Re: [Rdkit-discuss] Compiling git RDKit on Mac OS X (was: Atoms with strange positions/bonds when drawer makes PNG)

2016-02-23 Thread Paul Emsley
On 23/02/2016 15:52, Greg Landrum wrote: On Tue, Feb 23, 2016 at 3:50 PM, Paul Emsley > wrote: This seems to be the relevant difference in the cmake output: [ 3%] Linking CXX shared library

Re: [Rdkit-discuss] Windows 7 ImportError: DLL load failed

2016-02-23 Thread Nico Cantone
Riccardo, Thanks for your reply! I did not have %PYTHONPATH% or %RDBASE% defined, and the qtconsole I used is installed in the same environment as rdkit. Until your reply, I had only tried to import Chem using qtconsole or jupyter notebook (being sure I was in the proper environment), without

Re: [Rdkit-discuss] Atoms with strange positions/bonds when drawer makes PNG

2016-02-23 Thread Brian Kelley
I have a fix for this in the conda recipes I can submit, it boils down to something like the following ( setting the CXXFLAGS for c++11 ) if otool -L "$PYROOT/lib/libboost_python.dylib" | grep libc++ ; then FLAGS="-std=c++11 -stdlib=libc++" else FLAGS="-stdlib=libstdc++" fi

Re: [Rdkit-discuss] Windows 7 ImportError: DLL load failed

2016-02-23 Thread Riccardo Vianello
Hi Nico, no environment variable settings should be in general required beyond those eventually set by the activate command (and even those should be optional). In case you manually set the %PYTHONPATH% or the %RDBASE% I would suggest removing them until the problem is resolved. It is not clear

[Rdkit-discuss] Windows 7 ImportError: DLL load failed

2016-02-23 Thread Nico Cantone
I am trying to run RDKit on Windows 7, and I am getting the DLL load error which, according to the documentation, is due to missing Microsoft Visual C++ Redistributable files. It is a 64-bit system with 64-bit python 2.7, and I have installed RDKit using conda as per the instructions. According to

Re: [Rdkit-discuss] Atoms with strange positions/bonds when drawer makes PNG

2016-02-23 Thread Greg Landrum
On Tue, Feb 23, 2016 at 3:50 PM, Paul Emsley wrote: > > This seems to be the relevant difference in the cmake output: > > > > [ 3%] Linking CXX shared library ../../lib/libRDBoost.dylib > Undefined symbols for architecture x86_64: >

Re: [Rdkit-discuss] Compiling git rdkit

2016-02-23 Thread Greg Landrum
I haven't seen this, but can you please try moving the #include of algorithm from line 18 up to line 11 (i.e. before the BoostStartInclude line) to see if that helps? -greg On Tue, Feb 23, 2016 at 2:28 PM, Paul Emsley wrote: > > Yes, but not for boost. > > On

Re: [Rdkit-discuss] Compiling git rdkit

2016-02-23 Thread Paul Emsley
Yes, but not for boost. On 23/02/2016 13:19, Giuseppe Marco Randazzo wrote: > Are you using homebrew? > >> On 23 Feb 2016, at 14:17, Paul Emsley wrote: >> >> >> Using: >> Apple LLVM version 6.1.0 (clang-602.0.49) (based on LLVM 3.6.0svn) >> Target:

Re: [Rdkit-discuss] Compiling git rdkit

2016-02-23 Thread Giuseppe Marco Randazzo
Are you using homebrew? > On 23 Feb 2016, at 14:17, Paul Emsley wrote: > > > Using: > Apple LLVM version 6.1.0 (clang-602.0.49) (based on LLVM 3.6.0svn) > Target: x86_64-apple-darwin14.5.0 > > and boost_1_54_0: > > Scanning dependencies of target testMatCalc > [

[Rdkit-discuss] Compiling git rdkit

2016-02-23 Thread Paul Emsley
Using: Apple LLVM version 6.1.0 (clang-602.0.49) (based on LLVM 3.6.0svn) Target: x86_64-apple-darwin14.5.0 and boost_1_54_0: Scanning dependencies of target testMatCalc [ 29%] Building CXX object Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o [ 30%] Building CXX