From: Liwei Li [mailto:[email protected]]
Sent: Tuesday, April 03, 2012 2:18 PM
To: Long, Ryan L
Subject: Re: [Rdkit-discuss] rdkit - ctest mulitiple failures
Hi, Ryan,
I ran some test commands and here are the output. Please forward it to the
forum if you don't mind.
Liwei
node1$ /home/liwei/RDKit_2011_12_1/build$ ctest -V -R pyBV
UpdateCTestConfiguration from
:/home/liwei/RDKit_2011_12_1/build/DartConfiguration.tcl
UpdateCTestConfiguration from
:/home/liwei/RDKit_2011_12_1/build/DartConfiguration.tcl
Test project /home/liwei/RDKit_2011_12_1/build
Constructing a list of tests
Done constructing a list of tests
Checking test dependency graph...
Checking test dependency graph end
test 3
Start 3: pyBV
3: Test command: /usr/bin/python
"/home/liwei/RDKit_2011_12_1/Code/DataStructs/Wrap/testBV.py"
3: Test timeout computed to be: 9.99988e+06
3: Traceback (most recent call last):
3: File "/home/liwei/RDKit_2011_12_1/Code/DataStructs/Wrap/testBV.py", line
1, in <module>
3: from rdkit import DataStructs
3: File "/home/liwei/RDKit_2011_12_1/rdkit/DataStructs/__init__.py", line 11,
in <module>
3: from rdkit import rdBase
3: ImportError: cannot import name rdBase
1/1 Test #3: pyBV .............................***Failed 0.03 sec
0% tests passed, 1 tests failed out of 1
Total Test time (real) = 0.04 sec
The following tests FAILED:
3 - pyBV (Failed)
Errors while running CTest
node1$/home/liwei/RDKit_2011_12_1/build$ python -c "from rdkit import rdBase"
Traceback (most recent call last):
File "<string>", line 1, in <module>
ImportError: cannot import name rdBase
node1$echo $PYTHONPATH
/home/liwei/RDKit_2011_12_1/:
node1$echo $LD_LIBRARY_PATH
/home/liwei/RDKit_2011_12_1//lib:/usr/lib/:/usr/local/lib/:
node1$echo $RDBASE
/home/liwei/RDKit_2011_12_1/
node1$ ls -ltrh /home/liwei/RDKit_2011_12_1/rdkit
total 120K
-rwxr-xr-x 1 liwei liwei 464 2010-01-14 11:10 test_list.py
-rw-r--r-- 1 liwei liwei 0 2010-01-26 00:29 __init__.py
-rw-r--r-- 1 liwei liwei 1.4K 2010-09-15 00:18 CMakeLists.txt
-rwxr-xr-x 1 liwei liwei 852 2010-09-26 13:04 RDRandom.py
-rw-r--r-- 1 liwei liwei 1.6K 2010-09-26 13:04 RDLogger.py
-rwxr-xr-x 1 liwei liwei 2.1K 2010-09-26 13:04 RDConfig.py
-rwxr-xr-x 1 liwei liwei 5.7K 2012-01-03 02:50 TestRunner.py
-rw-r--r-- 1 liwei liwei 436 2012-01-07 02:30 epydoc.config
drwxr-xr-x 2 liwei liwei 4.0K 2012-01-14 09:49 Logger
drwxr-xr-x 15 liwei liwei 4.0K 2012-01-14 09:49 sping
drwxr-xr-x 3 liwei liwei 4.0K 2012-01-14 09:49 SimDivFilters
drwxr-xr-x 2 liwei liwei 4.0K 2012-01-14 09:49 ForceField
drwxr-xr-x 2 liwei liwei 4.0K 2012-01-14 09:49 Excel
drwxr-xr-x 2 liwei liwei 4.0K 2012-01-14 09:49 Avalon
-rw-r--r-- 1 liwei liwei 132 2012-04-03 13:30 __init__.pyc
drwxr-xr-x 3 liwei liwei 4.0K 2012-04-03 13:59 DataStructs
-rw-r--r-- 1 liwei liwei 2.0K 2012-04-03 13:59 RDConfig.pyc
drwxr-xr-x 2 liwei liwei 4.0K 2012-04-03 13:59 Numerics
drwxr-xr-x 2 liwei liwei 4.0K 2012-04-03 13:59 DistanceGeometry
-rw-r--r-- 1 liwei liwei 2.6K 2012-04-03 14:00 RDLogger.pyc
drwxr-xr-x 3 liwei liwei 4.0K 2012-04-03 14:00 DataManip
-rw-r--r-- 1 liwei liwei 670 2012-04-03 14:00 RDRandom.pyc
-rw-r--r-- 1 liwei liwei 4.9K 2012-04-03 14:00 TestRunner.pyc
drwxr-xr-x 4 liwei liwei 4.0K 2012-04-03 14:00 Dbase
drwxr-xr-x 17 liwei liwei 4.0K 2012-04-03 14:00 ML
drwxr-xr-x 2 liwei liwei 4.0K 2012-04-03 14:01 utils
drwxr-xr-x 16 liwei liwei 4.0K 2012-04-03 14:01 Chem
drwxr-xr-x 2 liwei liwei 4.0K 2012-04-03 14:01 Geometry
drwxr-xr-x 3 liwei liwei 4.0K 2012-04-03 14:01 VLib
On Tue, Apr 3, 2012 at 12:21 AM, Greg Landrum
<[email protected]<mailto:[email protected]>> wrote:
Dear Ryan,
On Mon, Apr 2, 2012 at 10:42 PM, Long, Ryan L
<[email protected]<mailto:[email protected]>> wrote:
>
> My name is Ryan Long. I am a computer technician for one of the labs at
> IUPUI. We have been trying to get rdkit running on a couple of our linux
> systems (a Ubuntu 10.10 and a Red Hat system) and the install seems to go
> ok, but when we run ctest we get at least 25 failures. Is this normal?
> Should we be able to run the program despite these errors? Any help is
> appreciated. Thanks!
The errors you are getting are all in the python tests. This is
usually the result of either your PYTHONPATH or your LD_LIBRARY_PATH
not being set properly.
PYTHONPATH needs to include the directory that contains the "rdkit"
directory and LD_LIBRARY_PATH needs to include the RDKit lib directory
(or wherever those files were installed to).
The easy test is to either do:
ctest -V -R pyBV
or:
python -c "from rdkit import rdBase"
and look at the output.
If you see an error message that python cannot find the module rdkit
it's a PYTHONPATH problem. Otherwise it's likely to be an
LD_LIBRARY_PATH problem.
Best,
-greg
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