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 <[email protected]> a écrit :
> Just as Christos said: you're missing boost path in LD_LIBRARY_PATH
>
> ----
> Pozdrawiam, | Best regards,
> Maciek Wójcikowski
> [email protected]
>
>
> 2014-07-28 15:53 GMT+02:00 Enrico Perspicace <
> [email protected]>:
>
>> 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 <[email protected]> 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 <
>> > [email protected]> 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 <[email protected]> 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 <[email protected]> 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 <
>> >> [email protected]>
>> >> >> 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 <[email protected]>:
>> >> >>>
>> >> >>> 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 <
>> >> [email protected]
>> >> >>>> >
>> >> >>>> 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/
>> >> >>>>> [email protected]/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
>> >> >>>>> [email protected]
>> >> >>>>> 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
>> >> > [email protected]
>> >> > 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
>> >> [email protected]
>> >> 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
>> [email protected]
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
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Build a bridge from your legacy apps to the future.
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