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/README.md

http://github.com/rajarshi/cdkr
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 1
 2<!-- README.md is generated from README.Rmd. Please edit that file -->
 3
 4[![Build
 5Status](https://api.travis-ci.org/CDK-R/cdkr.svg?branch=master)](https://travis-ci.org/CDK-R/cdkr)
 6[![CRAN
 7Version](https://www.r-pkg.org/badges/version/rcdk?color=green)](https://cran.r-project.org/package=rcdk)
 8[![CRAN
 9Downloads](http://cranlogs.r-pkg.org/badges/grand-total/rcdk?color=green)](https://cran.r-project.org/package=rcdk)
10[![CRAN Downloads
11Monthyl](http://cranlogs.r-pkg.org/badges/last-month/rcdk?color=green)](https://cran.r-project.org/package=rcdk)
12
13# rcdk: a chemistry library
14
15The goal of cdkr is to provide easy access to
16[CDK](https://github.com/cdk/cdk) chemoinformatics library to combine
17the simplicity and power of R with CDK’s powerful, tested API.
18
19# Installation
20
21rCDK package releases are available on CRAN or on Github via Devtools:
22
23``` r
24
25# releases
26install.packages("rcdk")
27
28# development releases of `cdkr` are also available on github uinsg devtools:
29library(devtools)
30install_github("https://github.com/CDK-R/rcdklibs")
31install_github("https://github.com/CDK-R/cdkr", subdir="rcdk")
32```
33
34## Building and Development
35
36Information on building and devloping the CDKR package is available in
37teh Otherwise if you prefer the command line
38
39``` 
40    cd /tmp/
41    git clone git@github.com:CDK-R/rcdklibs.git
42    R CMD INSTALL rcdklibs
43    git clone git@github.com:CDK-R/cdkr.git
44    cd cdkr/rcdkjar
45    ant clean jar
46    cd ../
47    R CMD INSTALL rcdk
48```
49
50Before performing the install, you should have the following
51dependencies installed:
52
53  - rJava
54  - fingerprint
55  - png
56  - RUnit
57  - Java JDK \>= 1.8
58
59For the png package, I have tested
60[png-0.1-7](http://www.rforge.net/png/files/)
61
62Some users have reported that `rcdk` methods (such as `parse.smiles`)
63are returning errors related to class not found or class version
64mismatch. This can happen when you are using a prepackaged version of
65`rJava` from [CRAN](https://cran.r-project.org/) and is caused by that
66package not finding the correct JRE home if you have multiple Java
67versions installed. In such a case, reinstalling `rJava` from sources
68appears to resolve this issue. See this
69[discussion](http://stackoverflow.com/questions/26948777/how-can-i-make-rjava-use-the-newer-version-of-java-on-osx).
70
71### Installing Java
72
73rCDK uses the CDK library that requires the Java JDK \>= 1.8. In order
74to install rCDK, this requirement must be satisfied. You can check your
75java version on the command line as follows:
76
77    > java -version
78    > java version "1.8.0"
79
80If your version is not 1.8 you may need to download and install a more
81recent installation of JAVA. If you have multiple versions of JAVA you
82may be using an older version. On Mac OSX, for example, the latest OS
83installs JAVA 1.6 and you will need to reconfigure your JAVA install.
84You can try the following:
85
86    # set the java version
87    R CMD javareconf  # or ....
88    sudo R CMD javareconf
89    
90    # re install fromfrom R
91    install.packages('rJava', type="source")
92
93Further informaiton about R’s use of Java can be [found
94here](https://cran.r-project.org/doc/manuals/r-release/R-admin.html#Java-support).