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
<module>
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 <[email protected]>
Sent: 14 April 2022 18:41
To: Charmaine Siu Man Chu <[email protected]>
Cc: [email protected]
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
<[email protected]<mailto:[email protected]>>
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) ->
"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
As during the compilation -- Could NOT find ZLIB (missing: ZLIB_LIBRARY
ZLIB_INCLUDE_DIR) was spotted, the command line was modified to point towards
the zlib folder as follow
cmake -DRDK_BUILD_PYTHON_WRAPPERS=ON -DBOOST_ROOT=C:/local/boost_1_78_0
-DZLIB_LIBRARY="C:/zlib-1.2.12/build/Release/zlib.lib"
-DZLIB_INCLUDE_DIR="C:/zlib-1.2.12" -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"
-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" -G"Visual Studio 17
2022" ..
This time running the INSTALL.vcxproj gave 93 warnings but no errors
However, when starting up python in KNIME it gives the following error:
Error while loading python type extension RDKitMolDeserializer
Cause: DLL load failed while importing rdBase: The specified module could not
be found.
And when loading the rdkit extension in pgAdmin gave
ERROR: could not load library "C:/Program Files/PostgreSQL/14/lib/rdkit.dll":
The specified module could not be found.
I’ve made sure I delete the rdkit build folder each time I redo the
compilation. Where had I gone wrong?
Regards,
Charmaine Chu
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