Hi Enrico,
In LD_LIBRARY_PATH you should also add the location of boost libraries.
Also since you are building using Python from anaconda then make sure that
/opt/anaconda/bin is in your PATH.
To summarize, the environment variables should be something like:
export RDBASE=/opt/RDKit/RDKit_2013_09_2
export LD_LIBRARY_PATH=$RDBASE/lib:path_to_boost_libs:$ LD_LIBRARY_PATH
export PYTHONPATH=$RDBASE:$PYTHONPATH
export PATH= /opt/anaconda/bin:$PATH
Best,
Christos
Christos Kannas
Researcher
Ph.D Student
Mob (UK): +44 (0) 7447700937
Mob (Cyprus): +357 99530608
[image: View Christos Kannas's profile on LinkedIn]
<http://cy.linkedin.com/in/christoskannas>
On 28 July 2014 11:13, Enrico Perspicace <e.perspic...@mx.uni-saarland.de>
wrote:
> Dear Christos,
>
> I'm back... So I upgraded my old Centos with Centos 6.5 and I updated it.
> I installed all packages needed as recommended on RDKit website
> followed by anaconda environment (which include Numpy) as you did.
> Now, I get no errors up to the test of the compilation of RDKit.
> Indeed, compilation of RDKit worked but now, after ctest I have some
> fails...
>
> I did first:
> [root@Pc-Eric-linux build]# cmake -D
> PYTHON_LIBRARY=/opt/anaconda/lib/python2.7/config/libpython2.7.a -D
> PYTHON_INCLUDE_DIR=/opt/anaconda/include/python2.7/ -D
> PYTHON_EXECUTABLE=/opt/anaconda/bin/python2.7 -D
> BOOST_ROOT=/opt/boost/boost_1_55_0 ..
> -- The C compiler identification is GNU 4.4.7
> -- The CXX compiler identification is GNU 4.4.7
> -- Check for working C compiler: /usr/bin/cc
> -- Check for working C compiler: /usr/bin/cc -- works
> -- Detecting C compiler ABI info
> -- Detecting C compiler ABI info - done
> -- Check for working CXX compiler: /usr/bin/c++
> -- Check for working CXX compiler: /usr/bin/c++ -- works
> -- Detecting CXX compiler ABI info
> -- Detecting CXX compiler ABI info - done
> -- Check if the system is big endian
> -- Searching 16 bit integer
> -- Looking for sys/types.h
> -- Looking for sys/types.h - found
> -- Looking for stdint.h
> -- Looking for stdint.h - found
> -- Looking for stddef.h
> -- Looking for stddef.h - found
> -- Check size of unsigned short
> -- Check size of unsigned short - done
> -- Using unsigned short
> -- Check if the system is big endian - little endian
> -- Found PythonLibs: /opt/anaconda/lib/python2.7/config/libpython2.7.a
> (found version "2.7.7")
> -- Found PythonInterp: /opt/anaconda/bin/python2.7 (found version "2.7.7")
> -- Boost version: 1.55.0
> -- Found the following Boost libraries:
> -- python
> -- Looking for include file pthread.h
> -- Looking for include file pthread.h - found
> -- Looking for pthread_create
> -- Looking for pthread_create - not found
> -- Looking for pthread_create in pthreads
> -- Looking for pthread_create in pthreads - not found
> -- Looking for pthread_create in pthread
> -- Looking for pthread_create in pthread - found
> -- Found Threads: TRUE
> -- Boost version: 1.55.0
> -- Found the following Boost libraries:
> -- regex
> -- Configuring done
> -- Generating done
> -- Build files have been written to: /opt/RDKit/RDKit_2014_03_1/build
> [root@Pc-Eric-linux build]#
>
> Then
>
> [root@Pc-Eric-linux build]# make
> [root@Pc-Eric-linux build]# make install
>
> RDKit is compiling correctly withour errors. I just had sometimes this
> warning:
>
> [ 46%] Building CXX object
> Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DataStructs.cpp.o
> Dans le fichier inclus à partir de
>
> /opt/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1761,
> à partir de
>
> /opt/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,
> à partir de
>
> /opt/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
> à partir de
> /opt/RDKit/RDKit_2014_03_1/Code/DataStructs/Wrap/DataStructs.cpp:20:
> /opt/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2:
> attention : #warning "Using deprecated NumPy API, disable it by "
> "#defining NPY_NO_DEPRECATED_API
> NPY_1_7_API_VERSION"
>
> Finally, I ran ctest:
>
> [root@Pc-Eric-linux build]# ctest
>
> And I got:
>
> Test project /opt/RDKit/RDKit_2014_03_1/build
> Start 1: testDict
> 1/78 Test #1: testDict ......................... Passed 0.03 sec
> Start 2: testDataStructs
> 2/78 Test #2: testDataStructs .................. Passed 0.01 sec
> Start 3: pyBV
> 3/78 Test #3: pyBV .............................***Failed 0.02 sec
> Start 4: pyDiscreteValueVect
> 4/78 Test #4: pyDiscreteValueVect ..............***Failed 0.03 sec
> Start 5: pySparseIntVect
> 5/78 Test #5: pySparseIntVect ..................***Failed 0.03 sec
> Start 6: testTransforms
> 6/78 Test #6: testTransforms ................... Passed 0.01 sec
> Start 7: testGrid
> 7/78 Test #7: testGrid ......................... Passed 0.03 sec
> Start 8: testPyGeometry
> 8/78 Test #8: testPyGeometry ...................***Failed 0.04 sec
> Start 9: testMatrices
> 9/78 Test #9: testMatrices ..................... Passed 0.00 sec
> Start 10: testAlignment
> 10/78 Test #10: testAlignment .................... Passed 0.00 sec
> Start 11: pyAlignment
> 11/78 Test #11: pyAlignment ......................***Failed 0.02 sec
> Start 12: testOptimizer
> 12/78 Test #12: testOptimizer .................... Passed 0.01 sec
> Start 13: testUFFForceField
> 13/78 Test #13: testUFFForceField ................ Passed 0.05 sec
> Start 14: testMMFFForceField
> 14/78 Test #14: testMMFFForceField ............... Passed 17.79 sec
> Start 15: pyForceFieldConstraints
> 15/78 Test #15: pyForceFieldConstraints ..........***Failed 0.03 sec
> Start 16: testDistGeom
> 16/78 Test #16: testDistGeom ..................... Passed 0.00 sec
> Start 17: pyDistGeom
> 17/78 Test #17: pyDistGeom .......................***Failed 0.10 sec
> Start 18: graphmolTest1
> 18/78 Test #18: graphmolTest1 .................... Passed 0.14 sec
> Start 19: graphmolcpTest
> 19/78 Test #19: graphmolcpTest ................... Passed 0.02 sec
> Start 20: graphmolqueryTest
> 20/78 Test #20: graphmolqueryTest ................ Passed 0.02 sec
> Start 21: graphmolMolOpsTest
> 21/78 Test #21: graphmolMolOpsTest ............... Passed 1.81 sec
> Start 22: graphmoltestCanon
> 22/78 Test #22: graphmoltestCanon ................ Passed 0.00 sec
> Start 23: graphmoltestChirality
> 23/78 Test #23: graphmoltestChirality ............ Passed 0.04 sec
> Start 24: graphmoltestPickler
> 24/78 Test #24: graphmoltestPickler .............. Passed 0.37 sec
> Start 25: graphmolIterTest
> 25/78 Test #25: graphmolIterTest ................. Passed 0.02 sec
> Start 26: testDepictor
> 26/78 Test #26: testDepictor ..................... Passed 0.41 sec
> Start 27: pyDepictor
> 27/78 Test #27: pyDepictor .......................***Failed 0.02 sec
> Start 28: smiTest1
> 28/78 Test #28: smiTest1 ......................... Passed 0.27 sec
> Start 29: smaTest1
> 29/78 Test #29: smaTest1 ......................... Passed 1.39 sec
> Start 30: fileParsersTest1
> 30/78 Test #30: fileParsersTest1 ................. Passed 7.46 sec
> Start 31: testMolSupplier
> 31/78 Test #31: testMolSupplier .................. Passed 0.18 sec
> Start 32: testMolWriter
> 32/78 Test #32: testMolWriter .................... Passed 0.41 sec
> Start 33: testTplParser
> 33/78 Test #33: testTplParser .................... Passed 0.02 sec
> Start 34: testMol2ToMol
> 34/78 Test #34: testMol2ToMol .................... Passed 0.02 sec
> Start 35: testSubstructMatch
> 35/78 Test #35: testSubstructMatch ............... Passed 0.02 sec
> Start 36: testReaction
> 36/78 Test #36: testReaction ..................... Passed 0.08 sec
> Start 37: pyChemReactions
> 37/78 Test #37: pyChemReactions ..................***Failed 0.02 sec
> Start 38: testChemTransforms
> 38/78 Test #38: testChemTransforms ............... Passed 0.07 sec
> Start 39: testSubgraphs1
> 39/78 Test #39: testSubgraphs1 ................... Passed 0.37 sec
> Start 40: testSubgraphs2
> 40/78 Test #40: testSubgraphs2 ................... Passed 0.02 sec
> Start 41: testFragCatalog
> 41/78 Test #41: testFragCatalog .................. Passed 1.19 sec
> Start 42: pyFragCatalog
> 42/78 Test #42: pyFragCatalog ....................***Failed 0.03 sec
> Start 43: testDescriptors
> 43/78 Test #43: testDescriptors .................. Passed 0.24 sec
> Start 44: pyMolDescriptors
> 44/78 Test #44: pyMolDescriptors .................***Failed 0.02 sec
> Start 45: testFingerprints
> 45/78 Test #45: testFingerprints ................. Passed 0.20 sec
> Start 46: pyPartialCharges
> 46/78 Test #46: pyPartialCharges .................***Failed 0.02 sec
> Start 47: testMolTransforms
> 47/78 Test #47: testMolTransforms ................ Passed 0.02 sec
> Start 48: pyMolTransforms
> 48/78 Test #48: pyMolTransforms ..................***Failed 0.02 sec
> Start 49: testMMFFForceFieldHelpers
> 49/78 Test #49: testMMFFForceFieldHelpers ........ Passed 0.65 sec
> Start 50: testUFFForceFieldHelpers
> 50/78 Test #50: testUFFForceFieldHelpers ......... Passed 1.51 sec
> Start 51: pyForceFieldHelpers
> 51/78 Test #51: pyForceFieldHelpers ..............***Failed 0.02 sec
> Start 52: testDistGeomHelpers
> 52/78 Test #52: testDistGeomHelpers .............. Passed 0.89 sec
> Start 53: pyDistGeom
> 53/78 Test #53: pyDistGeom .......................***Failed 0.02 sec
> Start 54: testMolAlign
> 54/78 Test #54: testMolAlign ..................... Passed 3.97 sec
> Start 55: pyMolAlign
> 55/78 Test #55: pyMolAlign .......................***Failed 0.03 sec
> Start 56: testFeatures
> 56/78 Test #56: testFeatures ..................... Passed 0.02 sec
> Start 57: pyChemicalFeatures
> 57/78 Test #57: pyChemicalFeatures ...............***Failed 0.02 sec
> Start 58: testShapeHelpers
> 58/78 Test #58: testShapeHelpers ................. Passed 0.02 sec
> Start 59: pyShapeHelpers
> 59/78 Test #59: pyShapeHelpers ...................***Failed 0.03 sec
> Start 60: testMolCatalog
> 60/78 Test #60: testMolCatalog ................... Passed 0.02 sec
> Start 61: pyMolCatalog
> 61/78 Test #61: pyMolCatalog .....................***Failed 0.03 sec
> Start 62: testSLNParse
> 62/78 Test #62: testSLNParse ..................... Passed 0.03 sec
> Start 63: pySLNParse
> 63/78 Test #63: pySLNParse .......................***Failed 0.01 sec
> Start 64: pyGraphMolWrap
> 64/78 Test #64: pyGraphMolWrap ...................***Failed 0.04 sec
> Start 65: pyTestConformerWrap
> 65/78 Test #65: pyTestConformerWrap ..............***Failed 0.02 sec
> Start 66: testQuery
> 66/78 Test #66: testQuery ........................ Passed 0.00 sec
> Start 67: testMatCalc
> 67/78 Test #67: testMatCalc ...................... Passed 0.00 sec
> Start 68: pyMatCalc
> 68/78 Test #68: pyMatCalc ........................***Failed 0.03 sec
> Start 69: pyRanker
> 69/78 Test #69: pyRanker .........................***Failed 0.03 sec
> Start 70: testChemicalFeatures
> 70/78 Test #70: testChemicalFeatures ............. Passed 0.01 sec
> Start 71: pyFeatures
> 71/78 Test #71: pyFeatures .......................***Failed 0.02 sec
> Start 72: pythonTestDbCLI
> 72/78 Test #72: pythonTestDbCLI ..................***Failed 0.23 sec
> Start 73: pythonTestDirML
> 73/78 Test #73: pythonTestDirML ..................***Failed 3.34 sec
> Start 74: pythonTestDirDataStructs
> 74/78 Test #74: pythonTestDirDataStructs ......... Passed 0.02 sec
> Start 75: pythonTestDirDbase
> 75/78 Test #75: pythonTestDirDbase ............... Passed 0.02 sec
> Start 76: pythonTestDirSimDivFilters
> 76/78 Test #76: pythonTestDirSimDivFilters ....... Passed 0.02 sec
> Start 77: pythonTestDirVLib
> 77/78 Test #77: pythonTestDirVLib ................ Passed 0.01 sec
> Start 78: pythonTestDirChem
> 78/78 Test #78: pythonTestDirChem ................***Failed 2.26 sec
>
> 64% tests passed, 28 tests failed out of 78
>
> Total Test time (real) = 46.52 sec
>
> The following tests FAILED:
> 3 - pyBV (Failed)
> 4 - pyDiscreteValueVect (Failed)
> 5 - pySparseIntVect (Failed)
> 8 - testPyGeometry (Failed)
> 11 - pyAlignment (Failed)
> 15 - pyForceFieldConstraints (Failed)
> 17 - pyDistGeom (Failed)
> 27 - pyDepictor (Failed)
> 37 - pyChemReactions (Failed)
> 42 - pyFragCatalog (Failed)
> 44 - pyMolDescriptors (Failed)
> 46 - pyPartialCharges (Failed)
> 48 - pyMolTransforms (Failed)
> 51 - pyForceFieldHelpers (Failed)
> 53 - pyDistGeom (Failed)
> 55 - pyMolAlign (Failed)
> 57 - pyChemicalFeatures (Failed)
> 59 - pyShapeHelpers (Failed)
> 61 - pyMolCatalog (Failed)
> 63 - pySLNParse (Failed)
> 64 - pyGraphMolWrap (Failed)
> 65 - pyTestConformerWrap (Failed)
> 68 - pyMatCalc (Failed)
> 69 - pyRanker (Failed)
> 71 - pyFeatures (Failed)
> 72 - pythonTestDbCLI (Failed)
> 73 - pythonTestDirML (Failed)
> 78 - pythonTestDirChem (Failed)
> Errors while running CTest
> [root@Pc-Eric-linux build]#
>
> I set variables environment as follow:
> export RDBASE=/opt/RDKit/RDKit_2013_09_2/
> export LD_LIBRARY_PATH=$RDBASE/lib
> export PYTHONPATH=$RDBASE
>
> What I did wrong?
>
> Do you have any idea?
>
> Thanks in advance for you reply.
>
> Best regards,
>
> Enrico
>
>
>
>
> Enrico Perspicace <e.perspic...@mx.uni-saarland.de> a écrit :
>
> > Dear Christos,
> >
> > Thanks for your reply.
> > I already tried but it didn't work...
> > I downloaded yesterday Centos 6.5 and I will install it.
> > I hope to get less problem with this version as RDKit is available
> > using rpm package.
> > I will let you know if I will succeed or not ;-)
> >
> > Best regards,
> >
> > Enrico
> >
> >
> > Christos Kannas <chriskan...@gmail.com> a écrit :
> >
> >> Enrico,
> >>
> >> According to Boost web site (
> >>
> http://www.boost.org/doc/libs/1_55_0/libs/log/doc/html/log/installation.html
> )
> >> it has been tested and working with gcc 4.5+.
> >> Try to update your gcc and gcc-c++ to the latest versions available... I
> >> know CentOS is not up to date...
> >> At the moment I do not recall if I did any update to gcc.
> >> I will get back to you on Monday for this, except if you are in a hurry
> >> I'll go from the office tomorrow to check my dev machine.
> >>
> >> Best,
> >>
> >> Christos
> >>
> >> Christos Kannas
> >>
> >> Researcher
> >> Ph.D Student
> >>
> >> Mob (UK): +44 (0) 7447700937
> >> Mob (Cyprus): +357 99530608
> >>
> >> [image: View Christos Kannas's profile on LinkedIn]
> >> <http://cy.linkedin.com/in/christoskannas>
> >>
> >>
> >> On 24 July 2014 15:02, Enrico Perspicace <
> e.perspic...@mx.uni-saarland.de>
> >> wrote:
> >>
> >>> Hi Christos,
> >>>
> >>> Thanks for your help.
> >>>
> >>> I tried what you said but I got an error with boost.
> >>>
> >>> I think the problem came from here...
> >>>
> >>> I use Canopy environment, it is like Anaconda which include Numpy and
> it
> >>> is detected when I did ./bootstrap.sh
> >>>
> >>> [root@eric-pc boost_1_55_0]# ./bootstrap.sh
> --with-libraries=python,regex
> >>> Building Boost.Build engine with toolset gcc...
> tools/build/v2/engine/bin.
> >>> linuxx86_64/b2
> >>> Detecting Python version... 2.7
> >>> Detecting Python root... /root/Enthought/Canopy_64bit/User
> >>> Unicode/ICU support for Boost.Regex?... not found.
> >>> Generating Boost.Build configuration in project-config.jam...
> >>>
> >>> Bootstrapping is done. To build, run:
> >>>
> >>> ./b2
> >>>
> >>> To adjust configuration, edit 'project-config.jam'.
> >>> Further information:
> >>>
> >>> - Command line help:
> >>> ./b2 --help
> >>>
> >>> - Getting started guide:
> >>> http://www.boost.org/more/getting_started/unix-variants.html
> >>>
> >>> - Boost.Build documentation:
> >>> http://www.boost.org/boost-build2/doc/html/index.html
> >>>
> >>> [root@eric-pc boost_1_55_0]#
> >>>
> >>> But, when I performed ./b2 address-model=64 cflags=-fPIC cxxflags=-fPIC
> >>> Install I got errors of compilation with gcc (I use gcc (GCC) 4.1.2
> >>> 20080704 (Red Hat 4.1.2-54)) and should be ok (miminum required gcc
> 3.3:
> >>>
> >>> ...failed gcc.compile.c++ bin.v2/libs/python/build/gcc-
> >>> 4.1.2/release/address-model-64/link-static/threading-
> >>> multi/object/function_doc_signature.o...
> >>> ...skipped <pbin.v2/libs/python/build/gcc-4.1.2/release/address-
> >>> model-64/link-static/threading-multi>libboost_python.a(clean) for lack
> of
> >>>
> <pbin.v2/libs/python/build/gcc-4.1.2/release/address-model-64/link-static/
> >>> threading-multi>numeric.o...
> >>> ...skipped <pbin.v2/libs/python/build/gcc-4.1.2/release/address-
> >>> model-64/link-static/threading-multi>libboost_python.a for lack of
> >>>
> <pbin.v2/libs/python/build/gcc-4.1.2/release/address-model-64/link-static/
> >>> threading-multi>numeric.o...
> >>> ...skipped <p/usr/local/lib>libboost_python.a for lack of
> >>>
> <pbin.v2/libs/python/build/gcc-4.1.2/release/address-model-64/link-static/
> >>> threading-multi>libboost_python.a...
> >>> common.copy /usr/local/lib/libboost_regex.a
> >>> ...failed updating 56 targets...
> >>> ...skipped 6 targets...
> >>> ...updated 3 targets...
> >>>
> >>>
> >>> Regards,
> >>>
> >>> Enrico
> >>>
> >>>
> >>>
> >>> Quoting Christos Kannas <chriskan...@gmail.com>:
> >>>
> >>> Hi Enrico,
> >>>>
> >>>> The latest version of RDKit does not require flex or bison,
> thankfully.
> >>>>
> >>>> In the attached file I list the commands that I used to build CMake
> >>>> (2.8.12.2), Boost libraries (1.55) and RDKit (2014_03_1) on a CentOS
> 5.10
> >>>> VM.
> >>>> In my case I was using an Anaconda Python environment so I didn't
> have to
> >>>> install NumPy, since it is bundled to it.
> >>>>
> >>>> Best,
> >>>>
> >>>> Christos
> >>>>
> >>>> Christos Kannas
> >>>>
> >>>> Researcher
> >>>> Ph.D Student
> >>>>
> >>>> Mob (UK): +44 (0) 7447700937
> >>>> Mob (Cyprus): +357 99530608
> >>>>
> >>>> [image: View Christos Kannas's profile on LinkedIn]
> >>>> <http://cy.linkedin.com/in/christoskannas>
> >>>>
> >>>>
> >>>>
> >>>> On 24 July 2014 10:05, Enrico Perspicace <
> e.perspic...@mx.uni-saarland.de
> >>>> >
> >>>> wrote:
> >>>>
> >>>>
> >>>>> Dear all,
> >>>>>
> >>>>> I would like to install RDKit 2014 on Centos 5.10 (Final) but I did
> not
> >>>>> succeed!
> >>>>>
> >>>>> I follow Instructions for Installation on RDKIT website but I got an
> >>>>> error
> >>>>> when I used cmake command line...
> >>>>>
> >>>>> Indeed, cmake is not able to find boost_python library.
> >>>>>
> >>>>> I installed: Python 2.7, atlas, lapack, blas, fftw3, numpy 1.8 via
> canopy
> >>>>> 1.4.1 (and is working with python import numpy), boost 1.55, flex
> 2.5.35
> >>>>> and bison 3.0.2 before performing the RDKit installation.
> >>>>>
> >>>>> I followed the procedure described here:
> https://www.mail-archive.com/
> >>>>> rdkit-discuss@lists.sourceforge.net/msg01376.html
> >>>>>
> >>>>> Please find in attached document related files which describe my
> problem.
> >>>>>
> >>>>> Thanks a lot for you help.
> >>>>>
> >>>>> Best regards,
> >>>>>
> >>>>> Enrico Perspicace
> >>>>>
> >>>>>
> >>>>> ------------------------------------------------------------
> >>>>> ------------------
> >>>>> Want fast and easy access to all the code in your enterprise? Index
> and
> >>>>> search up to 200,000 lines of code with a free copy of Black Duck
> >>>>> Code Sight - the same software that powers the world's largest code
> >>>>> search on Ohloh, the Black Duck Open Hub! Try it now.
> >>>>> http://p.sf.net/sfu/bds
> >>>>> _______________________________________________
> >>>>> Rdkit-discuss mailing list
> >>>>> Rdkit-discuss@lists.sourceforge.net
> >>>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
> >>>>>
> >>>>>
> >>>>>
> >>>
> >>>
> >>>
> >
> >
> >
> >
> >
> ------------------------------------------------------------------------------
> > Want fast and easy access to all the code in your enterprise? Index and
> > search up to 200,000 lines of code with a free copy of Black Duck
> > Code Sight - the same software that powers the world's largest code
> > search on Ohloh, the Black Duck Open Hub! Try it now.
> > http://p.sf.net/sfu/bds
> > _______________________________________________
> > Rdkit-discuss mailing list
> > Rdkit-discuss@lists.sourceforge.net
> > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>
>
>
>
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