I have modified the configure file to work on summit.
- Its 'grep/sed' command for determining the version of the boost library was failing because of a leading space present in the version.h file.
As of Thu Jan 25 11:08:56 MST 2018
ml is a shortcut for module load.
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ml intel
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ml impi
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ml boost
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ml R
A local install path must be set inside R. For us, your project space is encouraged, and I recommend creating an R directory:
mkdir /projects/username@colostate.edu/R
$ R
.libPaths('/projects/username@colostate.edu/R)
The original repository uses devtools, but that may be insufficient to install dependencies on Summit. To try it, update the url in that command.
require(devtools)
devtools::install_github('meekrob/spp', build_vignettes = FALSE)
Preferably, download this package using git clone and the url of this repository, it should create a directory called spp. In the same directory, start R, and do
.libPaths('/projects/username@colostate.edu/R') # Set your local install path
install.packages("spp", repos=NULL) # Should install dependancies
This will also compile SPP, and may take a while.
In R:
.libPaths('/projects/username@colostate.edu/R') # Set your local install path
require(spp)
If the require succeeds without reporting errors, the installation worked.
An R package for anlaysis of ChIP-seq and other functional sequencing data. Please see package homepage for details.
A unix-flavored OS with R and Boost C++ installed.
You can use modtools to install SPP:
require(devtools)
devtools::install_github('hms-dbmi/spp', build_vignettes = FALSE)
Alternatively, download a .tar.gz containing the latest release and use the standard R installation command, e.g.:
R CMD INSTALL spp_1.13.tar.gz
Note: if Boost libraries are installed in a non-standard location, please specify the location in a BOOST_ROOT environment variable prior to running the installation.
export BOOST_ROOT=/path/boost_1_58_0/