Re: [Rdkit-discuss] Building RDKit on Windows. Only static libraries produced? How to make the Python wrapper work?
> Joos Kiener hat am 11.05.2023 16:11 CEST geschrieben: > > > Hi Ernst-Georg, > > maybe you are running into the same issue as I was: > > https://github.com/rdkit/rdkit/discussions/6148#discussioncomment-5450102 > > You have to explicitly tell python where the dlls are: > > os.add_dll_directory(r"C:\path\to\rdkit\lib") > > before importing rdkit. > > From python documentation: > > DLL dependencies for extension modules and DLLs loaded with ctypes > https://docs.python.org/3/library/ctypes.html#module-ctypes on Windows are > now resolved more securely. Only the system paths, the directory containing > the DLL or PYD file, and directories added with add_dll_directory() > https://docs.python.org/3/library/os.html#os.add_dll_directory are searched > for load-time dependencies. Specifically, PATH and the current working > directory are no longer used, and modifications to these will no longer have > any effect on normal DLL resolution. > > Best Regards, > > Joos > > Hello Joos, that was the problem indeed. Thank you very much for your help. best regards Ernst-Georg ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Building RDKit on Windows. Only static libraries produced? How to make the Python wrapper work?
Hi Ernst-Georg, maybe you are running into the same issue as I was: https://github.com/rdkit/rdkit/discussions/6148#discussioncomment-5450102 You have to explicitly tell python where the dlls are: os.add_dll_directory(r"C:\path\to\rdkit\lib") before importing rdkit. >From python documentation: DLL dependencies for extension modules and DLLs loaded with ctypes <https://docs.python.org/3/library/ctypes.html#module-ctypes> on Windows are now resolved more securely. Only the system paths, the directory containing the DLL or PYD file, and directories added with add_dll_directory() <https://docs.python.org/3/library/os.html#os.add_dll_directory> are searched for load-time dependencies. *Specifically, PATH and the current working directory are no longer used, and modifications to these will no longer have any effect on normal DLL resolution*. Best Regards, Joos > > -- Forwarded message -- > From: pgchem pgchem > To: "rdkit-discuss@lists.sourceforge.net" < > rdkit-discuss@lists.sourceforge.net> > Cc: > Bcc: > Date: Wed, 10 May 2023 16:32:31 +0200 (CEST) > Subject: [Rdkit-discuss] Building RDKit on Windows. Only static libraries > produced? How to make the Python wrapper work? > Hello all, > > I'm currently trying to build RDKit 2023_03_1 on Windows 11 with Visual > Studio 2022 Community. The building itself works: > > - No errors during the build > - I get a working extension against PostgreSQL 15.2 > - I get working static libraries for Visual Studio (RDGeneral.lib etc.) > - I get a rdkit package for Python 3.10 > > BUT this does not work: > > from rdkit import Chem > > Traceback (most recent call last): > File "", line 1, in > File "C:\RDKit\lib\site-packages\rdkit\__init__.py", line 6, in > from . import rdBase > ImportError: DLL load failed while importing rdBase: The specified module > could not be found. > > I am pretty sure, that the environment is ok, I have checked with the > dependency walker that rdBase.pyd sees everything it needs. > > However, when I take a look at the rdkit package from PyPI, there are a > lot of *.dlls. while my build only produces static libraries (*.lib). > > When I compare the sizes of rdBase.pyd from PyPI and mine, mine is much > larger, so I assume that it also is statically linked - so it should work?, > but it doesn't. > > Any pointers to what I am doing wrong here? > > This is my cmake command: > > c:/cmake/bin/cmake -DRDK_BUILD_PYTHON_WRAPPERS=ON > -DBOOST_ROOT=C:/Devel/RDBuild/boost -DRDK_BUILD_CAIRO_SUPPORT=ON > -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_BUILD_AVALON_SUPPORT=ON > -DRDK_BUILD_PGSQL=ON -DPostgreSQL_ROOT="C:\PostgreSQL\15" > -DRDK_INSTALL_INTREE=OFF -DCMAKE_INSTALL_PREFIX=c:/RDKit > -DEIGEN3_INCLUDE_DIR=C:/Devel/RDBuild/eigen3 > -DFREETYPE_INCLUDE_DIRS=c:/Devel/RDbuild/freetype/include > -DFREETYPE_LIBRARY="c:/Devel/RDBuild/freetype/release > dll/win64/freetype.lib" -DZLIB_INCLUDE_DIR=c:/Devel/RDBuild/zlib/include > -DZLIB_LIBRARY=c:/Devel/RDBuild/zlib/libz.lib > -DCAIRO_INCLUDE_DIRS=c:/Devel/RDBuild/cairo/include > -DCAIRO_LIBRARIES=c:/Devel/RDBuild/cairo/lib/x64/cairo.lib > -DRDK_BUILD_FREETYPE_SUPPORT=ON -DRDK_BUILD_COMPRESSED_SUPPLIERS=ON > -G"Visual Studio 17 2022" -A x64 .. > > and the MSBuild command: > > & "C:\Program Files\Microsoft Visual > Studio\2022\Community\MSBuild\Current\Bin\MSBuild.exe" > /p:Configuration=Release INSTALL.vcxproj > > best regards > > Ernst-Georg > > > > -- Forwarded message -- > From: Ernst-Georg Schmid > To: "rdkit-discuss@lists.sourceforge.net" < > rdkit-discuss@lists.sourceforge.net> > Cc: > Bcc: > Date: Thu, 11 May 2023 14:35:23 +0200 > Subject: Re: [Rdkit-discuss] Building RDKit on Windows. Only static > libraries produced? How to make the Python wrapper work? > Am 10.05.2023 um 16:32 schrieb pgchem pgchem: > > I'm currently trying to build RDKit 2023_03_1 on Windows 11 with Visual > > Studio 2022 Community. The building itself works: > > - No errors during the build > > - I get a working extension against PostgreSQL 15.2 > > - I get working static libraries for Visual Studio (RDGeneral.lib etc.) > > - I get a rdkit package for Python 3.10 > > BUT this does not work: > > from rdkit import Chem > > Traceback (most recent call last): > > File "", line 1, in > > File "C:\RDKit\lib\site-packages\rdkit\__init__.py", line 6, in > > from . import rdBase > > ImportError: DLL load failed while importing rdBase: The specified > > module could not be found. > > Hello again, > > I have managed to
Re: [Rdkit-discuss] Building RDKit on Windows. Only static libraries produced? How to make the Python wrapper work?
Am 10.05.2023 um 16:32 schrieb pgchem pgchem: I'm currently trying to build RDKit 2023_03_1 on Windows 11 with Visual Studio 2022 Community. The building itself works: - No errors during the build - I get a working extension against PostgreSQL 15.2 - I get working static libraries for Visual Studio (RDGeneral.lib etc.) - I get a rdkit package for Python 3.10 BUT this does not work: from rdkit import Chem Traceback (most recent call last): File "", line 1, in File "C:\RDKit\lib\site-packages\rdkit\__init__.py", line 6, in from . import rdBase ImportError: DLL load failed while importing rdBase: The specified module could not be found. Hello again, I have managed to build the shared objects also by now. I had to carve this out of the azure pipelines, apparently it only works correctly if you build like there, i.e. using cmake instead of MSBuild directly. E.g. C:\CMake\bin\cmake --build . --config=Release --target install instead of & "C:\Program Files\Microsoft Visual Studio\2022\Community\MSBuild\Current\Bin\MSBuild.exe" /p:Configuration=Release INSTALL.vcxproj (as the RDKit Book says) But the rdkit Python package still throws abovementioned error. I did the same build on Ubuntu, and everything worked out of the box. I have also checked various "solutions" from the WWW but to no avail. I cannot see any unresolved dependencies for rdBase.pyd. Any helpful suggestions or pointers are appreciated. best regards Ernst-Georg ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Building RDKit on Windows. Only static libraries produced? How to make the Python wrapper work?
Hello all, I'm currently trying to build RDKit 2023_03_1 on Windows 11 with Visual Studio 2022 Community. The building itself works: - No errors during the build - I get a working extension against PostgreSQL 15.2 - I get working static libraries for Visual Studio (RDGeneral.lib etc.) - I get a rdkit package for Python 3.10 BUT this does not work: from rdkit import Chem Traceback (most recent call last): File "", line 1, in File "C:\RDKit\lib\site-packages\rdkit\__init__.py", line 6, in from . import rdBase ImportError: DLL load failed while importing rdBase: The specified module could not be found. I am pretty sure, that the environment is ok, I have checked with the dependency walker that rdBase.pyd sees everything it needs. However, when I take a look at the rdkit package from PyPI, there are a lot of *.dlls. while my build only produces static libraries (*.lib). When I compare the sizes of rdBase.pyd from PyPI and mine, mine is much larger, so I assume that it also is statically linked - so it should work?, but it doesn't. Any pointers to what I am doing wrong here? This is my cmake command: c:/cmake/bin/cmake -DRDK_BUILD_PYTHON_WRAPPERS=ON -DBOOST_ROOT=C:/Devel/RDBuild/boost -DRDK_BUILD_CAIRO_SUPPORT=ON -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_BUILD_AVALON_SUPPORT=ON -DRDK_BUILD_PGSQL=ON -DPostgreSQL_ROOT="C:\PostgreSQL\15" -DRDK_INSTALL_INTREE=OFF -DCMAKE_INSTALL_PREFIX=c:/RDKit -DEIGEN3_INCLUDE_DIR=C:/Devel/RDBuild/eigen3 -DFREETYPE_INCLUDE_DIRS=c:/Devel/RDbuild/freetype/include -DFREETYPE_LIBRARY="c:/Devel/RDBuild/freetype/release dll/win64/freetype.lib" -DZLIB_INCLUDE_DIR=c:/Devel/RDBuild/zlib/include -DZLIB_LIBRARY=c:/Devel/RDBuild/zlib/libz.lib -DCAIRO_INCLUDE_DIRS=c:/Devel/RDBuild/cairo/include -DCAIRO_LIBRARIES=c:/Devel/RDBuild/cairo/lib/x64/cairo.lib -DRDK_BUILD_FREETYPE_SUPPORT=ON -DRDK_BUILD_COMPRESSED_SUPPLIERS=ON -G"Visual Studio 17 2022" -A x64 .. and the MSBuild command: & "C:\Program Files\Microsoft Visual Studio\2022\Community\MSBuild\Current\Bin\MSBuild.exe" /p:Configuration=Release INSTALL.vcxproj best regards Ernst-Georg___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Building RDKit on Windows for pgAdmin (Postgres)
Hi Paolo,
I finally had some time to look at this again and I tried building from a conda
environment.
I looked at the instruction on https://github.com/rdkit/conda-rdkit and after
getting a bit lost as to where the recipe for building boost is (found it
through
https://docs.conda.io/projects/conda-build/en/latest/user-guide/recipes/sample-recipes.html)
I tried first building boost but got stuck.
Running $ conda build boost through command prompt ends up giving me this error
message where the process is aborted:
(%BUILD_PREFIX%) %SRC_DIR%>call bootstrap.bat
Building Boost.Build engine
** B A T C H R E C U R S I O N exceeds STACK limits **
Recursion Count=336, Stack Usage=90 percent
** B A T C H PROCESSING IS A B O R T E D **
Traceback (most recent call last):
File "C:\Users\candy\anaconda3\Scripts\conda-build-script.py", line 10, in
sys.exit(main())
File
"C:\Users\candy\anaconda3\lib\site-packages\conda_build\cli\main_build.py",
line 488, in main
execute(sys.argv[1:])
File
"C:\Users\candy\anaconda3\lib\site-packages\conda_build\cli\main_build.py",
line 477, in execute
outputs = api.build(args.recipe, post=args.post,
test_run_post=args.test_run_post,
File "C:\Users\candy\anaconda3\lib\site-packages\conda_build\api.py", line
186, in build
return build_tree(
File "C:\Users\candy\anaconda3\lib\site-packages\conda_build\build.py", line
3088, in build_tree
packages_from_this = build(metadata, stats,
File "C:\Users\candy\anaconda3\lib\site-packages\conda_build\build.py", line
2179, in build
windows.build(m, build_file, stats=build_stats,
provision_only=provision_only)
File "C:\Users\candy\anaconda3\lib\site-packages\conda_build\windows.py",
line 297, in build
check_call_env(cmd, cwd=m.config.work_dir, stats=stats,
rewrite_stdout_env=rewrite_env)
File "C:\Users\candy\anaconda3\lib\site-packages\conda_build\utils.py", line
410, in check_call_env
return _func_defaulting_env_to_os_environ('call', *popenargs, **kwargs)
File "C:\Users\candy\anaconda3\lib\site-packages\conda_build\utils.py", line
390, in _func_defaulting_env_to_os_environ
raise subprocess.CalledProcessError(proc.returncode, _args)
subprocess.CalledProcessError: Command '['cmd.exe', '/d', '/c',
'conda_build.bat']' returned non-zero exit status 255.
Any idea as to why this is happening and how to fix this?
Regards,
Charmaine Chu
Computational Chemist
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From: Paolo Tosco
Sent: 14 April 2022 18:41
To: Charmaine Siu Man Chu
Cc: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] Building RDKit on Windows for pgAdmin (Postgres)
Hi Charmaine,
my suggestion is to build starting from a conda environment. That will
significantly simplify your dependencies, since most packages are available
pre-built.
You can look into .azure-pipelines\vs_build_dll.yml for how to set up your
conda environment and for the cmake flags to use.
For Postgres, these are the cmake flags that I use to configure the PostgreSQL
DLL build:
-D RDK_BUILD_PGSQL=ON ^
-D RDK_PGSQL_STATIC=OFF ^
-D PostgreSQL_INCLUDE_DIR="C:/Program Files/PostgreSQL/14/include" ^
-D PostgreSQL_TYPE_INCLUDE_DIR="C:/Program
Files/PostgreSQL/14/include/server" ^
-D PostgreSQL_LIBRARY="C:/Program Files/PostgreSQL/14/lib/postgres.lib" ^
..
Note that this is to build against Postgres installed using the Windows
installer from the PostgreSQL website, not the version provided by conda.
Cheers,
p.
On Thu, Apr 14, 2022 at 11:36 AM Charmaine Siu Man Chu
mailto:charmaine@liverpoolchirochem.com>>
wrote:
Hello,
I’ve been trying to build RDKit on Windows so that I can get the RDKit
extension in pgAdmin (Postgres) but I’ve been unsuccessful.
I’ve tried to follow the instruction on https://www.rdkit.org/docs/Install.html
to build RDKit and encountered several problems.
Some of them I mana
Re: [Rdkit-discuss] Building RDKit on Windows for pgAdmin (Postgres)
Hi Charmaine, my suggestion is to build starting from a conda environment. That will significantly simplify your dependencies, since most packages are available pre-built. You can look into .azure-pipelines\vs_build_dll.yml for how to set up your conda environment and for the cmake flags to use. For Postgres, these are the cmake flags that I use to configure the PostgreSQL DLL build: -D RDK_BUILD_PGSQL=ON ^ -D RDK_PGSQL_STATIC=OFF ^ -D PostgreSQL_INCLUDE_DIR="C:/Program Files/PostgreSQL/14/include" ^ -D PostgreSQL_TYPE_INCLUDE_DIR="C:/Program Files/PostgreSQL/14/include/server" ^ -D PostgreSQL_LIBRARY="C:/Program Files/PostgreSQL/14/lib/postgres.lib" ^ .. Note that this is to build against Postgres installed using the Windows installer from the PostgreSQL website, not the version provided by conda. Cheers, p. On Thu, Apr 14, 2022 at 11:36 AM Charmaine Siu Man Chu < charmaine@liverpoolchirochem.com> wrote: > Hello, > > > > I’ve been trying to build RDKit on Windows so that I can get the RDKit > extension in pgAdmin (Postgres) but I’ve been unsuccessful. > > I’ve tried to follow the instruction on > https://www.rdkit.org/docs/Install.html to build RDKit and encountered > several problems. > > Some of them I manage to resolve myself but can someone help on this? > > > > Here is what I’ve tried: > > > > To start off, I’m using the Windows 11 64-bit OS and Postgres 14 was > installed. > > I then went to install the following: > > Python 3.10 along with numpy and Pillow > > Visual Studio 2022 with Visual Studio Community 2022, Visual Studio Build > Tools 2022 > > Cmake 3.23.0 > > Boost_1_78_0 using the .exe installer > > And downloaded and extracted the rdkit-Release_2022_03_1 > > > > After install the above, I ran the below in Comand Prompt > > cmake -DRDK_BUILD_PYTHON_WRAPPERS=ON -DBOOST_ROOT=C:/locall/boost_1_78_0 > -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_BUILD_AVALON_SUPPORT=ON > -DRDK_BUILD_PGSQL=ON -DPostgreSQL_ROOT="C:\Program Files\PostgreSQL\14" > -G"Visual Studio 17 2022" .. > > came back with error: > > The following variants have been tried and rejected: > > > > * boost_python310-vc143-mt-gd-x64-1_78.lib (shared, default on Windows is > > static, set Boost_USE_STATIC_LIBS=OFF to override) > > > > * boost_python310-vc143-mt-x64-1_78.lib (shared, default on Windows is > > static, set Boost_USE_STATIC_LIBS=OFF to override) > > > > I then edit the command line to > > cmake -DRDK_BUILD_PYTHON_WRAPPERS=ON -DBOOST_ROOT=C:/locall/boost_1_78_0 > -DBoost_USE_STATIC_LIBS=OFF -DRDK_BUILD_INCHI_SUPPORT=ON > -DRDK_BUILD_AVALON_SUPPORT=ON -DRDK_BUILD_PGSQL=ON > -DPostgreSQL_ROOT="C:\Program Files\PostgreSQL\14" -G"Visual Studio 17 > 2022" .. > > and this time following error occured > > Could NOT find Eigen3 (missing: EIGEN3_INCLUDE_DIR EIGEN3_VERSION_OK) > (Required is at least version "2.91.0") > > CMake Error at C:/Program > Files/CMake/share/cmake-3.23/Modules/ExternalProject.cmake:2540 (message): > > error: could not find git for clone of Eigen > > > > So I went to download and extracted eigen 3.4.0 and edit the command line > to > > cmake -DRDK_BUILD_PYTHON_WRAPPERS=ON -DBOOST_ROOT=C:/locall/boost_1_78_0 > -DBoost_USE_STATIC_LIBS=OFF -DEIGEN3_INCLUDE_DIR="C:/eigen-3.4.0" > -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_BUILD_AVALON_SUPPORT=ON > -DRDK_BUILD_PGSQL=ON -DPostgreSQL_ROOT="C:\Program Files\PostgreSQL\14" > -G"Visual Studio 17 2022" .. > > which gave the following error > > CMake Error at C:/Program > Files/CMake/share/cmake-3.23/Modules/FindPackageHandleStandardArgs.cmake:230 > (message): > > Could NOT find Freetype (missing: FREETYPE_LIBRARY FREETYPE_INCLUDE_DIRS) > > > > So again I went to obtain freetype-2.12.0 and build it following the > instructions on > https://bobhowto.wordpress.com/2020/11/10/build-freetype-on-windows-10-using-visual-studio-2017/, > using VS 2022 instead, and edit the command line to > > cmake -DRDK_BUILD_PYTHON_WRAPPERS=ON -DBOOST_ROOT=C:/local/boost_1_78_0 > -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_BUILD_AVALON_SUPPORT=ON > -DBoost_USE_STATIC_LIBS=OFF -DEIGEN3_INCLUDE_DIR="C:/eigen-3.4.0" > -DFREETYPE_INCLUDE_DIRS="C:/freetype-2.12.0/include" > -DFREETYPE_LIBRARY="C:/freetype-2.12.0/objs/freetype.lib" > -DRDK_BUILD_PGSQL=ON -DPostgreSQL_ROOT="C:\Program Files\PostgreSQL\14" > -G"Visual Studio 17 2022" .. > > and it managed to compile > > However, when running > > "C:\Program Files\Microsoft Visual > Studio\2022\Community\MSBuild\Current\Bin\MSBuild.exe" /m:4 > /p:Configuration=Release INSTALL.vcxproj > > Gave the following error with 47 other warnings > > "C:\rdkit-Release_2022_03_1\build\INSTALL.vcxproj" (default target) (1) -> > >"C:\rdkit-Release_2022_03_1\build\ALL_BUILD.vcxproj" (default > target) (3) -> > > > "C:\rdkit-Release_2022_03_1\build\Code\GraphMol\Deprotect\Wrap\rdDeprotect.vcxproj" > (default target) (20) -> > > > "C:\rdkit-Release_2022_03_1\build\Code\GraphMol\ChemReactions\ChemReactions.vcxproj" > (default target) (48) -> > >
[Rdkit-discuss] Building RDKit on Windows for pgAdmin (Postgres)
Hello, I've been trying to build RDKit on Windows so that I can get the RDKit extension in pgAdmin (Postgres) but I've been unsuccessful. I've tried to follow the instruction on https://www.rdkit.org/docs/Install.html to build RDKit and encountered several problems. Some of them I manage to resolve myself but can someone help on this? Here is what I've tried: To start off, I'm using the Windows 11 64-bit OS and Postgres 14 was installed. I then went to install the following: Python 3.10 along with numpy and Pillow Visual Studio 2022 with Visual Studio Community 2022, Visual Studio Build Tools 2022 Cmake 3.23.0 Boost_1_78_0 using the .exe installer And downloaded and extracted the rdkit-Release_2022_03_1 After install the above, I ran the below in Comand Prompt cmake -DRDK_BUILD_PYTHON_WRAPPERS=ON -DBOOST_ROOT=C:/locall/boost_1_78_0 -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_BUILD_AVALON_SUPPORT=ON -DRDK_BUILD_PGSQL=ON -DPostgreSQL_ROOT="C:\Program Files\PostgreSQL\14" -G"Visual Studio 17 2022" .. came back with error: The following variants have been tried and rejected: * boost_python310-vc143-mt-gd-x64-1_78.lib (shared, default on Windows is static, set Boost_USE_STATIC_LIBS=OFF to override) * boost_python310-vc143-mt-x64-1_78.lib (shared, default on Windows is static, set Boost_USE_STATIC_LIBS=OFF to override) I then edit the command line to cmake -DRDK_BUILD_PYTHON_WRAPPERS=ON -DBOOST_ROOT=C:/locall/boost_1_78_0 -DBoost_USE_STATIC_LIBS=OFF -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_BUILD_AVALON_SUPPORT=ON -DRDK_BUILD_PGSQL=ON -DPostgreSQL_ROOT="C:\Program Files\PostgreSQL\14" -G"Visual Studio 17 2022" .. and this time following error occured Could NOT find Eigen3 (missing: EIGEN3_INCLUDE_DIR EIGEN3_VERSION_OK) (Required is at least version "2.91.0") CMake Error at C:/Program Files/CMake/share/cmake-3.23/Modules/ExternalProject.cmake:2540 (message): error: could not find git for clone of Eigen So I went to download and extracted eigen 3.4.0 and edit the command line to cmake -DRDK_BUILD_PYTHON_WRAPPERS=ON -DBOOST_ROOT=C:/locall/boost_1_78_0 -DBoost_USE_STATIC_LIBS=OFF -DEIGEN3_INCLUDE_DIR="C:/eigen-3.4.0" -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_BUILD_AVALON_SUPPORT=ON -DRDK_BUILD_PGSQL=ON -DPostgreSQL_ROOT="C:\Program Files\PostgreSQL\14" -G"Visual Studio 17 2022" .. which gave the following error CMake Error at C:/Program Files/CMake/share/cmake-3.23/Modules/FindPackageHandleStandardArgs.cmake:230 (message): Could NOT find Freetype (missing: FREETYPE_LIBRARY FREETYPE_INCLUDE_DIRS) So again I went to obtain freetype-2.12.0 and build it following the instructions on https://bobhowto.wordpress.com/2020/11/10/build-freetype-on-windows-10-using-visual-studio-2017/, using VS 2022 instead, and edit the command line to cmake -DRDK_BUILD_PYTHON_WRAPPERS=ON -DBOOST_ROOT=C:/local/boost_1_78_0 -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_BUILD_AVALON_SUPPORT=ON -DBoost_USE_STATIC_LIBS=OFF -DEIGEN3_INCLUDE_DIR="C:/eigen-3.4.0" -DFREETYPE_INCLUDE_DIRS="C:/freetype-2.12.0/include" -DFREETYPE_LIBRARY="C:/freetype-2.12.0/objs/freetype.lib" -DRDK_BUILD_PGSQL=ON -DPostgreSQL_ROOT="C:\Program Files\PostgreSQL\14" -G"Visual Studio 17 2022" .. and it managed to compile However, when running "C:\Program Files\Microsoft Visual Studio\2022\Community\MSBuild\Current\Bin\MSBuild.exe" /m:4 /p:Configuration=Release INSTALL.vcxproj Gave the following error with 47 other warnings "C:\rdkit-Release_2022_03_1\build\INSTALL.vcxproj" (default target) (1) -> "C:\rdkit-Release_2022_03_1\build\ALL_BUILD.vcxproj" (default target) (3) -> "C:\rdkit-Release_2022_03_1\build\Code\GraphMol\Deprotect\Wrap\rdDeprotect.vcxproj" (default target) (20) -> "C:\rdkit-Release_2022_03_1\build\Code\GraphMol\ChemReactions\ChemReactions.vcxproj" (default target) (48) -> "C:\rdkit-Release_2022_03_1\build\Code\GraphMol\Descriptors\Descriptors.vcxproj" (default target) (55) -> "C:\rdkit-Release_2022_03_1\build\Code\GraphMol\FileParsers\FileParsers.vcxproj" (default target) (56) -> (ClCompile target) -> C:\rdkit-Release_2022_03_1\Code\GraphMol\FileParsers\PNGParser.cpp(25,10): fatal error C1083: Cannot open incl ude file: 'zlib.h': No such file or directory [C:\rdkit-Release_2022_03_1\build\Code\GraphMol\FileParsers\FilePa rsers.vcxproj] So I went to obtain zlib 1.2.12 and build it via cmake -G"Visual Studio 17 2022" .. "C:\Program Files\Microsoft Visual Studio\2022\Community\MSBuild\Current\Bin\MSBuild.exe" zlib.sln copy /Y zconf.h .. and compiled the boost libraries via b2 --prefix=C:\local\boost_1_78_0 -sZLIB_SOURCE="C:/zlib-1.2.12" -sZLIB_INCLUDE="C:/zlib-1.2.12" -sZLIB_LIBPATH="C:/zlib-1.2.12/build/Release" -sZLIB_BINARY="C:/zlib-1.2.12/build/Release/zlib.lib" --debug-configuration -d0 address-model=64 link=shared install and changed the PATH in the environment variables to C:\local\boost_1_78_0\lib but running the build code and the INSTALL.vcxproj gave the same error
Re: [Rdkit-discuss] Building RDKit on Windows
Dear RDKit Community, Dear Paolo, I have now managed to build the RDKit on a fresh Windows environment. I was unable to do so before due to the following issue: According to https://gitlab.kitware.com/cmake/cmake/issues/16391 the python suffixes for Boost have changed since 1.67. I tried to build with the 1.68 but always got a... Could not find the following Boost libraries: boost_python The solution was to use a boost version below 1.67, then the build works. Thanks for considering this solution, and thanks again for your support and the awesome RDKit! Cheers, Roman Von: Roman Bolzern Gesendet: Mittwoch, 29. August 2018 07:24 An: 'Paolo Tosco' ; Rdkit-discuss@lists.sourceforge.net Betreff: AW: [Rdkit-discuss] Building RDKit on Windows Hi Paolo Thanks a lot! I tried building using your libraries, but unfortunately I still have the same issue.. I know they work for you so now I triple checked every detail: environment variables are set, and I built with -DBOOST_LIBRARYDIR=C:/boost/lib and without. And according to CMakeLists.txt it should be able to find both of boost_pythons (in your build as well as in my installed build)... I'm not experienced with cmake building so maybe it's a beginner mistake? Below again the command I currently trust the most (along with environment variables BOOST_ROOT, BOOST_LIBRARYDIR and the boost library dir set in PATH): Thank you for your time! Roman C:\RDKit\build>cmake -DRDK_BUILD_PYTHON_WRAPPERS=ON -DBOOST_ROOT=C:/boost -DBOOST_LIBRARYDIR=C:/boost/lib -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_BUILD_AVALON_SUPPORT=ON -DRDK_BUILD_PGSQL=ON -G"Visual Studio 15 2017 Win64" .. -- Could NOT find InChI in system locations (missing: INCHI_LIBRARY INCHI_INCLUDE_DIR) CUSTOM_INCHI_PATH = C:/RDKit/External/INCHI-API -- Found InChI software locally CMake Warning at C:/Program Files/CMake/share/cmake-3.12/Modules/FindBoost.cmake:1723 (message): No header defined for python-py36; skipping header check Call Stack (most recent call first): CMakeLists.txt:191 (find_package) CMake Error at C:/Program Files/CMake/share/cmake-3.12/Modules/FindBoost.cmake:2044 (message): Unable to find the requested Boost libraries. Boost version: 1.68.0 Boost include path: C:/boost Could not find the following Boost libraries: boost_python No Boost libraries were found. You may need to set BOOST_LIBRARYDIR to the directory containing Boost libraries or BOOST_ROOT to the location of Boost. ... Von: Paolo Tosco mailto:paolo.tosco.m...@gmail.com>> Gesendet: Dienstag, 28. August 2018 20:32 An: Roman Bolzern mailto:roman.bolz...@chemspeed.com>>; Rdkit-discuss@lists.sourceforge.net<mailto:Rdkit-discuss@lists.sourceforge.net> Betreff: Re: [Rdkit-discuss] Building RDKit on Windows Hi Roman, I have a pre-built version of Boost 1.64 for Windows/Python 3.6 built using VS2017. I always use it to build my own copy of the RDKit and I know it works fine. You may find it here: https://www.dropbox.com/s/xqzv71r2lllhww1/boost_py36-vc152-mt-1_64.zip?dl=0 HTH, cheers, p. On 28/08/2018 13:52, Roman Bolzern wrote: Dear RDKit community, I'm trying to build RDKit on Windows, yet Cmake is unable to find boost_python. It finds "serialization" though, and the path "C:\boost\libs\python" exists. Also, I've replaced all boost versions in CMakeLists.txt with my installed version of boost (1.56.0 -> 1.68.0). As the code in CMakeLists.txt seems to me as if it searches for "python3" and not just "python", I tried to rename the folder in boost to "python3", but it still doesn't find boost_python. The boost library was installed by downloading the exe from SourceForge. I pasted the full console output below for reference. What should I try next? Thank you and kind regards, Roman C:\RDKit\build>cmake -DRDK_BUILD_PYTHON_WRAPPERS=ON -DBOOST_ROOT=C:/boost -DBOOST_LIBRARYDIR=C:/boost/libs -DRDK_BOOST_PYTHON3_NAME="python" -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_BUILD_AVALON_SUPPORT=ON -DRDK_BUILD_PGSQL=ON -G"Visual Studio 15 2017 Win64" .. -- Could NOT find InChI in system locations (missing: INCHI_LIBRARY INCHI_INCLUDE_DIR) CUSTOM_INCHI_PATH = C:/RDKit/External/INCHI-API -- Found InChI software locally CMake Warning at C:/Program Files/CMake/share/cmake-3.12/Modules/FindBoost.cmake:1723 (message): No header defined for python-py36; skipping header check Call Stack (most recent call first): CMakeLists.txt:191 (find_package) CMake Error at C:/Program Files/CMake/share/cmake-3.12/Modules/FindBoost.cmake:2044 (message): Unable to find the requested Boost libraries. Boost version: 1.68.0 Boost include path: C:/boost Could not find the following Boost libraries: boost_python No Boost libraries were found. You may need to set BOOST_LIBRARYDIR to the directory containing Boost libraries or BOOST
Re: [Rdkit-discuss] Building RDKit on Windows
Hi Paolo Thanks a lot! I tried building using your libraries, but unfortunately I still have the same issue.. I know they work for you so now I triple checked every detail: environment variables are set, and I built with -DBOOST_LIBRARYDIR=C:/boost/lib and without. And according to CMakeLists.txt it should be able to find both of boost_pythons (in your build as well as in my installed build)... I'm not experienced with cmake building so maybe it's a beginner mistake? Below again the command I currently trust the most (along with environment variables BOOST_ROOT, BOOST_LIBRARYDIR and the boost library dir set in PATH): Thank you for your time! Roman C:\RDKit\build>cmake -DRDK_BUILD_PYTHON_WRAPPERS=ON -DBOOST_ROOT=C:/boost -DBOOST_LIBRARYDIR=C:/boost/lib -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_BUILD_AVALON_SUPPORT=ON -DRDK_BUILD_PGSQL=ON -G"Visual Studio 15 2017 Win64" .. -- Could NOT find InChI in system locations (missing: INCHI_LIBRARY INCHI_INCLUDE_DIR) CUSTOM_INCHI_PATH = C:/RDKit/External/INCHI-API -- Found InChI software locally CMake Warning at C:/Program Files/CMake/share/cmake-3.12/Modules/FindBoost.cmake:1723 (message): No header defined for python-py36; skipping header check Call Stack (most recent call first): CMakeLists.txt:191 (find_package) CMake Error at C:/Program Files/CMake/share/cmake-3.12/Modules/FindBoost.cmake:2044 (message): Unable to find the requested Boost libraries. Boost version: 1.68.0 Boost include path: C:/boost Could not find the following Boost libraries: boost_python No Boost libraries were found. You may need to set BOOST_LIBRARYDIR to the directory containing Boost libraries or BOOST_ROOT to the location of Boost. ... Von: Paolo Tosco Gesendet: Dienstag, 28. August 2018 20:32 An: Roman Bolzern ; Rdkit-discuss@lists.sourceforge.net Betreff: Re: [Rdkit-discuss] Building RDKit on Windows Hi Roman, I have a pre-built version of Boost 1.64 for Windows/Python 3.6 built using VS2017. I always use it to build my own copy of the RDKit and I know it works fine. You may find it here: https://www.dropbox.com/s/xqzv71r2lllhww1/boost_py36-vc152-mt-1_64.zip?dl=0 HTH, cheers, p. On 28/08/2018 13:52, Roman Bolzern wrote: Dear RDKit community, I'm trying to build RDKit on Windows, yet Cmake is unable to find boost_python. It finds "serialization" though, and the path "C:\boost\libs\python" exists. Also, I've replaced all boost versions in CMakeLists.txt with my installed version of boost (1.56.0 -> 1.68.0). As the code in CMakeLists.txt seems to me as if it searches for "python3" and not just "python", I tried to rename the folder in boost to "python3", but it still doesn't find boost_python. The boost library was installed by downloading the exe from SourceForge. I pasted the full console output below for reference. What should I try next? Thank you and kind regards, Roman C:\RDKit\build>cmake -DRDK_BUILD_PYTHON_WRAPPERS=ON -DBOOST_ROOT=C:/boost -DBOOST_LIBRARYDIR=C:/boost/libs -DRDK_BOOST_PYTHON3_NAME="python" -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_BUILD_AVALON_SUPPORT=ON -DRDK_BUILD_PGSQL=ON -G"Visual Studio 15 2017 Win64" .. -- Could NOT find InChI in system locations (missing: INCHI_LIBRARY INCHI_INCLUDE_DIR) CUSTOM_INCHI_PATH = C:/RDKit/External/INCHI-API -- Found InChI software locally CMake Warning at C:/Program Files/CMake/share/cmake-3.12/Modules/FindBoost.cmake:1723 (message): No header defined for python-py36; skipping header check Call Stack (most recent call first): CMakeLists.txt:191 (find_package) CMake Error at C:/Program Files/CMake/share/cmake-3.12/Modules/FindBoost.cmake:2044 (message): Unable to find the requested Boost libraries. Boost version: 1.68.0 Boost include path: C:/boost Could not find the following Boost libraries: boost_python No Boost libraries were found. You may need to set BOOST_LIBRARYDIR to the directory containing Boost libraries or BOOST_ROOT to the location of Boost. Call Stack (most recent call first): CMakeLists.txt:198 (find_package) -- Could NOT find Eigen3 (missing: EIGEN3_INCLUDE_DIR EIGEN3_VERSION_OK) (Required is at least version "2.91.0") Eigen3 not found, disabling the Descriptors3D build. -- Boost version: 1.68.0 -- Found the following Boost libraries: -- serialization CMake Warning (dev) at CMakeLists.txt:317 (find_package): Policy CMP0074 is not set: find_package uses PackageName_ROOT variables. Run "cmake --help-policy CMP0074" for policy details. Use the cmake_policy command to set the policy and suppress this warning. CMake variable PostgreSQL_ROOT is set to: C:\Program Files\PostgreSQL\10 Environment variable PostgreSQL_ROOT is set to: C:\Program Files\PostgreSQL\10 For compatibility, CMake is ignoring the variable. This warning is for project developers. Use
Re: [Rdkit-discuss] Building RDKit on Windows
Hi Roman, I have a pre-built version of Boost 1.64 for Windows/Python 3.6 built using VS2017. I always use it to build my own copy of the RDKit and I know it works fine. You may find it here: https://www.dropbox.com/s/xqzv71r2lllhww1/boost_py36-vc152-mt-1_64.zip?dl=0 HTH, cheers, p. On 28/08/2018 13:52, Roman Bolzern wrote: Dear RDKit community, I’m trying to build RDKit on Windows, yet Cmake is unable to find boost_python. It finds “serialization” though, and the path “C:\boost\libs\python” exists. Also, I’ve replaced all boost versions in CMakeLists.txt with my installed version of boost (1.56.0 -> 1.68.0). As the code in CMakeLists.txt seems to me as if it searches for “python3” and not just “python”, I tried to rename the folder in boost to “python3”, but it still doesn’t find boost_python. The boost library was installed by downloading the exe from SourceForge. I pasted the full console output below for reference. What should I try next? Thank you and kind regards, Roman C:\RDKit\build>cmake -DRDK_BUILD_PYTHON_WRAPPERS=ON -DBOOST_ROOT=C:/boost -DBOOST_LIBRARYDIR=C:/boost/libs -DRDK_BOOST_PYTHON3_NAME="python" -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_BUILD_AVALON_SUPPORT=ON -DRDK_BUILD_PGSQL=ON -G"Visual Studio 15 2017 Win64" .. -- Could NOT find InChI in system locations (missing: INCHI_LIBRARY INCHI_INCLUDE_DIR) CUSTOM_INCHI_PATH = C:/RDKit/External/INCHI-API -- Found InChI software locally CMake Warning at C:/Program Files/CMake/share/cmake-3.12/Modules/FindBoost.cmake:1723 (message): No header defined for python-py36; skipping header check Call Stack (most recent call first): CMakeLists.txt:191 (find_package) CMake Error at C:/Program Files/CMake/share/cmake-3.12/Modules/FindBoost.cmake:2044 (message): Unable to find the requested Boost libraries. Boost version: 1.68.0 Boost include path: C:/boost Could not find the following Boost libraries: boost_python No Boost libraries were found. You may need to set BOOST_LIBRARYDIR to the directory containing Boost libraries or BOOST_ROOT to the location of Boost. Call Stack (most recent call first): CMakeLists.txt:198 (find_package) -- Could NOT find Eigen3 (missing: EIGEN3_INCLUDE_DIR EIGEN3_VERSION_OK) (Required is at least version "2.91.0") Eigen3 not found, disabling the Descriptors3D build. -- Boost version: 1.68.0 -- Found the following Boost libraries: -- serialization CMake Warning (dev) at CMakeLists.txt:317 (find_package): Policy CMP0074 is not set: find_package uses PackageName_ROOT variables. Run "cmake --help-policy CMP0074" for policy details. Use the cmake_policy command to set the policy and suppress this warning. CMake variable PostgreSQL_ROOT is set to: C:\Program Files\PostgreSQL\10 Environment variable PostgreSQL_ROOT is set to: C:\Program Files\PostgreSQL\10 For compatibility, CMake is ignoring the variable. This warning is for project developers. Use -Wno-dev to suppress it. == Using strict rotor definition -- Found MAEParser source in C:/RDKit/External/CoordGen/maeparser -- Found coordgenlibs source in C:/RDKit/External/CoordGen/coordgenlibs == Updating Filters.cpp from pains file == Done updating pains files -- Found RapidJSON source in C:/RDKit/External CMake Warning (dev) at Code/PgSQL/rdkit/CMakeLists.txt:11 (find_package): Policy CMP0074 is not set: find_package uses PackageName_ROOT variables. Run "cmake --help-policy CMP0074" for policy details. Use the cmake_policy command to set the policy and suppress this warning. CMake variable PostgreSQL_ROOT is set to: C:\Program Files\PostgreSQL\10 Environment variable PostgreSQL_ROOT is set to: C:\Program Files\PostgreSQL\10 For compatibility, CMake is ignoring the variable. This warning is for project developers. Use -Wno-dev to suppress it. postgres: C:/Program Files/PostgreSQL/10/include;C:/Program Files/PostgreSQL/10/include/server = After building, check C:/RDKit/build/Code/PgSQL/rdkit/pgsql_install.bat for correctness of installation paths. If everything is OK, gain administrator privileges, stop the PostgreSQL service, run C:/RDKit/build/Code/PgSQL/rdkit/pgsql_install.bat to install the PostgreSQL RDKit cartridge, then start again the PostgreSQL service = -- Configuring incomplete, errors occurred! See also "C:/RDKit/build/CMakeFiles/CMakeOutput.log". See also "C:/RDKit/build/CMakeFiles/CMakeError.log". -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -
[Rdkit-discuss] Building RDKit on Windows
Dear RDKit community, I'm trying to build RDKit on Windows, yet Cmake is unable to find boost_python. It finds "serialization" though, and the path "C:\boost\libs\python" exists. Also, I've replaced all boost versions in CMakeLists.txt with my installed version of boost (1.56.0 -> 1.68.0). As the code in CMakeLists.txt seems to me as if it searches for "python3" and not just "python", I tried to rename the folder in boost to "python3", but it still doesn't find boost_python. The boost library was installed by downloading the exe from SourceForge. I pasted the full console output below for reference. What should I try next? Thank you and kind regards, Roman C:\RDKit\build>cmake -DRDK_BUILD_PYTHON_WRAPPERS=ON -DBOOST_ROOT=C:/boost -DBOOST_LIBRARYDIR=C:/boost/libs -DRDK_BOOST_PYTHON3_NAME="python" -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_BUILD_AVALON_SUPPORT=ON -DRDK_BUILD_PGSQL=ON -G"Visual Studio 15 2017 Win64" .. -- Could NOT find InChI in system locations (missing: INCHI_LIBRARY INCHI_INCLUDE_DIR) CUSTOM_INCHI_PATH = C:/RDKit/External/INCHI-API -- Found InChI software locally CMake Warning at C:/Program Files/CMake/share/cmake-3.12/Modules/FindBoost.cmake:1723 (message): No header defined for python-py36; skipping header check Call Stack (most recent call first): CMakeLists.txt:191 (find_package) CMake Error at C:/Program Files/CMake/share/cmake-3.12/Modules/FindBoost.cmake:2044 (message): Unable to find the requested Boost libraries. Boost version: 1.68.0 Boost include path: C:/boost Could not find the following Boost libraries: boost_python No Boost libraries were found. You may need to set BOOST_LIBRARYDIR to the directory containing Boost libraries or BOOST_ROOT to the location of Boost. Call Stack (most recent call first): CMakeLists.txt:198 (find_package) -- Could NOT find Eigen3 (missing: EIGEN3_INCLUDE_DIR EIGEN3_VERSION_OK) (Required is at least version "2.91.0") Eigen3 not found, disabling the Descriptors3D build. -- Boost version: 1.68.0 -- Found the following Boost libraries: -- serialization CMake Warning (dev) at CMakeLists.txt:317 (find_package): Policy CMP0074 is not set: find_package uses PackageName_ROOT variables. Run "cmake --help-policy CMP0074" for policy details. Use the cmake_policy command to set the policy and suppress this warning. CMake variable PostgreSQL_ROOT is set to: C:\Program Files\PostgreSQL\10 Environment variable PostgreSQL_ROOT is set to: C:\Program Files\PostgreSQL\10 For compatibility, CMake is ignoring the variable. This warning is for project developers. Use -Wno-dev to suppress it. == Using strict rotor definition -- Found MAEParser source in C:/RDKit/External/CoordGen/maeparser -- Found coordgenlibs source in C:/RDKit/External/CoordGen/coordgenlibs == Updating Filters.cpp from pains file == Done updating pains files -- Found RapidJSON source in C:/RDKit/External CMake Warning (dev) at Code/PgSQL/rdkit/CMakeLists.txt:11 (find_package): Policy CMP0074 is not set: find_package uses PackageName_ROOT variables. Run "cmake --help-policy CMP0074" for policy details. Use the cmake_policy command to set the policy and suppress this warning. CMake variable PostgreSQL_ROOT is set to: C:\Program Files\PostgreSQL\10 Environment variable PostgreSQL_ROOT is set to: C:\Program Files\PostgreSQL\10 For compatibility, CMake is ignoring the variable. This warning is for project developers. Use -Wno-dev to suppress it. postgres: C:/Program Files/PostgreSQL/10/include;C:/Program Files/PostgreSQL/10/include/server = After building, check C:/RDKit/build/Code/PgSQL/rdkit/pgsql_install.bat for correctness of installation paths. If everything is OK, gain administrator privileges, stop the PostgreSQL service, run C:/RDKit/build/Code/PgSQL/rdkit/pgsql_install.bat to install the PostgreSQL RDKit cartridge, then start again the PostgreSQL service = -- Configuring incomplete, errors occurred! See also "C:/RDKit/build/CMakeFiles/CMakeOutput.log". See also "C:/RDKit/build/CMakeFiles/CMakeError.log". -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Building RDKit on Windows
On Wednesday, March 5, 2014, James Davidson wrote: > Thanks Greg - that did the trick! > (I still see pythonTestDbCLI - as previously posted) Those problems are due to windows not being able to delete files that it has just closed. I need to put the deletion bit in a try..except block. The failures probably do not indicate any actual problem. -greg > Kind regards > > James > > __ > PLEASE READ: This email is confidential and may be privileged. It is > intended for the named addressee(s) only and access to it by anyone else is > unauthorised. If you are not an addressee, any disclosure or copying of the > contents of this email or any action taken (or not taken) in reliance on it > is unauthorised and may be unlawful. If you have received this email in > error, please notify the sender or postmas...@vernalis.com . > Email is not a secure method of communication and the Company cannot accept > responsibility for the accuracy or completeness of this message or any > attachment(s). Please check this email for virus infection for which the > Company accepts no responsibility. If verification of this email is sought > then please request a hard copy. Unless otherwise stated, any views or > opinions presented are solely those of the author and do not represent > those of the Company. > > The Vernalis Group of Companies > 100 Berkshire Place > Wharfedale Road > Winnersh, Berkshire > RG41 5RD, England > Tel: +44 (0)118 938 > > To access trading company registration and address details, please go to > the Vernalis website at www.vernalis.com and click on the "Company > address and registration details" link at the bottom of the page.. > __ > -- Subversion Kills Productivity. Get off Subversion & Make the Move to Perforce. With Perforce, you get hassle-free workflows. Merge that actually works. Faster operations. Version large binaries. Built-in WAN optimization and the freedom to use Git, Perforce or both. Make the move to Perforce. http://pubads.g.doubleclick.net/gampad/clk?id=122218951&iu=/4140/ostg.clktrk___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Building RDKit on Windows
Thanks Greg - that did the trick! (I still see pythonTestDbCLI - as previously posted) Kind regards James __ PLEASE READ: This email is confidential and may be privileged. It is intended for the named addressee(s) only and access to it by anyone else is unauthorised. If you are not an addressee, any disclosure or copying of the contents of this email or any action taken (or not taken) in reliance on it is unauthorised and may be unlawful. If you have received this email in error, please notify the sender or postmas...@vernalis.com. Email is not a secure method of communication and the Company cannot accept responsibility for the accuracy or completeness of this message or any attachment(s). Please check this email for virus infection for which the Company accepts no responsibility. If verification of this email is sought then please request a hard copy. Unless otherwise stated, any views or opinions presented are solely those of the author and do not represent those of the Company. The Vernalis Group of Companies 100 Berkshire Place Wharfedale Road Winnersh, Berkshire RG41 5RD, England Tel: +44 (0)118 938 To access trading company registration and address details, please go to the Vernalis website at www.vernalis.com and click on the "Company address and registration details" link at the bottom of the page.. __ -- Subversion Kills Productivity. Get off Subversion & Make the Move to Perforce. With Perforce, you get hassle-free workflows. Merge that actually works. Faster operations. Version large binaries. Built-in WAN optimization and the freedom to use Git, Perforce or both. Make the move to Perforce. http://pubads.g.doubleclick.net/gampad/clk?id=122218951&iu=/4140/ostg.clktrk ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Building RDKit on Windows
Ok, the updated file is checked in. Hopefully the windows build will now
work.
Apologies for the mistake.
-greg
On Tue, Mar 4, 2014 at 3:38 PM, Greg Landrum wrote:
> You're right. That's the wrong file. It's lex.yysmarts.cpp.cmake, and I
> forgot to check it in.
> I will do that tomorrow morning.
>
>
> On Tue, Mar 4, 2014 at 8:49 AM, James Davidson wrote:
>
>> Hi Greg,
>>
>>
>>
>> Before building yesterday, I updated RDKit to rev3060, then removed the
>> 'build' directory and re-set / configured cmake. I just checked the
>> 'smarts.tab.cpp' file, and it is certainly dated with yesterday's date... So
>> I presume it was freshly regenerated at the time(?)
>>
>>
>>
>> Kind regards
>>
>>
>>
>> James
>>
>>
>>
>> *From:* Greg Landrum [mailto:greg.land...@gmail.com]
>> *Sent:* 04 March 2014 04:12
>> *To:* James Davidson; RDKit Discuss
>> *Subject:* Re: [Rdkit-discuss] Building RDKit on Windows
>>
>>
>>
>> Hi James,
>>
>>
>>
>> On Mon, Mar 3, 2014 at 6:45 PM, James Davidson
>> wrote:
>>
>>
>>
>> I have just rebuilt RDKit on Windows using the latest source, and am
>> seeing a problem with smaTest1 failing (as well as still seeing the same
>> DbCLI failure posted previously...)
>>
>> The smaTest1 failure seems a little strange because it actually throws a
>> Windows executable error ("smaTest1.exe has stopped working", etc).
>>
>> If I run ctest -V -R smaTest1 I see the output below. Any thoughts?
>>
>>
>>
>> I checked in some changes to allow the aromatic "b" in mid-February. When
>> I did so, I added a test to make sure it's working. You've got the test
>> (that's the one that is failing), but it looks like the build did not
>> regenerate the parser files it needs to. You should be able to clear this
>> up by re-configuring cmake and regenerating the build files. After you do
>> this, check to see that $RDBASE/Code/GraphMol/SmilesParse/smarts.tab.cpp
>> has been freshly re-created.
>>
>>
>>
>> -greg
>>
>>
>>
>> __
>> PLEASE READ: This email is confidential and may be privileged. It is
>> intended for the named addressee(s) only and access to it by anyone else is
>> unauthorised. If you are not an addressee, any disclosure or copying of the
>> contents of this email or any action taken (or not taken) in reliance on it
>> is unauthorised and may be unlawful. If you have received this email in
>> error, please notify the sender or postmas...@vernalis.com. Email is not
>> a secure method of communication and the Company cannot accept
>> responsibility for the accuracy or completeness of this message or any
>> attachment(s). Please check this email for virus infection for which the
>> Company accepts no responsibility. If verification of this email is sought
>> then please request a hard copy. Unless otherwise stated, any views or
>> opinions presented are solely those of the author and do not represent
>> those of the Company.
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>> The Vernalis Group of Companies
>> 100 Berkshire Place
>> Wharfedale Road
>> Winnersh, Berkshire
>> RG41 5RD, England
>> Tel: +44 (0)118 938
>>
>> To access trading company registration and address details, please go to
>> the Vernalis website at www.vernalis.com and click on the "Company
>> address and registration details" link at the bottom of the page..
>> __
>>
>
>
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Re: [Rdkit-discuss] Building RDKit on Windows
You're right. That's the wrong file. It's lex.yysmarts.cpp.cmake, and I
forgot to check it in.
I will do that tomorrow morning.
On Tue, Mar 4, 2014 at 8:49 AM, James Davidson wrote:
> Hi Greg,
>
>
>
> Before building yesterday, I updated RDKit to rev3060, then removed the
> 'build' directory and re-set / configured cmake. I just checked the
> 'smarts.tab.cpp' file, and it is certainly dated with yesterday's date... So
> I presume it was freshly regenerated at the time(?)
>
>
>
> Kind regards
>
>
>
> James
>
>
>
> *From:* Greg Landrum [mailto:greg.land...@gmail.com]
> *Sent:* 04 March 2014 04:12
> *To:* James Davidson; RDKit Discuss
> *Subject:* Re: [Rdkit-discuss] Building RDKit on Windows
>
>
>
> Hi James,
>
>
>
> On Mon, Mar 3, 2014 at 6:45 PM, James Davidson
> wrote:
>
>
>
> I have just rebuilt RDKit on Windows using the latest source, and am
> seeing a problem with smaTest1 failing (as well as still seeing the same
> DbCLI failure posted previously...)
>
> The smaTest1 failure seems a little strange because it actually throws a
> Windows executable error ("smaTest1.exe has stopped working", etc).
>
> If I run ctest -V -R smaTest1 I see the output below. Any thoughts?
>
>
>
> I checked in some changes to allow the aromatic "b" in mid-February. When
> I did so, I added a test to make sure it's working. You've got the test
> (that's the one that is failing), but it looks like the build did not
> regenerate the parser files it needs to. You should be able to clear this
> up by re-configuring cmake and regenerating the build files. After you do
> this, check to see that $RDBASE/Code/GraphMol/SmilesParse/smarts.tab.cpp
> has been freshly re-created.
>
>
>
> -greg
>
>
>
> __
> PLEASE READ: This email is confidential and may be privileged. It is
> intended for the named addressee(s) only and access to it by anyone else is
> unauthorised. If you are not an addressee, any disclosure or copying of the
> contents of this email or any action taken (or not taken) in reliance on it
> is unauthorised and may be unlawful. If you have received this email in
> error, please notify the sender or postmas...@vernalis.com. Email is not
> a secure method of communication and the Company cannot accept
> responsibility for the accuracy or completeness of this message or any
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> Company accepts no responsibility. If verification of this email is sought
> then please request a hard copy. Unless otherwise stated, any views or
> opinions presented are solely those of the author and do not represent
> those of the Company.
>
> The Vernalis Group of Companies
> 100 Berkshire Place
> Wharfedale Road
> Winnersh, Berkshire
> RG41 5RD, England
> Tel: +44 (0)118 938
>
> To access trading company registration and address details, please go to
> the Vernalis website at www.vernalis.com and click on the "Company
> address and registration details" link at the bottom of the page..
> __
>
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Re: [Rdkit-discuss] Building RDKit on Windows
Hi Greg,
Before building yesterday, I updated RDKit to rev3060, then removed the 'build'
directory and re-set / configured cmake. I just checked the 'smarts.tab.cpp'
file, and it is certainly dated with yesterday's date... So I presume it was
freshly regenerated at the time(?)
Kind regards
James
From: Greg Landrum [mailto:greg.land...@gmail.com]
Sent: 04 March 2014 04:12
To: James Davidson; RDKit Discuss
Subject: Re: [Rdkit-discuss] Building RDKit on Windows
Hi James,
On Mon, Mar 3, 2014 at 6:45 PM, James Davidson
mailto:j.david...@vernalis.com>> wrote:
I have just rebuilt RDKit on Windows using the latest source, and am seeing a
problem with smaTest1 failing (as well as still seeing the same DbCLI failure
posted previously...)
The smaTest1 failure seems a little strange because it actually throws a
Windows executable error ("smaTest1.exe has stopped working", etc).
If I run ctest -V -R smaTest1 I see the output below. Any thoughts?
I checked in some changes to allow the aromatic "b" in mid-February. When I did
so, I added a test to make sure it's working. You've got the test (that's the
one that is failing), but it looks like the build did not regenerate the parser
files it needs to. You should be able to clear this up by re-configuring cmake
and regenerating the build files. After you do this, check to see that
$RDBASE/Code/GraphMol/SmilesParse/smarts.tab.cpp has been freshly re-created.
-greg
__
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Winnersh, Berkshire
RG41 5RD, England
Tel: +44 (0)118 938
To access trading company registration and address details, please go to the
Vernalis website at www.vernalis.com and click on the "Company address and
registration details" link at the bottom of the page..
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Re: [Rdkit-discuss] Building RDKit on Windows
Hi James,
On Mon, Mar 3, 2014 at 6:45 PM, James Davidson wrote:
>
>
> I have just rebuilt RDKit on Windows using the latest source, and am
> seeing a problem with smaTest1 failing (as well as still seeing the same
> DbCLI failure posted previously...)
>
> The smaTest1 failure seems a little strange because it actually throws a
> Windows executable error ("smaTest1.exe has stopped working", etc).
>
> If I run ctest -V -R smaTest1 I see the output below. Any thoughts?
>
I checked in some changes to allow the aromatic "b" in mid-February. When I
did so, I added a test to make sure it's working. You've got the test
(that's the one that is failing), but it looks like the build did not
regenerate the parser files it needs to. You should be able to clear this
up by re-configuring cmake and regenerating the build files. After you do
this, check to see that $RDBASE/Code/GraphMol/SmilesParse/smarts.tab.cpp
has been freshly re-created.
-greg
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Re: [Rdkit-discuss] Building RDKit on Windows
Hi All,
I have just rebuilt RDKit on Windows using the latest source, and am seeing a
problem with smaTest1 failing (as well as still seeing the same DbCLI failure
posted previously...)
The smaTest1 failure seems a little strange because it actually throws a
Windows executable error ("smaTest1.exe has stopped working", etc).
If I run ctest -V -R smaTest1 I see the output below. Any thoughts?
Kind regards
James
C:\RDKit\build>ctest -V -R smaTest1
UpdateCTestConfiguration from :C:/RDKit/build/DartConfiguration.tcl
UpdateCTestConfiguration from :C:/RDKit/build/DartConfiguration.tcl
Test project C:/RDKit/build
Constructing a list of tests
Done constructing a list of tests
Checking test dependency graph...
Checking test dependency graph end
test 32
Start 32: smaTest1
32: Test command: C:\RDKit\build\Code\GraphMol\SmilesParse\Release\smaTest1.exe
32: Test timeout computed to be: 9.99988e+006
32: [17:42:57] -
32: [17:42:57] Testing patterns which should parse.
32: [17:42:57] SMARTS Parse Error: syntax error for input: c1b1
32: [17:42:57]
32:
32:
32: Invariant Violation
32: c1b1
32: Violation occurred on line 90 in file
..\..\..\..\Code\GraphMol\SmilesParse\smatest.cpp
32: Failed Expression: mol
32:
32:
1/1 Test #32: smaTest1 .***Failed4.03 sec
0% tests passed, 1 tests failed out of 1
Total Test time (real) = 4.29 sec
The following tests FAILED:
32 - smaTest1 (Failed)
Errors while running CTest
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RG41 5RD, England
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Re: [Rdkit-discuss] Building RDKit on Windows
Hi Greg, > Try: ctest -V -R DbCLI > that should run the test in Verbose mode so that you can see the failures. Thanks - I have pasted the output below - looks like a file access issue (but I don't know why...). Kind regards James C:\RDKit\build>ctest -V -R DbCLI UpdateCTestConfiguration from :C:/RDKit/build/DartConfiguration.tcl UpdateCTestConfiguration from :C:/RDKit/build/DartConfiguration.tcl Test project C:/RDKit/build Constructing a list of tests Done constructing a list of tests Checking test dependency graph... Checking test dependency graph end test 76 Start 76: pythonTestDbCLI 76: Test command: C:\Python27\python.exe "C:/RDKit/Projects/test_list.py" "--testDir" "C:/RDKit/Projects" 76: Test timeout computed to be: 9.99988e+006 76: [10:13:51] INFO: Reading molecules and constructing molecular database. 76: [10:13:51] INFO: Generating molecular database in file testData/bzr\Compounds.sqlt 76: [10:13:51] INFO: Processing 10 molecules 76: [10:13:51] INFO: Generating fingerprints and descriptors: 76: [10:13:51] INFO: Finished. 76: [10:13:52] INFO: Reading molecules and constructing molecular database. 76: [10:13:52] INFO: Generating molecular database in file testData/bzr\Compounds.sqlt 76: [10:13:52] INFO: Processing 163 molecules 76: [10:13:53] INFO: done 100 76: [10:13:53] INFO: Generating fingerprints and descriptors: 76: [10:14:02] INFO: Finished. 76: [10:14:02] INFO: Reading query molecules and generating fingerprints 76: [10:14:03] INFO: Finding Neighbors 76: [10:14:04] INFO: The search took 0.6 seconds 76: [10:14:04] INFO: Creating output 76: [10:14:04] INFO: Done! 76: [10:14:05] INFO: Reading query molecules and generating fingerprints 76: [10:14:05] INFO: Finding Neighbors 76: [10:14:05] INFO: The search took 0.3 seconds 76: [10:14:05] INFO: Creating output 76: [10:14:05] INFO: Done! 76: [10:14:06] INFO: Reading query molecules and generating fingerprints 76: [10:14:06] INFO: Finding Neighbors 76: [10:14:06] INFO: The search took 0.1 seconds 76: [10:14:06] INFO: Creating output 76: [10:14:06] INFO: Done! 76: [10:14:07] INFO: Doing property query 76: [10:14:07] INFO: Found 30 molecules matching the query 76: [10:14:07] INFO: Creating output 76: [10:14:07] INFO: Done! 76: [10:14:08] INFO: Doing property query 76: [10:14:08] INFO: Found 30 molecules matching the query 76: [10:14:08] INFO: Creating output 76: [10:14:08] INFO: Done! 76: [10:14:08] INFO: Doing substructure query 76: [10:14:09] INFO:Fingerprint screenout rate: 112 of 163 (%68.71) 76: [10:14:09] INFO: Found 49 molecules matching the query 76: [10:14:09] INFO: Creating output 76: [10:14:09] INFO: Done! 76: [10:14:09] INFO: Doing substructure query 76: [10:14:09] INFO:Fingerprint screenout rate: 112 of 163 (%68.71) 76: [10:14:09] INFO: Found 49 molecules matching the query 76: [10:14:09] INFO: Creating output 76: [10:14:09] INFO: Done! 76: [10:14:10] INFO: Doing substructure query 76: [10:14:10] INFO: Found 114 molecules matching the query 76: [10:14:10] INFO: Creating output 76: [10:14:10] INFO: Done! 76: [10:14:11] INFO: Doing substructure query 76: [10:14:11] INFO:Fingerprint screenout rate: 23 of 30 (%76.67) 76: [10:14:11] INFO: Found 5 molecules matching the query 76: [10:14:11] INFO: Creating output 76: [10:14:11] INFO: Done! 76: [10:14:12] INFO: Doing substructure query 76: [10:14:12] INFO: Found 25 molecules matching the query 76: [10:14:12] INFO: Creating output 76: [10:14:12] INFO: Done! 76: [10:14:13] INFO: Reading query molecules and generating fingerprints 76: [10:14:18] INFO: Finding Neighbors 76: [10:14:19] INFO: The search took 0.9 seconds 76: [10:14:19] INFO: Creating output 76: [10:14:19] INFO: Done! 76: [10:14:20] INFO: Reading query molecules and generating fingerprints 76: [10:14:20] INFO: Finding Neighbors 76: [10:14:20] INFO: The search took 0.0 seconds 76: [10:14:20] INFO: Creating output 76: [10:14:20] INFO: Done! 76: [10:14:21] INFO: Reading molecules and constructing molecular database. 76: [10:14:21] INFO: Generating molecular database in file testData/bzr\Compounds.sqlt 76: [10:14:21] INFO: Processing 10 molecules 76: [10:14:21] INFO: Generating fingerprints and descriptors: 76: [10:14:21] INFO: Finished. 76: [10:14:23] INFO: Reading molecules and constructing molecular database. 76: [10:14:23] INFO: Generating molecular database in file testData/bzr\Compounds.sqlt 76: [10:14:23] INFO: Processing 10 molecules 76: [10:14:23] INFO: Generating fingerprints and descriptors: 76: [10:14:23] INFO: Finished. 76: .Traceback (most recent call last): 76: File "CreateDb.py", line 460, in 76: CreateDb(options,dataFilename) 76: File "CreateDb.py", line 214, in CreateDb 76: startAnew=not options.updateDb 76: File "C:\RDKit\rdkit\Chem\MolDb\Loader_sa.py", line 111, in LoadDb 76: os.unlink(dbName) 76: WindowsError: [Error 32] The process cannot access the file because it is being used by another process: 'testData/bzr\\Compounds.sqlt' 76: [10:14:24] INFO: R
Re: [Rdkit-discuss] Building RDKit on Windows
On Wed, Jan 29, 2014 at 9:22 AM, James Davidson wrote: > > > > 7. Re-ran configure, then generate, then followed the rest of the > > > wiki instructions to build and test - all tests passed except the > > > dbCli one. > > > > > What was the DbCLI test failure? > > I just see " 76/82 Test #76: pythonTestDbCLI ..***Failed > 50.66 sec" > > Try: ctest -V -R DbCLI that should run the test in Verbose mode so that you can see the failures. > I have now included the INCHI 1.04 source, and followed your Avalon steps > above. The AVALONTOOLS_DIR currently needs to be added manually in CMake > (but that's ok). I should also say that, just in case, I deleted the build > folder and cleared the CMake cache before this build attempt. I also > *definitely* re-ran the 'generate' command (a few times!) before > 'configure'. > Anyway, I now see more tests when running 'ctest' - which I think is due > to the addition of testInchi, testAvalonLib1, and pyAvalonTools - all of > which pass! I can also confirm that Chem.inchi.INCHI_AVAILABLE now returns > "True". > (pythonTestDbCLI still fails as before.) > Glad you got something working! -greg -- WatchGuard Dimension instantly turns raw network data into actionable security intelligence. It gives you real-time visual feedback on key security issues and trends. Skip the complicated setup - simply import a virtual appliance and go from zero to informed in seconds. http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Building RDKit on Windows
Hi Greg, > > 5. Downloaded the INCHI src as described in the wiki and set the > > RDK_BUILD_INCHI_SUPPORT option later in cmake. Incidentally, the > > location for the downloads from IUPAC have changed (ie the info in the > > README is out of date): > > http://www.iupac.org/home/publications/e-resources/inchi/download.html > > The link that is in the README, which is to a more recent version (1.04 > instead of 1.03), does still work for me. Did you have problems with that? I realised that in my first attempts I had mistakenly linked to the RDKit repo on SourceForge (following the wiki). The README there points to http://www.iupac.org/inchi/download/version1.03/INCHI-1-API.zip which no longer exists. I am now using the INCHI download link from the current README - thanks! > > 7. Re-ran configure, then generate, then followed the rest of the > > wiki instructions to build and test - all tests passed except the > > dbCli one. > > > What was the DbCLI test failure? I just see " 76/82 Test #76: pythonTestDbCLI ..***Failed 50.66 sec" > > I thought I did everything right for adding INCHI support. However, I > > see the following: > > > > In [1]: from rdkit import Chem > > In [2]: Chem.inchi.INCHI_AVAILABLE > > Out[2]: False > > > > Do I also need to download the InChi binary and set these two > > variables appropriately in CMake? > > > No; that should not be necessary. > If you have the source in the right place (and that cmake message makes it > look like you do) and have RDK_BUILD_INCHI_SUPPORT set, run "generate", > and then do a build and an install, it should produce the binaries you need > and update that file so that Chem.inchi.INCHI_AVAILABLE is True. Did you > re-run "generate" after installing the INCHI source? I thought I had re-run 'generate'... Perhaps it was an issue with using older INCHI source? > > Also, I am struggling to build with Avalon support... > > 1) download the beta source distribution from sf.net; > http://sourceforge.net/projects/avalontoolkit/files/AvalonToolkit_1.1_beta/AvalonToolkit_1.1_beta.source.tar/download > 2) extract that tar file somewhere. It's going to create SourceDistribution > and a StandardFiles directories > 3) set the cmake variable AVALONTOOLS_DIR to point to the SourceDistribution > directory > 3) set RDK_BUILD_AVALON_SUPPORT=ON in cmake > 4) run a build and install. > > Note: one or two of the avalontools tests may fail on windows. This is > currently expected. I have now included the INCHI 1.04 source, and followed your Avalon steps above. The AVALONTOOLS_DIR currently needs to be added manually in CMake (but that's ok). I should also say that, just in case, I deleted the build folder and cleared the CMake cache before this build attempt. I also *definitely* re-ran the 'generate' command (a few times!) before 'configure'. Anyway, I now see more tests when running 'ctest' - which I think is due to the addition of testInchi, testAvalonLib1, and pyAvalonTools - all of which pass! I can also confirm that Chem.inchi.INCHI_AVAILABLE now returns "True". (pythonTestDbCLI still fails as before.) Thanks very much for the help! Kind regards James __ PLEASE READ: This email is confidential and may be privileged. It is intended for the named addressee(s) only and access to it by anyone else is unauthorised. If you are not an addressee, any disclosure or copying of the contents of this email or any action taken (or not taken) in reliance on it is unauthorised and may be unlawful. If you have received this email in error, please notify the sender or postmas...@vernalis.com. Email is not a secure method of communication and the Company cannot accept responsibility for the accuracy or completeness of this message or any attachment(s). Please check this email for virus infection for which the Company accepts no responsibility. If verification of this email is sought then please request a hard copy. Unless otherwise stated, any views or opinions presented are solely those of the author and do not represent those of the Company. The Vernalis Group of Companies 100 Berkshire Place Wharfedale Road Winnersh, Berkshire RG41 5RD, England Tel: +44 (0)118 938 To access trading company registration and address details, please go to the Vernalis website at www.vernalis.com and click on the "Company address and registration details" link at the bottom of the page.. __ -- WatchGuard Dimension instantly turns raw network data into actionable security intelligence. It gives you real-time visual feedback on key security issues and trends. Skip the complicated setup - simply import a virtual appliance and go from zero to informed in seconds. http://pubads.g.doubleclick.net/gampad/clk
Re: [Rdkit-discuss] Building RDKit on Windows
Dear James, On Tue, Jan 28, 2014 at 4:09 PM, James Davidson wrote: > > > As part of a New Year's resolution, I decided I should try to enjoy the > benefits of a cutting-edge version of RDKit built from source(!) So far > this has proven to be much more realistic than eg 'not drinking for > January' - as I now have a working build to show for my efforts. > > congrats! > > > However, I wonder if I could quickly list the steps I took; and also ask a > couple of questions (relating to InChi and Avalon)? > Attempts at some answers are below. > For reference I am running on Windows7 64-bit, but use python 2.7.6 32bit, > so am building 32-bit RDKit. I essentially followed the guide on the wiki ( > https://code.google.com/p/rdkit/wiki/BuildingOnWindows) but thought the > version info of boost, etc may be of use to others, and the steps may help > put my questions into context: > > > > 1. Downloaded Visual Studio Express 2012 for Desktop, installed, > and accepted the updates > > 2. Downloaded matching version of Windows boost binaries > (boost_1_55_0-msvc-11.0-32.exe) from > http://sourceforge.net/projects/boost/files/boost-binaries/ and extracted > to the default path > hmm, I didn't know about that source of boost binaries. That is very good to know; I was afraid there was going to be real hole after the boostpro guys stopped doing binaries. > 3. Used TortoiseSVN to add a repository link to > https://github.com/rdkit/rdkit.git/trunk (and not the SF path as > currently shown in the wiki guide) in C:/RDKit > > 4. Set the environment variables as described on the wiki. > > 5. Downloaded the INCHI src as described in the wiki and set the > RDK_BUILD_INCHI_SUPPORT option later in cmake. Incidentally, the location > for the downloads from IUPAC have changed (ie the info in the README is out > of date): > http://www.iupac.org/home/publications/e-resources/inchi/download.html > The link that is in the README, which is to a more recent version (1.04 instead of 1.03), does still work for me. Did you have problems with that? > 6. Ran CMake configure (GUI) following the wiki, and based on the > output, made some boost-related additions to environment variables > > a. Added C:\local\boost_1_55_0\lib32-msvc-11.0 to PATH > > b. Created BOOST_ROOT=C:\local\boost_1_55_0 > > c. Created BOOST_LIBRARYDIR=C:\local\boost_1_55_0\lib32-msvc-11.0 > > 7. Re-ran configure, then generate, then followed the rest of the > wiki instructions to build and test - all tests passed except the dbCli > one. > What was the DbCLI test failure? Thanks for pointing out the places where the documentation needs to be updated. Since the wiki docs are out of date, I will go back and replace them with a pointer to the main documentation ( http://www.rdkit.org/docs/Install.html#installation-from-source) and be sure that is up to date based on the above. > > So now for the questions: > > I thought I did everything right for adding INCHI support. However, I see > the following: > > > > In [1]: from rdkit import Chem > > In [2]: Chem.inchi.INCHI_AVAILABLE > > Out[2]: False > > > > CMake shows: > > > > Could NOT find InChI in system locations (missing: INCHI_LIBRARY > INCHI_INCLUDE_DIR) > > Found InChI software locally > > > > Do I also need to download the InChi binary and set these two variables > appropriately in CMake? > No; that should not be necessary. If you have the source in the right place (and that cmake message makes it look like you do) and have RDK_BUILD_INCHI_SUPPORT set, run "generate", and then do a build and an install, it should produce the binaries you need and update that file so that Chem.inchi.INCHI_AVAILABLE is True. Did you re-run "generate" after installing the INCHI source? > Also, I am struggling to build with Avalon support... Choosing the > RDK_BUILD_AVALON_SUPPORT appears to configure fine, but when I try to > 'Generate' I see the following error: > > > > CMake Error at Code/cmake/Modules/RDKitUtils.cmake:26 (add_library): > Cannot find source file: > > /common/layout.c > > Tried extensions .c .C .c++ .cc .cpp .cxx .m .M .mm .h .hh .h++ .hm .hpp > .hxx .in .txx > Call Stack (most recent call first): > External/AvalonTools/CMakeLists.txt:43 (rdkit_library) > > > > Any thought on how to get around this? Do I need to download the Avalon > project src and put it somewhere? > Yeah, you do, but there's no documentation for that (yet...). Here's a first pass at something 1) download the beta source distribution from sf.net; http://sourceforge.net/projects/avalontoolkit/files/AvalonToolkit_1.1_beta/AvalonToolkit_1.1_beta.source.tar/download 2) extract that tar file somewhere. It's going to create SourceDistribution and a StandardFiles directories 3) set the cmake variable AVALONTOOLS_DIR to point to the SourceDistribution directory 3) set RDK_BUILD_AVALON_SUPPORT=ON in cmake 4) run a build and install. Note: one or two of the avalontools tests may fail on
[Rdkit-discuss] Building RDKit on Windows
Dear All, As part of a New Year's resolution, I decided I should try to enjoy the benefits of a cutting-edge version of RDKit built from source(!) So far this has proven to be much more realistic than eg 'not drinking for January' - as I now have a working build to show for my efforts. However, I wonder if I could quickly list the steps I took; and also ask a couple of questions (relating to InChi and Avalon)? For reference I am running on Windows7 64-bit, but use python 2.7.6 32bit, so am building 32-bit RDKit. I essentially followed the guide on the wiki (https://code.google.com/p/rdkit/wiki/BuildingOnWindows) but thought the version info of boost, etc may be of use to others, and the steps may help put my questions into context: 1. Downloaded Visual Studio Express 2012 for Desktop, installed, and accepted the updates 2. Downloaded matching version of Windows boost binaries (boost_1_55_0-msvc-11.0-32.exe) from http://sourceforge.net/projects/boost/files/boost-binaries/ and extracted to the default path 3. Used TortoiseSVN to add a repository link to https://github.com/rdkit/rdkit.git/trunk (and not the SF path as currently shown in the wiki guide) in C:/RDKit 4. Set the environment variables as described on the wiki. 5. Downloaded the INCHI src as described in the wiki and set the RDK_BUILD_INCHI_SUPPORT option later in cmake. Incidentally, the location for the downloads from IUPAC have changed (ie the info in the README is out of date): http://www.iupac.org/home/publications/e-resources/inchi/download.html 6. Ran CMake configure (GUI) following the wiki, and based on the output, made some boost-related additions to environment variables a. Added C:\local\boost_1_55_0\lib32-msvc-11.0 to PATH b. Created BOOST_ROOT=C:\local\boost_1_55_0 c. Created BOOST_LIBRARYDIR=C:\local\boost_1_55_0\lib32-msvc-11.0 7. Re-ran configure, then generate, then followed the rest of the wiki instructions to build and test - all tests passed except the dbCli one. So now for the questions: I thought I did everything right for adding INCHI support. However, I see the following: In [1]: from rdkit import Chem In [2]: Chem.inchi.INCHI_AVAILABLE Out[2]: False CMake shows: Could NOT find InChI in system locations (missing: INCHI_LIBRARY INCHI_INCLUDE_DIR) Found InChI software locally Do I also need to download the InChi binary and set these two variables appropriately in CMake? Also, I am struggling to build with Avalon support... Choosing the RDK_BUILD_AVALON_SUPPORT appears to configure fine, but when I try to 'Generate' I see the following error: CMake Error at Code/cmake/Modules/RDKitUtils.cmake:26 (add_library): Cannot find source file: /common/layout.c Tried extensions .c .C .c++ .cc .cpp .cxx .m .M .mm .h .hh .h++ .hm .hpp .hxx .in .txx Call Stack (most recent call first): External/AvalonTools/CMakeLists.txt:43 (rdkit_library) Any thought on how to get around this? Do I need to download the Avalon project src and put it somewhere? And final question - can I happily ignore the CMake messages about not finding FLEX and BISON, or are these needed when incorporating any of the non-default entries (SWIG wrappers, etc)? Kind regards James __ PLEASE READ: This email is confidential and may be privileged. It is intended for the named addressee(s) only and access to it by anyone else is unauthorised. If you are not an addressee, any disclosure or copying of the contents of this email or any action taken (or not taken) in reliance on it is unauthorised and may be unlawful. If you have received this email in error, please notify the sender or postmas...@vernalis.com. Email is not a secure method of communication and the Company cannot accept responsibility for the accuracy or completeness of this message or any attachment(s). Please check this email for virus infection for which the Company accepts no responsibility. If verification of this email is sought then please request a hard copy. Unless otherwise stated, any views or opinions presented are solely those of the author and do not represent those of the Company. The Vernalis Group of Companies 100 Berkshire Place Wharfedale Road Winnersh, Berkshire RG41 5RD, England Tel: +44 (0)118 938 To access trading company registration and address details, please go to the Vernalis website at www.vernalis.com and click on the "Company address and registration details" link at the bottom of the page.. __-- WatchGuard Dimension instantly turns raw network data into actionable security intelligence. It gives you real-time visual feedback on key security issues and trends. Skip the complicated setup - simply import a virtual applianc
