Hi RDKitters,
I managed to get RDKit 2013_09_2 built on CentOS 5.3. Will post a short
recipe later.
Right now, I am still left with three tests that fail, but I think
(hope) that I can live with that ? Failing tests are:
72:pythonTestDbCLI
73:pythonTestDirML
78:pythonTestDirChem
The test log shows that test 72 won't run because of missing SQLite support.
72/78 Testing: pythonTestDbCLI
72/78 Test: pythonTestDbCLI
Command: "/usr/bin/python26"
"/u01/software/RDKit_2013_09_2/Projects/test_list.py" "--testDir"
"/u01/software/RDKit_2013_09_2/Projects"
Directory: /u01/software/RDKit_2013_09_2/build/Projects
"pythonTestDbCLI" start time: Mar 05 11:07 CET
Output:
----------------------------------------------------------
Traceback (most recent call last):
File "TestDbCLI.py", line 9, in ?
from rdkit.Dbase.DbConnection import DbConnect
File "/u01/software/RDKit_2013_09_2/rdkit/Dbase/DbConnection.py",
line 21, in ?
from rdkit.Dbase import DbUtils,DbInfo
File "/u01/software/RDKit_2013_09_2/rdkit/Dbase/DbUtils.py", line
17, in ?
from rdkit.Dbase.DbResultSet import
DbResultSet,RandomAccessDbResultSet
File "/u01/software/RDKit_2013_09_2/rdkit/Dbase/DbResultSet.py",
line 12, in ?
from rdkit.Dbase import DbInfo
File "/u01/software/RDKit_2013_09_2/rdkit/Dbase/DbInfo.py", line
12, in ?
import DbModule
File "/u01/software/RDKit_2013_09_2/rdkit/Dbase/DbModule.py",
line 61, in ?
raise ImportError,"Neither sqlite nor PgSQL support found."
ImportError: Neither sqlite nor PgSQL support found.
A bit puzzling, since I can "import sqlite3" just fine from Python when
run interactively. As far as I can understand RDConfig.py a successful
import of sqlite3 should make it report that SQLite support is availabe
? For my purposes, failing this test is probably fine - I don't expect I
need sqlite support on this machine.
Tests 73 has this in the log:
Traceback (most recent call last):
File "UnitTestBuildComposite.py", line 16, in ?
from rdkit.ML import BuildComposite
File "/u01/software/RDKit_2013_09_2/rdkit/ML/BuildComposite.py",
line 203, in ?
from rdkit.ML.Composite import Composite,BayesComposite
File
"/u01/software/RDKit_2013_09_2/rdkit/ML/Composite/Composite.py",
line 25, in ?
from rdkit.ML.Data import DataUtils
File "/u01/software/RDKit_2013_09_2/rdkit/ML/Data/DataUtils.py",
line 57, in ?
from rdkit.ML.Data import MLData
File "/u01/software/RDKit_2013_09_2/rdkit/ML/Data/MLData.py",
line 8, in ?
import numpy
ImportError: No module named numpy
...
and test 78:
Output:
----------------------------------------------------------
File "UnitTestInchi.py", line 187
except InchiReadWriteError as inst:
^
SyntaxError: invalid syntax
File "PandasTools.py", line 100
except Exception as e:
^
SyntaxError: invalid syntax
Traceback (most recent call last):
File "UnitTestEState.py", line 17, in ?
import numpy
ImportError: No module named numpy
Traceback (most recent call last):
File "UnitTestFingerprints.py", line 17, in ?
import numpy
ImportError: No module named numpy
...
The numpy module loads fine when run interactively. So maybe it is
something else that is wrong - just that the error reported from Python
is a bit misleading (?).
I haven't run into stuff that doesn't work yet because of these test
failures, so I think that I can get by without them passing. But it
would be nice to know if it is potentially critical or not.
Cheers
-- Jan
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