> On Apr 23, 2018, at 10:43, Greg Landrum <greg.land...@gmail.com> wrote:
>
> I'm pleased to announce that the next version of the RDKit - 2018.03 - is
> released. The release notes are below.
...
> Please let me know if you find any problems with the release or have
> suggestions for the next one, which is scheduled for Octobera 2018.
I'm likely one of the few who builds RDKit manually. I also build on a Mac but
I don't use the system/homebrew Python or Boost but rather have my own
installations under a virtual environment. Which makes updates "fun".
The build step produced errors like:
"links to target 'Boost::serialization' but the target was not found."
"links to target 'Boost::python3' but the target was not found."
The solution was to upgrade my cmake from 3.7.2 to 3.11.1.
Note however that the Install.md says:
cmake. You need version 3.1 (or more recent)
This should be updated. I don't know which cmake version is the minimum
required.
By the way, how do I install RDKit into a specified location? I usually expect
something like --prefix /usr/local, and there's a CMAKE_INSTALL_PREFIX which
defaults to "/usr/local" but "make install" puts it in the build directory, like
/Users/dalke/ftps/rdkit-Release_2018_03_1
My solution is to install it myself, like:
cd ~/venvs/py36-2018-4/lib/python3.6/site-packages/
cp -rp ~/ftps/rdkit-Release_2018_03_1/rdkit .
python -m compileall rdkit
cd ~/venvs/py36-2018-4/lib
cp -p ~/ftps/rdkit-Release_2018_03_1/lib/lib* .
but the shared libraries uses a relative path:
File
"/Users/dalke/venvs/py36-2018-4/lib/python3.6/site-packages/rdkit/__init__.py",
line 2, in <module>
from .rdBase import rdkitVersion as __version__
ImportError:
dlopen(/Users/dalke/venvs/py36-2018-4/lib/python3.6/site-packages/rdkit/rdBase.so,
2): Library not loaded: @rpath/libboost_python36.dylib
Referenced from:
/Users/dalke/venvs/py36-2018-4/lib/python3.6/site-packages/rdkit/rdBase.so
Reason: image not found
% otool -L
/Users/dalke/venvs/py36-2018-4/lib/python3.6/site-packages/rdkit/rdBase.so
/Users/dalke/venvs/py36-2018-4/lib/python3.6/site-packages/rdkit/rdBase.so:
@rpath/libRDKitRDBoost.1.dylib (compatibility version 1.0.0, current
version 2018.3.1)
@rpath/libboost_python36.dylib (compatibility version 0.0.0, current
version 0.0.0)
@rpath/libboost_serialization.dylib (compatibility version 0.0.0,
current version 0.0.0)
@rpath/libRDKitRDGeneral.1.dylib (compatibility version 1.0.0, current
version 2018.3.1)
/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version
307.4.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current
version 1238.0.0)
which means I've always had to tweak my virtualenv 'activate' command to
set/unset DYLD_LIBRARY_PATH.
(It looks like there are ways to tweak the @rpath but I haven't figured it out.)
I would prefer to have something like
cmake ..... --prefix ~/venvs/py36-2018-4
make install
and skip all of this by-hand tweaking.
Does it exist already and I just missed it?
Andrew
da...@dalkescientific.com
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