Difference between revisions of "R"
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You may want to install R locally in your home directory. This puts you in control of the version installed, the packages installed and you can tweak the installation according to your needs. Consequently, before you can use R, you have to do the following: | You may want to install R locally in your home directory. This puts you in control of the version installed, the packages installed and you can tweak the installation according to your needs. Consequently, before you can use R, you have to do the following: | ||
| − | * | + | * Install R and the relevant packages |
* Write the code to be executed on the cluster | * Write the code to be executed on the cluster | ||
* Write the submit script to be submitted via qsub | * Write the submit script to be submitted via qsub | ||
| Line 9: | Line 9: | ||
== System-wide install == | == System-wide install == | ||
| − | The system-wide install of R has been compiled and installed with the commands given below. If this is sufficient for your purposes, you don't have to install your own version in your home directory. Available in '''/apps/R | + | The system-wide install of R has been compiled and installed with the commands given below. If this is sufficient for your purposes, you don't have to install your own version in your home directory. Available in '''/apps/R/3.0.2'''. Feel free to ask for extra modules to be loaded. |
<pre> | <pre> | ||
| − | $ ./configure --prefix=/apps/R | + | $ ./configure --prefix=/apps/R/3.0.2 --enable-R-shlib --with-system-zlib --with-system-bzlib --with-system-pcre --with-x=no |
$ make | $ make | ||
$ make check | $ make check | ||
| Line 21: | Line 21: | ||
<pre> | <pre> | ||
| − | /apps/R | + | $ module load openmpi-x86_64 |
| − | + | $ /apps/R/3.0.2/bin/R CMD INSTALL \ | |
| − | + | -l /apps/R/3.0.2/lib64/R/library/ \ | |
| − | + | --configure-args="--with-mpi=$MPI_HOME --with-Rmpi-libpath=$MPI_LIB --with-Rmpi-include=$MPI_INCLUDE --with-Rmpi-type=OPENMPI" \ | |
| − | + | Rmpi_0.6-3.tar.gz | |
| − | + | </pre> | |
| − | + | ||
| − | / | + | === biomod2 3.1-25 === |
| + | |||
| + | <pre> | ||
| + | $ for i in abind_1.4-0.tar.gz mda_0.4-4.tar.gz plyr_1.8.tar.gz pROC_1.5.4.tar.gz randomForest_4.6-7.tar.gz \ | ||
| + | RColorBrewer_1.0-5.tar.gz latticeExtra_0.6-26.tar.gz gbm_2.1.tar.gz hexbin_1.26.3.tar.gz sp_1.0-14.tar.gz \ | ||
| + | raster_2.1-66.tar.gz zoo_1.7-10.tar.gz rasterVis_0.24.tar.gz biomod2_3.1-25.tar.gz; do | ||
| + | /apps/R/3.0.2/bin/R CMD INSTALL -l /apps/R/3.0.2/lib64/R/library/ $i; | ||
| + | done | ||
| + | </pre> | ||
| + | |||
| + | === plyr 1.8.1 === | ||
| + | |||
| + | <pre> | ||
| + | $ for i in Rcpp_0.11.1.tar.gz plyr_1.8.1.tar.gz; do | ||
| + | /apps/R/3.0.2/bin/R CMD INSTALL -l /apps/R/3.0.2/lib64/R/library/ $i; | ||
| + | done | ||
| + | </pre> | ||
| + | |||
| + | === foreign 0.8-61 === | ||
| + | |||
| + | <pre> | ||
| + | $ /apps/R/3.0.2/bin/R CMD INSTALL -l /apps/R/3.0.2/lib64/R/library/ foreign_0.8-61.tar.gz | ||
</pre> | </pre> | ||
Latest revision as of 11:02, 1 April 2014
Contents
Personalised install
You may want to install R locally in your home directory. This puts you in control of the version installed, the packages installed and you can tweak the installation according to your needs. Consequently, before you can use R, you have to do the following:
- Install R and the relevant packages
- Write the code to be executed on the cluster
- Write the submit script to be submitted via qsub
System-wide install
The system-wide install of R has been compiled and installed with the commands given below. If this is sufficient for your purposes, you don't have to install your own version in your home directory. Available in /apps/R/3.0.2. Feel free to ask for extra modules to be loaded.
$ ./configure --prefix=/apps/R/3.0.2 --enable-R-shlib --with-system-zlib --with-system-bzlib --with-system-pcre --with-x=no $ make $ make check $ make install
Rmpi 0.6-3
$ module load openmpi-x86_64
$ /apps/R/3.0.2/bin/R CMD INSTALL \
-l /apps/R/3.0.2/lib64/R/library/ \
--configure-args="--with-mpi=$MPI_HOME --with-Rmpi-libpath=$MPI_LIB --with-Rmpi-include=$MPI_INCLUDE --with-Rmpi-type=OPENMPI" \
Rmpi_0.6-3.tar.gz
biomod2 3.1-25
$ for i in abind_1.4-0.tar.gz mda_0.4-4.tar.gz plyr_1.8.tar.gz pROC_1.5.4.tar.gz randomForest_4.6-7.tar.gz \
RColorBrewer_1.0-5.tar.gz latticeExtra_0.6-26.tar.gz gbm_2.1.tar.gz hexbin_1.26.3.tar.gz sp_1.0-14.tar.gz \
raster_2.1-66.tar.gz zoo_1.7-10.tar.gz rasterVis_0.24.tar.gz biomod2_3.1-25.tar.gz; do
/apps/R/3.0.2/bin/R CMD INSTALL -l /apps/R/3.0.2/lib64/R/library/ $i;
done
plyr 1.8.1
$ for i in Rcpp_0.11.1.tar.gz plyr_1.8.1.tar.gz; do
/apps/R/3.0.2/bin/R CMD INSTALL -l /apps/R/3.0.2/lib64/R/library/ $i;
done
foreign 0.8-61
$ /apps/R/3.0.2/bin/R CMD INSTALL -l /apps/R/3.0.2/lib64/R/library/ foreign_0.8-61.tar.gz
