Other than the R software itself, most Linux distributions (e.g. Ubuntu, CentOS, Debian, Slackware among other) include the developer tools required to compile R library packages. The instructions below should work for the majority of Linux distributions.
We will use shell commands within a Linux terminal to edit, recompile, and install the package. First, change directories to that which contains the BiasedUrn package source code. Here, we assume this directory is called Downloads and is found under our home directory (i.e. ~/Downloads/).
jdoe@somewhere ~ $ cd ~/Downloads
Next, use the tar command to extract the BiasedUrn source code.
jdoe@somewhere ~/Downloads $ tar -zxf BiasedUrn_1.04.tar.gz
The default contents of the Makevars file within the package src directory is displayed here:
jdoe@somewhere ~/Downloads $ cat BiasedUrn/src/Makevars # Makevars for BiasedUrn # The value of MAXCOLORS may be modified PKG_CPPFLAGS= -DR_BUILD=1 -DMAXCOLORS=32
Using any text editor, change the value of MAXCOLORS from 32 to 10000. After performing this edit and saving the changes, the file should look like this:
jdoe@somewhere ~/Downloads $ cat BiasedUrn/src/Makevars # Makevars for BiasedUrn # The value of MAXCOLORS may be modified PKG_CPPFLAGS= -DR_BUILD=1 -DMAXCOLORS=10000
Before building the package, one should execute the R check script to resolve any problems that may arise from compiling the package, e.g., missing developer tools. The command line execution of this step along with example output is shown here:
jdoe@somewhere ~/Downloads $ R CMD check BiasedUrn * using log directory '/home/jdoe/Downloads/BiasedUrn.Rcheck' * using R version 2.15.0 (2012-03-30) * using platform: i686-pc-linux-gnu (32-bit) * using session charset: ASCII * checking for file 'BiasedUrn/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'BiasedUrn' version '1.04' * checking package namespace information ... OK ... * checking re-building of vignette PDFs ... OK * checking PDF version of manual ... OK
The full output generated from the check command can be found in the log file BiasedUrn.Rcheck/00check.log.
Next we use the build command to compile the modified package and create an installable package file. This step will overwrite the original source file BiasedUrn_1.04.tar.gz with the installable modified package file.
jdoe@somewhere ~/Downloads $ R CMD build BiasedUrn * checking for file 'BiasedUrn/DESCRIPTION' ... OK * preparing 'BiasedUrn': * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to re-build vignettes * creating vignettes ... OK * cleaning src * checking for LF line-endings in source and make files * checking for empty or unneeded directories * building 'BiasedUrn_1.04.tar.gz'
The final step is to install this modified package. If you have root privileges, a global install can be performed; otherwise, installation to a local directory tree can be performed. Next we describe these two cases.
If you have root or sudo privileges and wish to make the new package available system-wide, then perform this action as superuser. Here we demonstrate this using the sudo command. Similarly, one could also perform this action from a root shell.
jdoe@somewhere ~/Downloads $ sudo R CMD INSTALL BiasedUrn_1.04.tar.gz Password: * installing to library '/usr/local/lib/R/library' * installing *source* package 'BiasedUrn' ... ** libs g++ -I/usr/local/lib/R/include -DNDEBUG -DR_BUILD=1 -DMAXCOLORS=10000 -I/usr/local/include -fpic -g -O2 -c fnchyppr.cpp -o fnchyppr.o g++ -I/usr/local/lib/R/include -DNDEBUG -DR_BUILD=1 -DMAXCOLORS=10000 -I/usr/local/include -fpic -g -O2 -c stoc1.cpp -o stoc1.o g++ -I/usr/local/lib/R/include -DNDEBUG -DR_BUILD=1 -DMAXCOLORS=10000 -I/usr/local/include -fpic -g -O2 -c stoc3.cpp -o stoc3.o g++ -I/usr/local/lib/R/include -DNDEBUG -DR_BUILD=1 -DMAXCOLORS=10000 -I/usr/local/include -fpic -g -O2 -c stocR.cpp -o stocR.o g++ -I/usr/local/lib/R/include -DNDEBUG -DR_BUILD=1 -DMAXCOLORS=10000 -I/usr/local/include -fpic -g -O2 -c urn1.cpp -o urn1.o g++ -I/usr/local/lib/R/include -DNDEBUG -DR_BUILD=1 -DMAXCOLORS=10000 -I/usr/local/include -fpic -g -O2 -c urn2.cpp -o urn2.o g++ -I/usr/local/lib/R/include -DNDEBUG -DR_BUILD=1 -DMAXCOLORS=10000 -I/usr/local/include -fpic -g -O2 -c wnchyppr.cpp -o wnchyppr.o g++ -shared -L/usr/local/lib -o BiasedUrn.so fnchyppr.o stoc1.o stoc3.o stocR.o urn1.o urn2.o wnchyppr.o installing to /usr/local/lib/R/library/BiasedUrn/libs ** R ** demo ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes 'UrnTheory.Rtex' ** testing if installed package can be loaded * DONE (BiasedUrn)
In the event one does not have root privileges, a local version of the package can be installed and used from the user account. Ensure that you have a directory set for local package installations; here we have created the directory ~/R/library/ for this purpose. In the output from this command you should see a line indicating installation to this local directory:
jdoe@somewhere ~/Downloads $ R CMD INSTALL BiasedUrn_1.04.tar.gz --library=~/R/library/ ... * installing *source* package 'BiasedUrn' ... ... installing to /home/jdoe/R/library/BiasedUrn/libs ...
The package should now be ready to use.
Epstein software | Human Genetics | School of Medicine | Emory University