Hi Greg,
I tried the xcode 6.1 but this didn’t seem to help. Hence I gave up on Anaconda
(should have gone deeper into it but I needed rdkit/postgres urgently so I went
for the quick-win solution…sorry about this), and managed to install
rdkit/postgres using the ‘normal' route. Just to keep things documented for
later reuse, I describe here the actual steps (OS X 10.10):
> which python
/usr/bin/python
> which python
/usr/local/bin/ipython
> which psql
/usr/local/pgsql/bin/psql
The I downloaded boost 1.57.0 and untarred it into /usr/local/src...
> cd /usr/local/src/boost_1_57_0
> ./bootstrap.sh --with-libraries=python,regex
> ./b2 -j4
Subsequently I downloaded rdkit 2014.09.1 and untarred it into /usr/local/src...
> cd /usr/local/src/rdkit-Release_2014_09_1
> mkdir build
> cd build
> export
> PYTHON_INCLUDE_DIR=/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7/
> export
> PYTHON_LIBRARY=/System/Library/Frameworks/Python.framework/Versions/2.7/lib/libpython2.7.dylib
> export BOOST_ROOT=/usr/local/src/boost_1_57_0
> cmake -DPYTHON_LIBRARY=$PYTHON_LIBRARY
> -DPYTHON_INCLUDE_DIR=$PYTHON_INCLUDE_DIR -DBOOST_ROOT=$BOOST_ROOT ..
> make -j4 install
> export BOOSTHOME=/usr/local/src/boost_1_57_0
> export RDBASE=/usr/local/src/rdkit-Release_2014_09_1
> export DYLD_LIBRARY_PATH=$RDBASE/lib
> export PYTHONPATH=$RDBASE
I also added these latter four lines to my .bash_profile file (although I am
not sure if this is required)
To install the postgres cartridge:
> cd $RDBASE/Code/PgSQL/rdkit
> make && make install
I then had to restart psql and I could check the installation by running the
following as postgres user:
> su postgres
> make installcheck
Sorry that I didn’t work further along the anaconda lines, but for now I need a
working rdkit/postgres copy to get along.
Regards,
Hans
On 15 Nov 2014, at 06:49, Greg Landrum
<greg.land...@gmail.com<mailto:greg.land...@gmail.com>> wrote:
Hi Hans,
I haven't tried to build on 10.10 yet, but it looks like you may need to have
xcode v6.1 installed:
http://stackoverflow.com/questions/26497606/porting-cmake-to-os-x-yosemite
-greg
On Fri, Nov 14, 2014 at 6:35 PM, Hans De Winter
<hdwinter1...@gmail.com<mailto:hdwinter1...@gmail.com>> wrote:
Hi all,
while trying to install rdkit as part of the Anacond distribution, I get the
following error:
> conda build rdkit
[ … messages skipped …]
==> git describe --tags --dirty <==
Release_2014_09_1
==> git status <==
HEAD detached at Release_2014_09_1
nothing to commit, working directory clean
Applying patch: u'/usr/local/src/conda-rdkit/rdkit/rdpaths.patch'
patching file rdkit/CMakeLists.txt
Package: rdkit-2014.09.1-np19py27_0
source tree in: /Users/hans/anaconda/conda-bld/work
+ /Users/hans/anaconda/envs/_build/bin/python
/usr/local/src/conda-rdkit/rdkit/fetch_inchi.py
Downloading: INCHI-1-API.zip
+ /Users/hans/anaconda/envs/_build/bin/python
/usr/local/src/conda-rdkit/rdkit/fetch_avalontools.py
Downloading: AvalonToolkit_1.1_beta.source.tar
+ cmake -D RDK_INSTALL_INTREE=OFF -D RDK_INSTALL_STATIC_LIBS=OFF -D
RDK_BUILD_INCHI_SUPPORT=ON -D RDK_BUILD_AVALON_SUPPORT=ON -D
RDK_USE_FLEXBISON=OFF -D
AVALONTOOLS_DIR=/Users/hans/anaconda/conda-bld/work/External/AvalonTools/src/SourceDistribution
-D CMAKE_SYSTEM_PREFIX_PATH=/Users/hans/anaconda/envs/_build -D
CMAKE_INSTALL_PREFIX=/Users/hans/anaconda/envs/_build -D
Python_ADDITIONAL_VERSIONS=2.7 -D
PYTHON_EXECUTABLE=/Users/hans/anaconda/envs/_build/bin/python -D
PYTHON_NUMPY_INCLUDE_PATH=/Users/hans/anaconda/envs/_build/lib/python2.7/site-packages/numpy/core/include
-D BOOST_ROOT=/Users/hans/anaconda/envs/_build -D Boost_NO_SYSTEM_PATHS=ON -D
CMAKE_BUILD_TYPE=Release .
-- The C compiler identification is Clang 6.0.0
-- The CXX compiler identification is Clang 6.0.0
CMake Error at
/Users/hans/anaconda/envs/_build/share/cmake-2.8/Modules/Platform/Darwin.cmake:150
(message):
CMAKE_OSX_DEPLOYMENT_TARGET (10.5) is greater than CMAKE_OSX_SYSROOT SDK
(/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk).
Please set CMAKE_OSX_DEPLOYMENT_TARGET to 10.1 or lower
Call Stack (most recent call first):
/Users/hans/anaconda/envs/_build/share/cmake-2.8/Modules/Platform/Darwin.cmake:156
(SanityCheckSDKAndDeployTarget)
/Users/hans/anaconda/envs/_build/share/cmake-2.8/Modules/CMakeSystemSpecificInformation.cmake:36
(INCLUDE)
CMakeLists.txt:6 (project)
-- Configuring incomplete, errors occurred!
Command failed: /bin/bash -x -e /usr/local/src/conda-rdkit/rdkit/build.sh
Clues that might help? I am on OS X 10.10.
Thanks in advance.
Hans
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