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module load mpi/openMPI/1.8.5-gcc4.9.0 R CMD INSTALL --configure-args="--with-Rmpi-include=/sw/openMPI/1.8.5-gcc4.9.0/include --with-Rmpi-libpath=/sw/openMPI/1.8.5-gcc4.9.0/lib/openmpi --with-Rmpi-type=OPENMPI" /tmp/Rmpi_0.6-5.tar.gz |
gpuR
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module load cuda/7.5.18
install.packages('gpuR', dependencies=TRUE, repos='http://cran.rstudio.com/') |
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install.packages("devtools")
library(devtools)
install_github("enriquea/feseR") |
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R-3.3.3 Installation
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Pre-Requisite
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Pre-Requisite ============ >>>>>>>>>>>Install xy to take care of lzma dependency >>>>>>>>>>>>>>>>>>>>>>>>>> xz-5.3.3 tar -zxvf xz-5.2.3.tar.gz ./configure --prefix=/sw/library/xz/5.3.3 make -j3 make install >>>>>>>>>>>>pcre>>>>>>>>>>>>>>> pcre-8.39 bunzip2 pcre-8.39.tar.bz2 tar -xvf pcre-8.39.tar ./configure --enable-utf8 --prefix=/sw/pcre/8.39 make -j3 make install >>>>>>>>curl>>> wget https://curl.haxx.se/download/curl-7.53.1.tar.gz ./configure --prefix=/sw/misc/curl/7.53.1 make -j3 make install >>>>>>bzip2>>>>>>>>> got error related to bizp2 “/sw/library/bzip2/1.0.6/lib/libbz2.a: could not read symbols: Bad value” >> >>>>>>bzip2 fix>>>>>>>>> cd /sw/library/bzip2/src/bzip2-1.0.6fpic vi Makefile CFLAGS=-Wall -Winline -O2 -g $(BIGFILES) -fPIC make 2>&1 | tee makeLog.txt make install PREFIX=/sw/library/bzip2/1.0.6fpic 2>&1 | tee makeInstallLog.txt >>>>>>> |
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module purge module load library/zlib/1.2.8 module load library/bzip2/1.0.6fpic module load library/xz/5.3.3 module load pcre/8.39 module load misc/curl/7.53.1 module load ATLAS/3.9.39 module load jdk/1.8.0_66 ./configure --prefix=/sw/R/3.3.3 '--with-cairo' '--with-jpeglib' '--with-readline' '--with-tcltk' '--with-blas' '--with-lapack' '--enable-R-profiling' '--enable-R-shlib' '--enable-memory-profiling' --enable-R-shlib --enable-BLAS-shlib LIBnn=lib64 JAVA_HOME=/sw/sdev/jdk/jdk1.8.0_66/jre 2>&1 | tee log.configure_R.txt make 2>&1 | tee makeLog.txt make install 2>&1 | tee makeInstallLog.txt |
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Ref: http://pj.freefaculty.org/blog/?p=315
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module purge module load library/zlib/1.2.8 module load library/bzip2/1.0.6fpic module load library/xz/5.3.3 module load pcre/8.39 module load misc/curl/7.53.1 module load ATLAS/3.9.39 module load jdk/1.8.0_66 module load gcc/4.9.3 module load misc/openssl/1.0.2 ./configure --prefix=/sw/R/3.4.0 '--with-cairo' '--with-jpeglib' '--with-readline' '--with-tcltk' '--with-blas' '--with-lapack' '--enable-R-profiling' '--enable-R-shlib' '--enable-memory-profiling' --enable-R-shlib --enable-BLAS-shlib LIBnn=lib64 JAVA_HOME=/sw/sdev/jdk/jdk1.8.0_66/jre LDFLAGS=" -L/sw/pcre/8.39/lib" CPPFLAGS="-I/sw/pcre/8.39/include" 2>&1 | tee log.configure_R.txt make 2>&1 | tee makeLog.txt make install 2>&1 | tee makeInstallLog.txt |
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Useful Commands to install additional packages in R
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install.packages("foobarbaz")
ap <- available.packages()
setRepositories()
install.packages("phyloseq")
library(devtools)
install_github("packageauthor/foobarbaz")
install_bitbucket("packageauthor/foobarbaz")
install_gitorious("packageauthor/foobarbaz")
install.packages("Rbbg", repos = "http://r.findata.org")
install.packages("lubridate", dependencies=TRUE, repos='http://cran.rstudio.com/')
source("https://bioconductor.org/biocLite.R")
biocLite("preprocessCore")
install_url("http://cran.r-project.org/src/contrib/Archive/sentiment/sentiment_0.2.tar.gz")
R CMD INSTALL /tmp/RcppParallel_4.3.20.tar.gz
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Sample PBS jobs
Serial jobs
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#! /bin/bash
# #PBS -m e
#PBS -N BigMemRjob
#PBS -l walltime=40:00:00
#PBS -q BigMemory
###Request 1.3TB of memory
#PBS -l nodes=1:ppn=24,mem=1331200mb,vmem=1331200mb
#PBS -A qris-gu
source $HOME/.bashrc
module load R/3.2.3
cd /home/userNameonFlashLite/pbs
export ROutfile=ROutfile001.txt
## RUN ##
echo "=== start R-3.2.3 ==="
Rscript --no-save myRscript.R &> $ROutfile
echo "Completed\n"
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List all R packages
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length(.packages(all.available=TRUE))
ip <- as.data.frame(installed.packages()[, c(1, 3:4)])
rownames(ip) <- NULL
ip <- ip[is.na(ip$Priority), 1:2, drop=FALSE]
print(ip, row.names=FALSE)
For example:
> length(.packages(all.available=TRUE))
[1] 200
> ip <- as.data.frame(installed.packages()[, c(1, 3:4)])
> rownames(ip) <- NULL
> ip <- ip[is.na(ip$Priority), 1:2, drop=FALSE]
> print(ip, row.names=FALSE)
Package Version
abind 1.4-5
acepack 1.4.1
anchors 3.0-8
askpass 1.1
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Reference
1. http://yusung.blogspot.com.au/2009/01/install-jags-and-rjags-in-fedora.html
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