Hi,
I guess I still couldn't resolve the path issue. After trying to set the path
the ctest still fail 70% of test case.
The most common error is ImportError: No module named rdkit; I guess I didn't
set the python path correctly.
Here is my current path on ubuntu
$RDBASE
bash: /opt/rdkit-Release_2018_09_1: Is a directory
$LD_LIBRARY_PATH
bash: /opt/rdkit-Release_2018_09_1:/usr/lib/x86_64-linux-gnu::: No such file or
directory
$PYTHONPATH
bash: /opt/rdkit-Release_2018_09_1::: No such file or directory
(I also tried:
/opt/rdkit-Release_2018_09_1:/usr/local/lib/python3.6/dis-packages:
and : /opt/rdkit-Release_2018_09_1:/usr/lib/python3.6:
)
Did I do something wrong?
Thank you!
Xuan
________________________________
From: Greg Landrum <[email protected]>
Sent: January 25, 2019 9:30
To: Xuan Cao
Cc: [email protected]
Subject: Re: [Rdkit-discuss] ctest failed while trying to build the rdkit from
source
After you change the path you should be able to just run ctest again.
On Fri, Jan 25, 2019 at 5:17 PM Xuan Cao
<[email protected]<mailto:[email protected]>> wrote:
Hi,
Thank you for your help!
I think I set the wrong path.
For $RDBASE, it should be something like this "/opt/rdkit-Release_2018_09_1"
For $LD_LIBRARY_PATH, the documents mentioned that it should include $RDBASE
and the boost library, so should it be like this:
"export LD_LIBRARY_PATH=$RDBASE:/usr/lib/x86_64-linux-gnu/:$LD_LIBRARY_PATH"
(/usr/lib/x86_64-linux-gnu/ is the boost shared library
For PYTHONPATH, I did "export PYTHONPATH:$RDBASE:$PYTHONPATH"
After I reconfigure the path, should I do the cmake .. again? or can I just run
make build, etc.?
Thank you!
Xuan
________________________________
From: Greg Landrum <[email protected]<mailto:[email protected]>>
Sent: January 24, 2019 20:52
To: Xuan Cao
Cc: Paolo Tosco;
[email protected]<mailto:[email protected]>
Subject: Re: [Rdkit-discuss] ctest failed while trying to build the rdkit from
source
Hi,
Please include the error messages you see when you run one of the tests.
For example, try doing:
ctest -R testData --output-on-failure
and send that output along.
On Thu, Jan 24, 2019 at 10:30 PM Xuan Cao
<[email protected]<mailto:[email protected]>> wrote:
Hi,
Thank you for the suggestion, but I have already setup the path with following
line before cmake ..
export RDBASE=/opt/RDKit_20XX_XX_X
export LD_LIBRARY_PATH=$RDBASE/lib:$LD_LIBRARY_PATH
export PYTHONPATH=$RDBASE:$PYTHONPATH
Xuan
________________________________
From: Paolo Tosco
<[email protected]<mailto:[email protected]>>
Sent: January 24, 2019 14:04
To:
[email protected]<mailto:[email protected]>
Subject: Re: [Rdkit-discuss] ctest failed while trying to build the rdkit from
source
Hi Xuan,
try to
export RDBASE=/absolute/path/to/rdkit
export PYTHONPATH=$RDBASE
export LD_LIBRARY_PATH=$RDBASE/lib:$LD_LIBRARY_PATH
then re-run ctest.
Cheers,
p.
On 01/24/19 20:48, Xuan Cao wrote:
Sorry, forgot to attach the file
________________________________
From: Xuan Cao <[email protected]><mailto:[email protected]>
Sent: January 24, 2019 13:44
To:
[email protected]<mailto:[email protected]>
Subject: [Rdkit-discuss] ctest failed while trying to build the rdkit from
source
Hi,
I am trying to build the rdkit from source on a fresh new ubuntu18.04 virutal
machine with virtual box (I did sudo apt update; sudo apt upgrade; etc.).
I successfully executed "sudo cmake ..", "sudo make", "sudo make install"
commands, but the sudo ctest gave me only 29% tests passed (I attached file
with failed test).
Then I tried the c++ example from rdkit/Docs/Book/. When I compile the code
with "#include <GraphMol/GraphMol.h>", the system couldn't find the the header
file: GraphMol/GraphMol.h.
I also tried to directly import rdkit by executing "from rdkit import Chem"
from python script, but it complain about no module named "rdkit".
I know that conda install works (I can import rdkit with conda), but I want to
use rdkit functionalities without any virtual environment, so I choose to build
from source.
Is there any suggestion that can help to use rdkit from source without any
virtualenv (python or cpp)?
Any help appreciated!
Thanks!
Xuan
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