Hi Matt, all;
I use RDKit from Scala/Java and experienced the same issue.
Despite having GraphMolWrap.so in the LD_LIBRARY_PATH the code fails
with a UnsatisfiedLinkError.
I've solved it by loading explicitly the native library:
System.load("/opt/collector/lib/libGraphMolWrap.so")
I don't know if there is some other way to solve it.
-
Regards,
*Oriol López Massaguer*
PharmacoInformatics Laboratory (PhI)
Research Program on Biomedical Informatics (GRIB) - IMIM/UPF
GRIB/PRBB Dr. Aiguader 88 | E08003 Barcelona (Spain)
olo...@imim.es <mailto:olo...@imim.es>
http://phi.imim.es/
On 13/01/14 22:58, Matthew Lardy wrote:
Thanks Greg and Gianluca,
The machine I had been build RDKit was having some major Cmake issues,
but I am through that now. I did a fresh install of CentOS (this time
version 6.5) and a new copy of Swig (2.0.10) and things compiled
without issue. So, I have the most recent version of RDKit built and
everything has passed the tests.
Still I have the following issue, using the Swig compiled jars in my
own code:
Exception in thread "main" java.lang.UnsatisfiedLinkError:
org.RDKit.RDKFuncsJNI.RWMol_MolFromMolFile__SWIG_2(Ljava/lang/String;)J at
org.RDKit.RDKFuncsJNI.RWMol_MolFromMolFile__SWIG_2(Native Method) at
org.RDKit.RWMol.MolFromMolFile(RWMol.java:472) at
autocorrelator.apps.SdfFilter.main(SdfFilter.java:71)
I don't have an issue compiling my java code, but I am doing that with
ant. I am executing this code (SdfFilter) from the command line. I
have the location (and jar file handle) to org.RDKit.jar in my
classpath, and I have the path to GraphMolWrap.so in my
LD_LIBRARY_PATH. Is there something else in the environment I need to
set up to get through the UnsatisfiedLinkError?
Thanks for your patience with my build issues!
Matt
On Sun, Jan 12, 2014 at 4:47 AM, Gianluca Sforna <gia...@gmail.com
<mailto:gia...@gmail.com>> wrote:
On Sat, Jan 11, 2014 at 1:45 AM, Matthew Lardy <mla...@gmail.com
<mailto:mla...@gmail.com>> wrote:
> I
> don't know who's fault it is (CentOS's for rolling with a
prehistoric
> version of boost, CMake for just being frustrating in general,
or Boost for
> not building the FindBoost.cmake from a user compile). If
anyone has a
> workaround, I am all ears. :)
The rpm I build for CentOS 6 works with the boost version included
with the distro, so I guess you are hitting some other issue. However,
further diagnosis without seeing specific commands given and output
received is very hard.
If you are interested, I recently rebuild rdkit in copr and you can
find the resulting binary RPMs here:
http://copr.fedoraproject.org/coprs/giallu/rdkit/
Regards
Gianluca
--
Gianluca Sforna
http://morefedora.blogspot.com
http://identi.ca/giallu - http://twitter.com/giallu
-
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