19 PM                Code
d-----         1/27/2024   1:19 PM                External
d-----         1/27/2024   1:19 PM                Testing
-a----         1/27/2024   1:19 PM         119922 ALL_BUILD.vcxproj
-a----         1/27/2024   1:19 PM            327 ALL_BUILD.vcxproj.filters
-a----         1/27/2024   1:19 PM          58884 CMakeCache.txt
-a----         1/27/2024   1:19 PM           9044 cmake_install.cmake
-a----         1/27/2024   1:19 PM          60365 Continuous.vcxproj
-a----         1/27/2024   1:19 PM            841 Continuous.vcxproj.filters
-a----         1/27/2024   1:19 PM           4119 CPackConfig.cmake
-a----         1/27/2024   1:19 PM           4614 CPackSourceConfig.cmake
-a----         1/27/2024   1:19 PM            350 CTestCustom.ctest
-a----         1/27/2024   1:19 PM            461 CTestTestfile.cmake
-a----         1/27/2024   1:19 PM           3162 DartConfiguration.tcl
-a----         1/27/2024   1:19 PM          60387 Experimental.vcxproj
-a----         1/27/2024   1:19 PM            845 Experimental.vcxproj.filters
-a----         1/27/2024   1:19 PM          10868 INSTALL.vcxproj
-a----         1/27/2024   1:19 PM            569 INSTALL.vcxproj.filters
-a----         1/27/2024   1:19 PM          60332 Nightly.vcxproj
-a----         1/27/2024   1:19 PM            835 Nightly.vcxproj.filters
-a----         1/27/2024   1:19 PM          60453 NightlyMemoryCheck.vcxproj
-a----         1/27/2024   1:19 PM            857 NightlyMemoryCheck.vcxproj.filters
-a----         1/27/2024   1:19 PM          11387 PACKAGE.vcxproj
-a----         1/27/2024   1:19 PM            569 PACKAGE.vcxproj.filters
-a----         1/27/2024   1:19 PM           1911 rdkit-config-version.cmake
-a----         1/27/2024   1:19 PM           1315 rdkit-config.cmake
-a----         1/27/2024   1:20 PM         534059 RDKit.sln
-a----         1/27/2024   1:19 PM          10281 RUN_TESTS.vcxproj
-a----         1/27/2024   1:19 PM            571 RUN_TESTS.vcxproj.filters
-a----         1/27/2024   1:19 PM         149287 ZERO_CHECK.vcxproj
-a----         1/27/2024   1:19 PM            570 ZERO_CHECK.vcxproj.filters

I then use Visual Studiio to build the rest of the libraries. However, when I run ctest, I only pass 10% of the tests:

10% tests passed, 138 tests failed out of 154

Total Test time (real) = 1580.56 sec

The following tests FAILED:
          1 - testCoordGen (Not Run)
          7 - testDataStructs (Failed)
          8 - testFPB (Failed)
          9 - testMultiFPB (Failed)
         11 - testGrid (Timeout)
         17 - testUFFForceField (Not Run)
         18 - testMMFFForceField (Not Run)
         20 - graphmolTest1 (Not Run)
         21 - graphmolcpTest (Not Run)
         22 - graphmolqueryTest (Not Run)
         23 - graphmolMolOpsTest (Not Run)
         24 - graphmoltestChirality (Not Run)
         25 - graphmoltestPickler (Not Run)
         26 - graphmoltestPicklerGlobalSetting (Not Run)
         27 - graphmolIterTest (Not Run)
         28 - hanoiTest (Not Run)
         29 - graphmolMemTest1 (Not Run)
         30 - resMolSupplierTest (Not Run)
         31 - molBundleTest (Not Run)
         32 - testSGroup (Not Run)
         33 - test-valgrind (Not Run)
         34 - graphmolTestsCatch (Not Run)
         35 - graphmolOrganometallicsCatch (Not Run)
         36 - graphmolSGroupCatch (Not Run)
         37 - graphmolAdjustQueryCatch (Not Run)
         38 - chiralityTestsCatch (Not Run)
         39 - canonTestsCatch (Not Run)
         40 - moliteratorTestsCatch (Not Run)
         41 - queryTestsCatch (Not Run)
         42 - molbundleTestsCatch (Not Run)
         43 - pickleTestsCatch (Not Run)
         44 - smiTest1 (Not Run)
         45 - smiTest2 (Not Run)
         46 - cxsmilesTest (Not Run)
         47 - smaTest1 (Not Run)
         48 - smiTestCatch (Not Run)
         49 - nontetrahedralCatch (Not Run)
         50 - testDepictor (Not Run)
         51 - depictorCatch (Not Run)
         52 - testMrvToMol (Not Run)
         53 - fileParsersTest1 (Not Run)
         54 - testMolSupplier (Not Run)
         55 - testGeneralFileReader (Not Run)
         56 - testMultithreadedMolSupplier (Not Run)
         57 - testMolWriter (Not Run)
         58 - testTplParser (Not Run)
         59 - testMol2ToMol (Not Run)
         60 - testSequence (Not Run)
         61 - testExtendedStereoParsing (Not Run)
         62 - fileParsersCatchTest (Not Run)
         63 - testPropertyLists (Not Run)
         64 - XYZFileParserCatchTest (Not Run)
         65 - cdxmlParserCatchTest (Not Run)
         66 - molfileStereoCatchTest (Not Run)
         67 - connectTheDotsTest (Not Run)
         68 - testSubstructMatch (Not Run)
         69 - substructTestCatch (Not Run)
         70 - testGenericGroups (Not Run)
         71 - testReaction (Not Run)
         72 - testReactionFingerprints (Not Run)
         73 - testEnumeration (Not Run)
         74 - rxnTestCatch (Not Run)
         75 - testChemTransforms (Not Run)
         76 - chemTransformsTestCatch (Not Run)
         77 - tautomerQueryTestCatch (Not Run)
         78 - testSubgraphs1 (Not Run)
         79 - testSubgraphs2 (Not Run)
         80 - subgraphsCatch (Not Run)
         81 - filterCatalogTest (Not Run)
         82 - testFragCatalog (Not Run)
         83 - testDescriptors (Not Run)
         84 - testAUTOCORR2D (Not Run)
         85 - testATF (Not Run)
         86 - testBCUT (Not Run)
         87 - testEEM (Not Run)
         88 - testPBF (Not Run)
         89 - testRDFcustom (Not Run)
         90 - testRDF (Not Run)
         91 - testMORSE (Not Run)
         92 - test3D (Not Run)
         93 - testWHIM (Not Run)
         94 - testGETAWAY (Not Run)
         95 - testAUTOCORR3D (Not Run)
         96 - testCoulombMat (Not Run)
         97 - descriptorsTestCatch (Not Run)
         98 - testFingerprints (Not Run)
         99 - testMHFPFingerprint (Not Run)
        100 - testFingerprintGenerators (Not Run)
        101 - fpTestCatch (Not Run)
        102 - fpGenTestCatch (Not Run)
        103 - testPartialCharges (Not Run)
        104 - testMolTransforms (Not Run)
        105 - testMMFFForceFieldHelpers (Not Run)
        106 - testMMFFForceFieldHelpersMultiThread (Not Run)
        107 - testUFFForceFieldHelpers (Not Run)
        108 - testCrystalForceField (Not Run)
        109 - testDistGeomHelpers (Not Run)
        110 - distGeomHelpersCatch (Not Run)
        111 - testMolAlign (Not Run)
        112 - testO3AAlign (Not Run)
        113 - molAlignCatchTest (Not Run)
        114 - testFeatures (Not Run)
        115 - testShapeHelpers (Not Run)
        116 - testMolCatalog (Not Run)
        117 - moldraw2DTest1 (Not Run)
        118 - moldraw2DTestCatch (Not Run)
        119 - moldraw2DRxnTest1 (Not Run)
        120 - testFMCS (Not Run)
        121 - FMCStest (Not Run)
        122 - molHashCatchTest (Not Run)
        123 - testMMPA (Not Run)
        124 - testRascalMCES (Not Run)
        125 - testRascalCluster (Not Run)
        126 - testCIPLabeler (Not Run)
        127 - deprotectTest (Not Run)
        128 - testReducedGraphs (Not Run)
        129 - trajectoryTest (Not Run)
        130 - substructLibraryTest (Not Run)
        131 - substructLibraryCatchTest (Not Run)
        132 - testRGroupDecomp (Not Run)
        133 - testRGroupDecompInternals (Not Run)
        134 - rgroupCatchTests (Not Run)
        135 - molInterchangeTest1 (Not Run)
        136 - molInterchangeCatchTest (Not Run)
        137 - testSLNParse (Not Run)
        138 - molStandardizeTest (Not Run)
        139 - molNormalizeTest (Not Run)
        140 - molValidateTest (Not Run)
        141 - molChargeTest (Not Run)
        142 - molTautomerTest (Not Run)
        143 - molStandardizeSmallTest (Not Run)
        144 - molFragmentTest (Not Run)
        145 - molStandardizeCatchTest (Not Run)
        146 - testScaffoldNetwork (Not Run)
        147 - testMolEnumerator (Not Run)
        148 - testAbbreviations (Not Run)
        149 - generalizedSubstructCatch (Not Run)
        153 - pickersTestsCatch (Failed)
Errors while running CTest

Can anyone help me with either rebuilding RDKit from source or tell me what I am doing wrong? Remember I cannot use Conda.

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Failing tests after building RDKit from source on Windows 11 #7105

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Failing tests after building RDKit from source on Windows 11 #7105

jzhang1705 Jan 29, 2024

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jzhang1705
Jan 29, 2024