Hi RDKitters,
Config : Linux CentOS 7 (64 bit)
Python 3.4 (Conda Installation)
Python system 2.7
R 3.2.3
I'm an RDKit newcomer and I would like to install R package named "rrdkit".
However, I obtained an error message during installation :
> library(devtools)
> install_github("pauca/rrdkit/rrdkit")
* installing *source* package ‘rrdkit’ ...
** libs
g++ -m64 -I/usr/include/R -DNDEBUG -I/Code -I/usr/lib64
-I/usr/local/include
-I"/home/canault/R/x86_64-redhat-linux-gnu-library/3.2/Rcpp/include"
-fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches
-m64 -mtune=generic -c RcppExports.cpp -o RcppExports.o
g++ -m64 -I/usr/include/R -DNDEBUG -I/Code -I/usr/lib64
-I/usr/local/include
-I"/home/canault/R/x86_64-redhat-linux-gnu-library/3.2/Rcpp/include"
-fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches
-m64 -mtune=generic -c inchi.cpp -o inchi.o
*inchi.cpp:57:36: fatal error: GraphMol/PeriodicTable.h: No such file or
directory*
* #include <GraphMol/PeriodicTable.h>*
^
compilation terminated.
make: *** [inchi.o] Error 1
ERROR: compilation failed for package ‘rrdkit’
* removing ‘/home/canault/R/x86_64-redhat-linux-gnu-library/3.2/rrdkit’
Error: Command failed (1)
> install_github("pauca/rrdkit/rrdkit")
Downloading GitHub repo pauca/rrdkit@master
from URL https://api.github.com/repos/pauca/rrdkit/zipball/master
Installing rrdkit
'/usr/lib64/R/bin/R' --no-site-file --no-environ --no-save --no-restore \
--quiet CMD INSTALL \
'/tmp/RtmpDYOheI/devtools7a513f76cf4/pauca-RRDKit-140b05d/rrdkit' \
--library='/home/canault/R/x86_64-redhat-linux-gnu-library/3.2' \
--install-tests
* installing *source* package ‘rrdkit’ ...
** libs
g++ -m64 -I/usr/include/R -DNDEBUG -I/Code -I/usr/lib64
-I/usr/local/include
-I"/home/canault/R/x86_64-redhat-linux-gnu-library/3.2/Rcpp/include"
-fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches
-m64 -mtune=generic -c RcppExports.cpp -o RcppExports.o
g++ -m64 -I/usr/include/R -DNDEBUG -I/Code -I/usr/lib64
-I/usr/local/include
-I"/home/canault/R/x86_64-redhat-linux-gnu-library/3.2/Rcpp/include"
-fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches
-m64 -mtune=generic -c inchi.cpp -o inchi.o
inchi.cpp:57:36: fatal error: GraphMol/PeriodicTable.h: No such file or
directory
#include <GraphMol/PeriodicTable.h>
^
compilation terminated.
make: *** [inchi.o] Error 1
ERROR: compilation failed for package ‘rrdkit’
* removing ‘/home/canault/R/x86_64-redhat-linux-gnu-library/3.2/rrdkit’
Error: Command failed (1)
But this Module work nicely in python :
python2.7
>>> from rdkit import Chem
>>> from rdkit.Chem import AllChem
>>> AllChem.INCHI_AVAILABLE
True
>>> from rdkit.Chem.rdchem import PeriodicTable
OK
my RDKit installation :
wget
https://copr.fedoraproject.org/coprs/giallu/rdkit/repo/epel-7/giallu-rdkit-epel-7.repo
yum search rdkit
yum install python2-rdkit.x86_64
I have no solution, could you please help me ?
Thanks in advance,
Baptiste
------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
