Monthly Archives: November 2012

Script for RStudio CentOS Linux install dependencies yum

 

Script for RStudio CentOS Linux install dependencies yum

This is supposed to work:

http://support.rstudio.org/help/discussions/problems/3353-installing-r-studio-server-on-redhat-446-4#comment_18902730
yum install r-studio-server.rpm

https://github.com/rstudio/rstudio/blob/master/dependencies/linux/install-dependencies-yum

 

#!/bin/bash
#
# install-dependencies-yum
#
# Copyright (C) 2009-12 by RStudio, Inc.
#
# This program is licensed to you under the terms of version 3 of the
# GNU Affero General Public License. This program is distributed WITHOUT
# ANY EXPRESS OR IMPLIED WARRANTY, INCLUDING THOSE OF NON-INFRINGEMENT,
# MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. Please refer to the
# AGPL (http://www.gnu.org/licenses/agpl-3.0.txt) for more details.
#
#
set -e
# build/development tools
sudo yum install -y make
sudo yum install -y gcc
sudo yum install -y gcc-c++
sudo yum install -y cmake
sudo yum install -y rpmdevtools
# core system libraries
sudo yum install -y libuuid-devel
sudo yum install -y openssl-devel
sudo yum install -y bzip2-devel
sudo yum install -y zlib-devel
sudo yum install -y pam-devel
# boost
sudo yum install -y boost-devel
# pango cairo
sudo yum install -y pango-devel
# gwt prereqs
sudo yum install -y java-1.6.0-openjdk
sudo yum install -y ant
sudo yum install -y xml-commons-apis
# common
cd ../common
./install-gwt
./install-dictionaries
./install-mathjax
cd ../linux
# boost
./install-boost
# desktop dependencies (qt)
if [ “$1” != “–exclude-qt-sdk” ]
then
   # install Qt 4.8 SDK (into a private /opt/RStudio-QtSDK directory so as to
   # not conflict with any other installed versions of Qt on the system)
   ./install-qt-sdk
fi

How to install R Base with latest update and Rstudio onto Debian Linux #rstats #linux

How to install R Base with latest update and Rstudio onto Debian Linux

apt-get install r-base

http://rwiki.sciviews.org/doku.php?id=getting-started:installation:debian#install_r

Then from http://tata-box-blog.blogspot.ca/2012/03/install-r-2142-in-debian-squeeze.html

First, open a Terminal and open the sources.list file: $ gksudo gedit /etc/apt/sources.list

Then, add these lines at the bottom of the file (Note, I use the UCLA server, but this can be easily changed taking a look here for the mirrors):

## R BACKPORTS deb http://cran.stat.ucla.edu/bin/linux/debian squeeze-cran/ #deb-src http://cran.stat.ucla.edu/bin/linux/debian squeeze-cran/ To install Rstudio download Rstudio deb file from http://www.rstudio.com/ide/download/desktop Install with deb http://linux.about.com/od/ubuntu_doc/a/ubudg21t2.htm

To install Rstudio

 

download Rstudio deb file from
http://www.rstudio.com/ide/download/desktop

Install with deb
http://linux.about.com/od/ubuntu_doc/a/ubudg21t2.htm

Damn, I really want to get RCPP and RInside working on my Netbeans for WIndows with Cygwin but..

Damn, I really want to get RCPP and RInside  working on my Netbeans for WIndows with Cygwin but..

I get these errors in my build attempt within Nebeans:

## -*- mode: makefile; tab-width: 8; -*-
##
## Simple Makefile for Windows

## This version is fairly directly derived from the Unix versions
## You may have to set R_HOME manually if this does not work
## It requires Rtools in the path — as does all R package building
#R_HOME := $(shell R RHOME | sed -e “s|\\|/|g”)
R_HOME := “/cygdrive/c/PROGRA~1/R/R-214~1.1”

## You may have to set this to one of the two values below to enforce a particular
## architecture in case the autodetection in the next line does not work correctly
R_ARCH := –arch $(shell echo ‘cat(.Platform$$r_arch)’ | R –vanilla –slave)
##R_ARCH := –arch i386
##R_ARCH := –arch x64

## You may need to set R_LIBS_USER if Rcpp or RInside are installed where R does not see them by default
#R_LIBS_USER := “C:/myRstuff/library”

sources := $(wildcard *.cpp)
programs := $(sources:.cpp=)

## include headers and libraries for R
RCPPFLAGS := $(shell $(R_HOME)/bin/R $(R_ARCH) CMD config –cppflags)
RLDFLAGS := $(shell $(R_HOME)/bin/R $(R_ARCH) CMD config –ldflags)
RBLAS := $(shell $(R_HOME)/bin/R $(R_ARCH) CMD config BLAS_LIBS)
RLAPACK := $(shell $(R_HOME)/bin/R $(R_ARCH) CMD config LAPACK_LIBS)
## include headers and libraries for Rcpp interface classes
RCPPINCL := $(shell echo ‘Rcpp:::CxxFlags()’ | $(R_HOME)/bin/R $(R_ARCH) –vanilla –slave)
RCPPLIBS := $(shell echo ‘Rcpp:::LdFlags()’ | $(R_HOME)/bin/R $(R_ARCH) –vanilla –slave)
## include headers and libraries for RInside embedding classes
RINSIDEINCL := $(shell echo ‘RInside:::CxxFlags()’ | $(R_HOME)/bin/R $(R_ARCH) –vanilla –slave)
RINSIDELIBS := $(shell echo ‘RInside:::LdFlags()’ | $(R_HOME)/bin/R $(R_ARCH) –vanilla –slave)
## compiler etc settings used in default make rules
CXX := $(shell $(R_HOME)/bin/R $(R_ARCH) CMD config CXX)
CPPFLAGS := -Wall $(shell $(R_HOME)/bin/R $(R_ARCH) CMD config CPPFLAGS)
CXXFLAGS := $(RCPPFLAGS) $(RCPPINCL) $(RINSIDEINCL) $(shell $(R_HOME)/bin/R $(R_ARCH) CMD config CXXFLAGS)
LDFLAGS = -s
LDLIBS := $(RLDFLAGS) $(RBLAS) $(RLAPACK) $(RINSIDELIBS) $(RCPPLIBS)
CC := $(shell $(R_HOME)/bin/R $(R_ARCH) CMD config CXX)

Error and warning  messages are:

(Note the strange MinGW path but I am not using that)

cygwin warning:
MS-DOS style path detected: C:PROGRA~1RR-214~1.1/bin/config.sh
Preferred POSIX equivalent is: /cygdrive/c/PROGRA~1/R/R-214~1.1/bin/config.sh
CYGWIN environment variable option “nodosfilewarning” turns off this warning.
Consult the user’s guide for more details about POSIX paths:
http://cygwin.com/cygwin-ug-net/using.html#using-pathnames
rm -vf rinside_sample8 rinside_sample12 rinside_test1 rinside_sample2 rinside_sample5 rinside_sample3 rinside_sample11 rinside_sample9 rinside_callbacks0 rinside_sample6 rinside_sample1 rinside_sample4 rinside_module_sample0 rinside_sample0 rinside_test0 rinside_sample10 rinside_sample7
CLEAN SUCCESSFUL (total time: 4s)

cygwin warning:
MS-DOS style path detected: C:PROGRA~1RR-214~1.1/bin/config.sh
Preferred POSIX equivalent is: /cygdrive/c/PROGRA~1/R/R-214~1.1/bin/config.sh
CYGWIN environment variable option “nodosfilewarning” turns off this warning.
Consult the user’s guide for more details about POSIX paths:
http://cygwin.com/cygwin-ug-net/using.html#using-pathnames
x86_64-w64-mingw32-g++ -IC:/PROGRA~1/R/R-214~1.1/include -IC:/PROGRA~1/R/R-214~1.1/include/x64 -IC:/Program Files/R/R-2.14.1/library/Rcpp/include -IC:/Program Files/R/R-2.14.1/library/RInside/include -O2 -Wall -mtune=core2 -Wall -s rinside_sample8.cpp -LC:/PROGRA~1/R/R-214~1.1/bin/x64 -lR -LC:/PROGRA~1/R/R-214~1.1/bin/x64 -lRblas -LC:/PROGRA~1/R/R-214~1.1/bin/x64 -lRlapack “C:/Program Files/R/R-2.14.1/library/RInside/lib/x64/libRInside.a” C:/Program Files/R/R-2.14.1/library/Rcpp/lib/x64/libRcpp.a -o rinside_sample8
/bin/sh: x86_64-w64-mingw32-g++: command not found
make: *** [rinside_sample8] Error 127
<builtin>: recipe for target `rinside_sample8′ failed
BUILD FAILED (exit value 2, total time: 4s)
all : $(programs)

clean:
rm -vf $(programs)

checkR:
echo “R is at $(R_HOME)”

 

Another complete list to push R for High-Performance Computing aka HPC and Parallel Computing: Includes grid, GPU

Another complete list to push R for High-Performance Computing aka HPC and Parallel Computing: Includes grid, GPU

Here is more to add to your list

http://cran.open-source-solution.org/web/views/HighPerformanceComputing.html