Dear Kirk and Greg,
I have got RDKit to compile!!!
Unfortunately almost all of the tests are failing when I run ctest - any
hints would be very welcome:
Linking CXX shared module ../../../rdkit/Chem/rdChemicalFeatures.so
[100%] Built target rdChemicalFeatures
[r...@mgcct25 build]# sqlite3 $RDBASE/Data/RDTests.sqlt <
$RDBASE/rdkit/Dbase/test_data/RDTests.sqlite
SQL error: table basic_2class already exists
SQL error: table ferro_noquant already exists
SQL error: table ferro_noquant_realact already exists
SQL error: table ferro_quant already exists
SQL error: table float_2class already exists
SQL error: table simple_mols already exists
SQL error: table simple_mols_fps already exists
SQL error: table simple_mols1 already exists
SQL error: table simple_mols1_fp already exists
SQL error: table ten_elements already exists
SQL error: table ten_elements_dups already exists
SQL error: table bit_ensemble_test already exists
SQL error: table fromtext already exists
SQL error: table fromtext2 already exists
SQL error: table StorageTest already exists
SQL error: column id is not unique
SQL error: column id is not unique
SQL error: column id is not unique
SQL error: table simple_combined already exists
[r...@mgcct25 build]# sqlite3 $RDBASE/Data/RDData.sqlt <
$RDBASE/rdkit/Dbase/test_data/RDData.sqlite
SQL error: table atomic_data already exists
SQL error: table lsd_data already exists
SQL error: table source_notes already exists
[r...@mgcct25 build]# ctest
Start processing tests
Test project /root/RDKit_2010_09_1/build
1/ 76 Testing testDict ***Failed
2/ 76 Testing testDataStructs ***Failed
3/ 76 Testing pyBV ***Failed
4/ 76 Testing pyDiscreteValueVect ***Failed
5/ 76 Testing pySparseIntVect ***Failed
6/ 76 Testing testTransforms ***Failed
7/ 76 Testing testGrid ***Failed
8/ 76 Testing testPyGeometry ***Failed
9/ 76 Testing testMatrices ***Failed
10/ 76 Testing testAlignment ***Failed
11/ 76 Testing pyAlignment ***Failed
12/ 76 Testing testOptimizer ***Failed
13/ 76 Testing testForceField ***Failed
14/ 76 Testing testDistGeom ***Failed
15/ 76 Testing pyDistGeom ***Failed
16/ 76 Testing graphmolTest1 ***Failed
17/ 76 Testing graphmolcpTest ***Failed
18/ 76 Testing graphmolqueryTest ***Failed
19/ 76 Testing graphmolMolOpsTest ***Failed
20/ 76 Testing graphmoltestCanon ***Failed
21/ 76 Testing graphmoltestChirality ***Failed
22/ 76 Testing graphmoltestPickler ***Failed
23/ 76 Testing graphmolIterTest ***Failed
24/ 76 Testing testDepictor ***Failed
25/ 76 Testing pyDepictor ***Failed
26/ 76 Testing smiTest1 ***Failed
27/ 76 Testing smaTest1 ***Failed
28/ 76 Testing fileParsersTest1 ***Failed
29/ 76 Testing testMolSupplier ***Failed
30/ 76 Testing testMolWriter ***Failed
31/ 76 Testing testTplParser ***Failed
32/ 76 Testing testMol2ToMol ***Failed
33/ 76 Testing testSubstructMatch ***Failed
34/ 76 Testing testReaction ***Failed
35/ 76 Testing pyChemReactions ***Failed
36/ 76 Testing testChemTransforms ***Failed
37/ 76 Testing testSubgraphs1 ***Failed
38/ 76 Testing testSubgraphs2 ***Failed
39/ 76 Testing testFragCatalog ***Failed
40/ 76 Testing pyFragCatalog ***Failed
41/ 76 Testing testDescriptors ***Failed
42/ 76 Testing pyMolDescriptors ***Failed
43/ 76 Testing testFingerprints ***Failed
44/ 76 Testing pyPartialCharges ***Failed
45/ 76 Testing testMolTransforms ***Failed
46/ 76 Testing pyMolTransforms ***Failed
47/ 76 Testing testForceFieldHelpers ***Failed
48/ 76 Testing pyForceFieldHelpers ***Failed
49/ 76 Testing testDistGeomHelpers ***Failed
50/ 76 Testing pyDistGeom ***Failed
51/ 76 Testing testMolAlign ***Failed
52/ 76 Testing pyMolAlign ***Failed
53/ 76 Testing testFeatures ***Failed
54/ 76 Testing pyChemicalFeatures ***Failed
55/ 76 Testing testShapeHelpers ***Failed
56/ 76 Testing pyShapeHelpers ***Failed
57/ 76 Testing testMolCatalog ***Failed
58/ 76 Testing pyMolCatalog ***Failed
59/ 76 Testing testSLNParse ***Failed
60/ 76 Testing pySLNParse ***Failed
61/ 76 Testing pyGraphMolWrap ***Failed
62/ 76 Testing pyTestConformerWrap ***Failed
63/ 76 Testing testQuery ***Failed
64/ 76 Testing testMatCalc ***Failed
65/ 76 Testing pyMatCalc ***Failed
66/ 76 Testing pyCMIM ***Failed
67/ 76 Testing pyRanker ***Failed
68/ 76 Testing testChemicalFeatures ***Failed
69/ 76 Testing pyFeatures ***Failed
70/ 76 Testing pythonTestDbCLI ***Failed
71/ 76 Testing pythonTestDirML ***Failed
72/ 76 Testing pythonTestDirDataStructs Passed
73/ 76 Testing pythonTestDirDbase Passed
74/ 76 Testing pythonTestDirSimDivFilters Passed
75/ 76 Testing pythonTestDirVLib Passed
76/ 76 Testing pythonTestDirChem ***Failed
5% tests passed, 72 tests failed out of 76
The following tests FAILED:
1 - testDict (Failed)
2 - testDataStructs (Failed)
3 - pyBV (Failed)
4 - pyDiscreteValueVect (Failed)
5 - pySparseIntVect (Failed)
6 - testTransforms (Failed)
7 - testGrid (Failed)
8 - testPyGeometry (Failed)
9 - testMatrices (Failed)
10 - testAlignment (Failed)
11 - pyAlignment (Failed)
12 - testOptimizer (Failed)
13 - testForceField (Failed)
14 - testDistGeom (Failed)
15 - pyDistGeom (Failed)
16 - graphmolTest1 (Failed)
17 - graphmolcpTest (Failed)
18 - graphmolqueryTest (Failed)
19 - graphmolMolOpsTest (Failed)
20 - graphmoltestCanon (Failed)
21 - graphmoltestChirality (Failed)
22 - graphmoltestPickler (Failed)
23 - graphmolIterTest (Failed)
24 - testDepictor (Failed)
25 - pyDepictor (Failed)
26 - smiTest1 (Failed)
27 - smaTest1 (Failed)
28 - fileParsersTest1 (Failed)
29 - testMolSupplier (Failed)
30 - testMolWriter (Failed)
31 - testTplParser (Failed)
32 - testMol2ToMol (Failed)
33 - testSubstructMatch (Failed)
34 - testReaction (Failed)
35 - pyChemReactions (Failed)
36 - testChemTransforms (Failed)
37 - testSubgraphs1 (Failed)
38 - testSubgraphs2 (Failed)
39 - testFragCatalog (Failed)
40 - pyFragCatalog (Failed)
41 - testDescriptors (Failed)
42 - pyMolDescriptors (Failed)
43 - testFingerprints (Failed)
44 - pyPartialCharges (Failed)
45 - testMolTransforms (Failed)
46 - pyMolTransforms (Failed)
47 - testForceFieldHelpers (Failed)
48 - pyForceFieldHelpers (Failed)
49 - testDistGeomHelpers (Failed)
50 - pyDistGeom (Failed)
51 - testMolAlign (Failed)
52 - pyMolAlign (Failed)
53 - testFeatures (Failed)
54 - pyChemicalFeatures (Failed)
55 - testShapeHelpers (Failed)
56 - pyShapeHelpers (Failed)
57 - testMolCatalog (Failed)
58 - pyMolCatalog (Failed)
59 - testSLNParse (Failed)
60 - pySLNParse (Failed)
61 - pyGraphMolWrap (Failed)
62 - pyTestConformerWrap (Failed)
63 - testQuery (Failed)
64 - testMatCalc (Failed)
65 - pyMatCalc (Failed)
66 - pyCMIM (Failed)
67 - pyRanker (Failed)
68 - testChemicalFeatures (Failed)
69 - pyFeatures (Failed)
70 - pythonTestDbCLI (Failed)
71 - pythonTestDirML (Failed)
76 - pythonTestDirChem (Failed)
Errors while running CTest
[r...@mgcct25 build]#
On Thu, 2011-01-06 at 12:26 -0500, rkdeli...@gmail.com wrote:
> Igor,
>
> I am very happy to hear that the script is helpful. And, yes,
> installation on CentOS 5.5 is a pain. The problem actually resides in
> the fact that the major CentOS and RHEL releases are very dated once
> they are released. GCC is my biggest complaint as the standard version
> on the current CentOS is known to have a major bug that causes the
> Boost compile and therefore RDKit compile to fail. I believe that the
> new RHEL 6 is somewhat better - based on Fedora 12 and 13 - and the
> upcoming CentOS 6 will obviously be better as well. Unfortunately,
> this is what we have to work with. Alternatively, I have also
> installed RDKit on Fedora 14 with no need for any updates to any other
> package. One step and I was done. The good news is that future
> releases of RDKit should go somewhat painlessly. I was able to install
> the current beta package by simply compiling the RDKit code. After 2
> minutes of hands on time, 15 minutes of waiting, and RDKit was up and
> running.
>
> If you run into any problems, please post them so that we can
> (hopefully) help and others can benefit in the future.
>
> -Kirk
>
>
>
> On Jan 6, 2011 10:11am, "Igor Filippov [Contr]" <ig...@helix.nih.gov>
> wrote:
> > Dear Kirk,
> >
> >
> >
> > Thank you so much! I'm in the process of compiling gcc-4.5.1 right
> now,
> >
> > having got gmp, mpc, and mpfr built with the older version of gcc.
> >
> > Your instructions have to be preserved for the others, I can't
> believe
> >
> > I'm the only one using CentOs/RHEL on a server/compute node.
> >
> >
> >
> > Greg, don't take it as a slam but compiling the Linux kernel is a
> walk
> >
> > in a park compared to a recent RDkit. I'm working on it second day
> and
> >
> > I'm barely half-way through the process of installing dependencies.
> Even
> >
> > without python the version of gcc which comes with CentOs 5 (4.1.2)
> >
> > cannot compile RDKit.
> >
> > On the other hand the RPM packages for Fedora have been painless to
> >
> > install, how nice it would be to have the RDKit RPMs for CentOs!
> >
> >
> >
> > Best,
> >
> > Igor
> >
> >
> >
> > On Wed, 2011-01-05 at 17:41 -0500, Robert DeLisle wrote:
> >
> > > I have been able to reproducibly build RDKit on CentOS 5.5, but it
> >
> > > required a significant amount of updating of the build components.
> >
> > > The attached walk-through script should get you there. I do not
> >
> > > recall ever seeing that particular error, however.
> >
> > >
> >
> > > -Kirk
> >
> > >
> >
> > >
> >
> > >
> >
> > >
> >
> > > On Wed, Jan 5, 2011 at 1:15 PM, Igor Filippov [Contr]
> >
> > > ig...@helix.nih.gov> wrote:
> >
> > > Dear All,
> >
> > >
> >
> > > Has anyone successfully compiled RDKit on CentOs 5? I'm
> >
> > > running into the
> >
> > > following error message:
> >
> > > [ 15%] Building CXX object
> >
> > >
> >
> > >
> Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o
> >
> > >
> >
> > >
> /root/RDKit_2010_09_1/Code/Numerics/Alignment/Wrap/rdAlignment.cpp:14:31:
> error: numpy/arrayobject.h: No such file or directory
> >
> > >
> >
> > > On CentOs 5 arrayobject.h is part of python-numeric
> package
> >
> > > and it's
> >
> > > located in:
> >
> > > /usr/include/python2.4/Numeric/arrayobject.h
> >
> > >
> >
> > > I'm attempting to compile RDKit_2010_09_1, using boost
> version
> >
> > > 1.39.0,
> >
> > > x86_64 system.
> >
> > >
> >
> > > Regards,
> >
> > > Igor
> >
> > >
> >
> > >
> >
> > >
> >
> > >
> >
> > >
> >
> > >
> ------------------------------------------------------------------------------
> >
> > > Learn how Oracle Real Application Clusters (RAC) One Node
> >
> > > allows customers
> >
> > > to consolidate database storage, standardize their
> database
> >
> > > environment, and,
> >
> > > should the need arise, upgrade to a full multi-node Oracle
> RAC
> >
> > > database
> >
> > > without downtime or disruption
> >
> > > http://p.sf.net/sfu/oracle-sfdevnl
> >
> > > _______________________________________________
> >
> > > Rdkit-discuss mailing list
> >
> > > Rdkit-discuss@lists.sourceforge.net
> >
> > > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
> >
> > >
> >
> >
> >
> >
> >
------------------------------------------------------------------------------
Learn how Oracle Real Application Clusters (RAC) One Node allows customers
to consolidate database storage, standardize their database environment, and,
should the need arise, upgrade to a full multi-node Oracle RAC database
without downtime or disruption
http://p.sf.net/sfu/oracle-sfdevnl
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