Dear all,

Finally I got:

99% tests passed, 1 tests failed out of 78

Total Test time (real) = 141.17 sec

The following tests FAILED:
         78 - pythonTestDirChem (Failed)
Errors while running CTest



I WOULD LIKE TO THANK ALL OF YOU FOR YOUR HELP!!!

It was not so easy for a Linux beginner like me and I spent a couple of hours!

I don't why, when I installed boost in /opt/boost folder, some  
libraries have been pasted into /usr/local/lib...

I just copy the missing file (libboost_python.so.1.55.0) from  
/usr/local/lib to /opt/anaconda/lib where I have the other...and set  
the LD_LIBRARY_PATH as follow:

export LD_LIBRARY_PATH=$RDBASE/lib:/opt/anaconda/lib:$LD_LIBRARY_PATH

Now everything is OK.

Thanks again.

Best regards,

Enrico





Maciek Wójcikowski <mac...@wojcikowski.pl> a écrit :

> Just as Christos said: you're missing boost path in LD_LIBRARY_PATH
>
> ----
> Pozdrawiam,  |  Best regards,
> Maciek Wójcikowski
> mac...@wojcikowski.pl
>
>
> 2014-07-28 15:53 GMT+02:00 Enrico Perspicace <
> e.perspic...@mx.uni-saarland.de>:
>
>> Dear Greg,
>>
>> Thanks for your help.
>>
>> I have this:
>> [root@Pc-Eric-linux build]# python -c 'from rdkit import rdBase'
>> Traceback (most recent call last):
>>    File "<string>", line 1, in <module>
>> ImportError: libboost_python.so.1.55.0: cannot open shared object
>> file: No such file or directory
>> [root@Pc-Eric-linux build]#
>>
>>
>> and
>>
>> [root@Pc-Eric-linux build]# ldd $RDBASE/rdkit/rdBase.so
>>         linux-vdso.so.1 =>  (0x00007fffe57ff000)
>>         libRDGeneral.so.1 =>
>> /opt/RDKit/RDKit_2014_03_1/lib/libRDGeneral.so.1
>> (0x00007ff4d1392000)
>>         libRDBoost.so.1 => /opt/RDKit/RDKit_2014_03_1/lib/libRDBoost.so.1
>> (0x00007ff4d0fc6000)
>>         libboost_python.so.1.55.0 => not found
>>         libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00007ff4d0cae000)
>>         libm.so.6 => /opt/anaconda/lib/libm.so.6 (0x00007ff4d0a2a000)
>>         libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007ff4d0814000)
>>         libc.so.6 => /lib64/libc.so.6 (0x00007ff4d0480000)
>>         /lib64/ld-linux-x86-64.so.2 (0x0000003148e00000)
>>         libboost_python.so.1.55.0 => not found
>> [root@Pc-Eric-linux build]#
>>
>> What do you think?
>>
>> Thanks
>>
>> Enrico
>>
>>
>>
>> Greg Landrum <greg.land...@gmail.com> a écrit :
>>
>> > given that the failures are all for python tests, I guess you don't have
>> > your PYTHONPATH set properly or that there's an LD_LIBRARY_PATH problem.
>> >
>> > What do you get when you run these two commands?
>> >
>> > python -c 'from rdkit import rdBase'
>> >
>> > ldd $RDBASE/rdkit/rdBase.so
>> >
>> >
>> > -greg
>> >
>> >
>> >
>> >
>> >
>> > -greg
>> >
>> >
>> >
>> > On Mon, Jul 28, 2014 at 12:13 PM, 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
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> ------------------------------------------------------------------------------
>> >> Infragistics Professional
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>> >> Build a bridge from your legacy apps to the future.
>> >>
>> >>
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>> >> _______________________________________________
>> >> Rdkit-discuss mailing list
>> >> Rdkit-discuss@lists.sourceforge.net
>> >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>> >>
>>
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Infragistics Professional
>> Build stunning WinForms apps today!
>> Reboot your WinForms applications with our WinForms controls.
>> Build a bridge from your legacy apps to the future.
>>
>> http://pubads.g.doubleclick.net/gampad/clk?id=153845071&iu=/4140/ostg.clktrk
>> _______________________________________________
>> Rdkit-discuss mailing list
>> Rdkit-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>




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