Compiling R 2.15.2 and SPRINT on HECToR Phase 3
Install R
Default compilation with gcc tool chain is trivial. First change compiler module to gcc by executing:
module swap PrgEnv-cray PrgEnv-gnu
Then run configure script with --prefix pointing to the package directory; use the system BLAS and LAPACK (--with-blas, --with-lapack); and remove the compilation of X-tools (--without-x).
export R_WORK_HOME=/usr/local/packages/rpackage/2.15.2-phase3/R-2.15.2 cd $R_WORK_HOME ./configure --prefix=$R_WORK_HOME --with-blas --with-lapack --without-x
Build the package.
make make check make install
Install SPRINT
Now install packages needed for SPRINT installation. Start R:
$R_WORK_HOME/bin/R --no-save
Install the packages that SPRINT depends on:
install.packages("rlecuyer")
install.packages("boot")
install.packages("e1071")
source("http://bioconductor.org/biocLite.R")
biocLite("ShortRead")
q()
Remove the old version of SPRINT (if you need to):
remove.packages("sprint")
Download the latest version of SPRINT (must be newer than 1.0.4). The SPRINT Makefile (sprint/src/Makefile) must have the following lines in it:
LONG_OS := $(shell uname -a)
ifeq (cray,$(findstring cray,$(LONG_OS)))
cc -shared -o $@ $^
else
Install SPRINT using the no test load command because mpi isn't installed on the front end.
R CMD INSTALL --no-test-load /usr/local/packages/rpackage/2.15.2-phase3/sprint
