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
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>>>>> _______________________________________________
>>>>> Rdkit-discuss mailing list
>>>>> Rdkit-discuss@lists.sourceforge.net
>>>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>>>
>>>>>
>>>>>
>>>
>>>
>>>
>
>
>
>
> ------------------------------------------------------------------------------
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