[Rdkit-discuss] ctest fails

[鈴木 倫太郎]

Dear All,

I have been used RDKit 2015_03_1 with self-build version of python 2.7 and 
boost 1.62 on CentOS 5.11.
Now I tried to built and install 2016_09_3 in the same environment and I got 13 
errors after ctest.


88% tests passed, 13 tests failed out of 112

The following tests FAILED:
  7 - pyBV (Failed)
  8 - pyDiscreteValueVect (Failed)
  9 - pySparseIntVect (Failed)
 13 - testPyGeometry (Failed)
 64 - pyMolTransforms (Failed)
 70 - pyDistGeom (Failed)
 72 - pyMolAlign (Failed)
 74 - pyChemicalFeatures (Failed)
 95 - pyGraphMolWrap (Failed)
 97 - pyTestTrajectory (Failed)
102 - pySimDivPickers (Failed)
108 - pythonTestDirDataStructs (Failed)
112 - pythonTestDirChem (Failed)
Errors while running CTest


I checked following commands. I could not find problems.


$ ldd $RDBASE/rdkit/Chem/rdchem.so
linux-vdso.so.1 =>  (0x7fff5e3fd000)
libSmilesParse.so.1 => /home/nmr/RDKit/lib/libSmilesParse.so.1 
(0x2b7ccfaa)
libChemTransforms.so.1 => /home/nmr/RDKit/lib/libChemTransforms.so.1 
(0x2b7ccfcf6000)
libSubstructMatch.so.1 => /home/nmr/RDKit/lib/libSubstructMatch.so.1 
(0x2b7ccff39000)
libGraphMol.so.1 => /home/nmr/RDKit/lib/libGraphMol.so.1 
(0x2b7cd0167000)
libRDGeometryLib.so.1 => /home/nmr/RDKit/lib/libRDGeometryLib.so.1 
(0x2b7cd04c9000)
libRDGeneral.so.1 => /home/nmr/RDKit/lib/libRDGeneral.so.1 
(0x2b7cd06e4000)
libRDBoost.so.1 => /home/nmr/RDKit/lib/libRDBoost.so.1 
(0x2b7cd08ff000)
libboost_python.so.1.62.0 => 
/usr/local/boost_1_62_0/lib/libboost_python.so.1.62.0 (0x2b7cd0ccb000)
libboost_thread.so.1.62.0 => 
/usr/local/boost_1_62_0/lib/libboost_thread.so.1.62.0 (0x2b7cd0f1f000)
libboost_system.so.1.62.0 => 
/usr/local/boost_1_62_0/lib/libboost_system.so.1.62.0 (0x2b7cd1145000)
libboost_serialization.so.1.62.0 => 
/usr/local/boost_1_62_0/lib/libboost_serialization.so.1.62.0 
(0x2b7cd1349000)
libDataStructs.so.1 => /home/nmr/RDKit/lib/libDataStructs.so.1 
(0x2b7cd1599000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x2b7cd18fd000)
libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x2b7cd1b1a000)
libm.so.6 => /lib64/libm.so.6 (0x2b7cd1e1a000)
libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x2b7cd209d000)
libc.so.6 => /lib64/libc.so.6 (0x2b7cd22ac000)
libdl.so.2 => /lib64/libdl.so.2 (0x2b7cd2605000)
libutil.so.1 => /lib64/libutil.so.1 (0x2b7cd280a000)
librt.so.1 => /lib64/librt.so.1 (0x2b7cd2a0d000)
/lib64/ld-linux-x86-64.so.2 (0x003ada20)


$ python -c 'from rdkit import rdBase; print rdBase.__file__'
/home/nmr/RDKit/rdkit/rdBase.so


Can you please suggest any solutions?

Thank you,
Rintarou


Suzuki, Rintarou
National Agriculture and Food Research Organization
Tsukuba, Japan

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Re: [Rdkit-discuss] ctest fails

[鈴木 倫太郎]

Dear Paolo,

Thank you for your response.

I built boost with the following commands.


$ ./bootstrap.sh --prefix=/usr/local/boost_1_62_0 
--with-python=/usr/local/bin/python --with-python-root=/usr/local
$ ./b2 threading=multi


/usr/local/bin/python is my self-built version of Python 2.7.

The command you suggested gives the following information but I can not 
interpret it.


$ ctest -I 7,7 -V
UpdateCTestConfiguration  from :/home/nmr/RDKit/build/DartConfiguration.tcl
Start processing tests
UpdateCTestConfiguration  from :/home/nmr/RDKit/build/DartConfiguration.tcl
Test project /home/nmr/RDKit/build
Constructing a list of tests
Done constructing a list of tests
Changing directory into /home/nmr/RDKit/build/External/INCHI-API
Changing directory into /home/nmr/RDKit/build/Code/RDGeneral
Changing directory into /home/nmr/RDKit/build/Code/DataStructs
Changing directory into /home/nmr/RDKit/build/Code/DataStructs/Wrap
  7/112 Testing pyBV
Test command: /usr/local/bin/python 
/home/nmr/RDKit/Code/DataStructs/Wrap/testBV.py
Test timeout computed to be: 9.99988e+06
..E...E..
==
ERROR: test3Bounds (__main__.TestCase)
--
Traceback (most recent call last):
  File "/home/nmr/RDKit/Code/DataStructs/Wrap/testBV.py", line 91, in 
test3Bounds
bv1[11]
RuntimeError: IndexErrorException

==
ERROR: test7FPS (__main__.TestCase)
--
Traceback (most recent call last):
  File "/home/nmr/RDKit/Code/DataStructs/Wrap/testBV.py", line 172, in test7FPS
self.assertRaises(ValueError, lambda: 
DataStructs.CreateFromFPSText("030082801"))
  File "/usr/local/lib/python2.7/unittest/case.py", line 475, in assertRaises
callableObj(*args, **kwargs)
  File "/home/nmr/RDKit/Code/DataStructs/Wrap/testBV.py", line 172, in 
self.assertRaises(ValueError, lambda: 
DataStructs.CreateFromFPSText("030082801"))
RuntimeError: ValueErrorException

--
Ran 13 tests in 0.753s

FAILED (errors=2)
-- Process completed
***Failed
Changing directory into /home/nmr/RDKit/build/Code/Geometry
Changing directory into /home/nmr/RDKit/build/Code/Geometry/Wrap
Changing directory into /home/nmr/RDKit/build/Code/Numerics
Changing directory into /home/nmr/RDKit/build/Code/Numerics/Alignment
Changing directory into /home/nmr/RDKit/build/Code/Numerics/Alignment/Wrap
Changing directory into /home/nmr/RDKit/build/Code/Numerics/Optimizer
Changing directory into /home/nmr/RDKit/build/Code/ForceField/UFF
Changing directory into /home/nmr/RDKit/build/Code/ForceField/MMFF
Changing directory into /home/nmr/RDKit/build/Code/ForceField/Wrap
Changing directory into /home/nmr/RDKit/build/Code/DistGeom
Changing directory into /home/nmr/RDKit/build/Code/DistGeom/Wrap
Changing directory into /home/nmr/RDKit/build/Code/GraphMol
Changing directory into /home/nmr/RDKit/build/Code/GraphMol/Depictor
Changing directory into /home/nmr/RDKit/build/Code/GraphMol/Depictor/Wrap
Changing directory into /home/nmr/RDKit/build/Code/GraphMol/SmilesParse
Changing directory into /home/nmr/RDKit/build/Code/GraphMol/FileParsers
Changing directory into /home/nmr/RDKit/build/Code/GraphMol/Substruct
Changing directory into /home/nmr/RDKit/build/Code/GraphMol/ChemReactions
Changing directory into /home/nmr/RDKit/build/Code/GraphMol/ChemReactions/Wrap
Changing directory into /home/nmr/RDKit/build/Code/GraphMol/ChemTransforms
Changing directory into /home/nmr/RDKit/build/Code/GraphMol/Subgraphs
Changing directory into /home/nmr/RDKit/build/Code/GraphMol/FilterCatalog
Changing directory into /home/nmr/RDKit/build/Code/GraphMol/FilterCatalog/Wrap
Changing directory into /home/nmr/RDKit/build/Code/GraphMol/FragCatalog
Changing directory into /home/nmr/RDKit/build/Code/GraphMol/FragCatalog/Wrap
Changing directory into /home/nmr/RDKit/build/Code/GraphMol/Descriptors
Changing directory into /home/nmr/RDKit/build/Code/GraphMol/Descriptors/Wrap
Changing directory into /home/nmr/RDKit/build/Code/GraphMol/Fingerprints
Changing directory into /home/nmr/RDKit/build/Code/GraphMol/PartialCharges
Changing directory into /home/nmr/RDKit/build/Code/GraphMol/PartialCharges/Wrap
Changing directory into /home/nmr/RDKit/build/Code/GraphMol/MolTransforms
Changing directory into /home/nmr/RDKit/build/Code/GraphMol/MolTransforms/Wrap
Changing directory into 
/home/nmr/RDKit/build/Code/GraphMol/ForceFieldHelpers/MMFF
Changing directory into 
/home/nmr/RDKit/build/Code/GraphMol/ForceFieldHelpers/UFF
Changing directory into 
/home/nmr/RDKit/build/Code/GraphMol/ForceFieldHelpers/CrystalFF
Changing directory into 
/home/nmr/RDKit/build/Code/GraphMol/ForceFieldHelpers/Wrap
Changing directory into /home/nmr/RDKit/build/Code/GraphMol/DistGeomHelpers
Changing directory into