Re: [Rdkit-discuss] Trouble compiling and installing on Ubuntu 14.04

Peter, Yes. In the interim just before you sent this message, I learned the install I was helping with had the source downloaded from SF rather than Github. Using the same version from github seems to resolve this issue. I apologize if this means I have wasted anyones time but I had not realised

Re: [Rdkit-discuss] Trouble compiling and installing on Ubuntu 14.04

One of the tests says: > ImportError: libInfoTheory.so.1: cannot open shared object file: No such file or directory Did you "make install" and does LD_LIBRARY_PATH contain $RDBASE/lib? Best, Peter On Tue, Oct 4, 2016 at 11:18 AM Philip Adler wrote: > Unfortunately

Re: [Rdkit-discuss] Trouble compiling and installing on Ubuntu 14.04

Unfortunately David Hall's suggestion has been unsuccessful, and adds new failures into the tests. The output from ctest --debug is here . Best, and thanks to all for helping so far, Phil On Mon, Oct 3, 2016 at

Re: [Rdkit-discuss] Trouble compiling and installing on Ubuntu 14.04

Hmmm, I didn't see anything below that looks odd. It's difficult for me to provide any more detailed help at the moment since I'm on vacation and don't have access to either my linux machine or to a good network connection (to get a proper docker environment set up). David Hall's suggestion to

Re: [Rdkit-discuss] Trouble compiling and installing on Ubuntu 14.04

What happens if you do this instead? cmake -DRDK_BUILD_INCHI_SUPPORT=ON -DPYTHON_EXECUTABLE=/usr/bin/python3.4 .. That seems to work for me on Ubuntu 14.04, also, delete your entire build directory and make it again before running the command. -David On Mon, Oct 3, 2016 at 11:05 AM, Philip

Re: [Rdkit-discuss] Trouble compiling and installing on Ubuntu 14.04

Phillip, if you run ctest --debug This may help us diagnose the issue with paths and such. Note that you will get a LOT of output. Brian Kelley > On Oct 3, 2016, at 4:05 PM, Philip Adler wrote: > > it does not seem that I am missing any dependencies. > >> On

Re: [Rdkit-discuss] Trouble compiling and installing on Ubuntu 14.04

it does not seem that I am missing any dependencies. On Mon, Oct 3, 2016 at 3:55 PM, Paolo Tosco wrote: > Hi Philip, > > Just wondering if CMake is pulling in Python 2.7 because you are missing > some Python dependencies on 3.4 (e.g., NumPy)? > > p. > > On 3 Oct 2016, at

Re: [Rdkit-discuss] Trouble compiling and installing on Ubuntu 14.04

Those variables were set correctly in my CMakeCache.txt. On Mon, Oct 3, 2016 at 2:47 PM, Peter Gedeck wrote: > You can also check the CMakeCache.txt file in the build directory. When I > last compiled for 3.5 on the Mac, I had to correct the PYTHON_INCLUDE_DIR. > > Greg,

Re: [Rdkit-discuss] Trouble compiling and installing on Ubuntu 14.04

You can also check the CMakeCache.txt file in the build directory. When I last compiled for 3.5 on the Mac, I had to correct the PYTHON_INCLUDE_DIR. Greg, PYTHON_INCLUDE_DIR was incorrectly set after "cmake ..". Executable and library correctly found. //Path to a program.

Re: [Rdkit-discuss] Trouble compiling and installing on Ubuntu 14.04

Greg (with apologies for the repeat for the benefit of the mailing list -gmail is great up until it isn't!), Please see below, import _frozen_importlib # frozen import imp # builtin import sys # builtin # installing zipimport hook # installed zipimport hook #

Re: [Rdkit-discuss] Trouble compiling and installing on Ubuntu 14.04

Yeah, but that ldd output indicates that python2.7 is being pulled in. As is, curiously, the python2.7 version of boost. Can you please try: python3.4 -v -c 'from rdkit import rdBase' and send the command and output from that? -greg On Mon, Oct 3, 2016 at 5:45 PM, Philip Adler

Re: [Rdkit-discuss] Trouble compiling and installing on Ubuntu 14.04

You built against python3.4, but it looks like you are running python2.7 -greg On Mon, Oct 3, 2016 at 5:39 PM, Philip Adler wrote: > Greg, > > The output of the commands is as follows: > > Segmentation fault (core dumped) > > and > > linux-vdso.so.1 =>

Re: [Rdkit-discuss] Trouble compiling and installing on Ubuntu 14.04

Greg, The output of the commands is as follows: Segmentation fault (core dumped) and linux-vdso.so.1 => (0x7fff3d6be000) libRDGeneral.so.1 => /usr/lib/libRDGeneral.so.1 (0x7f03d51df000) libRDBoost.so.1 => /usr/lib/libRDBoost.so.1 (0x7f03d4fdc000)

Re: [Rdkit-discuss] Trouble compiling and installing on Ubuntu 14.04

Hi Phil, I can't think of any particular reason that Ubuntu 14.04 should be a problem, so this should be solvable. This kind of thing (every python test failing) is typically a problem with either the python version or the boost libraries. The first check is to see what error message you get

Re: [Rdkit-discuss] Trouble compiling and installing on Ubuntu 14.04

Hello Python failures are usually an indication of problems with the boost library. You might pickup libraries for the wrong Python version. Best Peter On Mon, Oct 3, 2016 at 11:06 AM Philip Adler wrote: > Dear All, > > I am trying to compile rdkit to run with Python3.4

[Rdkit-discuss] Trouble compiling and installing on Ubuntu 14.04

Dear All, I am trying to compile rdkit to run with Python3.4 on Ubuntu 14.04 as per the instructions at http://www.rdkit.org/docs/Install.html For reasons which I don't really want to get into we would prefer to avoid anaconda for the time being. That being said, when I try to test the build, I