D4Science Infrastructure

R 3.2.3 is crucial to let IRD personnel work and test their processes. Furthermore, the 'withr' package requires a recent version of R.
@andrea.dellamico@isti.cnr.it built an R 3.2.3 installation suite that reproduces a very functional environment, which can be installed on the online-RStudio machine (rstudio.d4science.org).
In the following, I report the packages/software which should be part of this RStudio environment by default. It's to be checked if they are already included in the installation suite.

GDAL:
 wget http://download.osgeo.org/gdal/1.11.0/gdal1110.zip
 unzip gdal1110.zip -d gdal1110
 ./configure --with-gdal-config=/usr/local/bin/gdal-config
JAGS:
 http://mcmc-jags.sourceforge.net/

 R Packages:
 data.table
 doBy
 multcomp
 mvtnorm
 survival
 splines
 TH.data
 MASS
 Matrix
 lattice
 abind 
 bayesmix 
 coda 
 R2jags 
 R2WinBUGS 
 rjags 
 runjags 
 abind 
 coda 
 maptools 
 rjags 
 sp 
 base 
 boot 
 class 
 cluster 
 codetools 
 compiler 
 datasets
 foreign 
 graphics
 grDevices
 grid 
 KernSmooth 
 lattice 
 MASS 
 Matrix 
 methods 
 mgcv 
 nlme 
 nnet 
 parallel 
 rpart 
 spatial
 splines
 stats
 stats4 
 survival
 tcltk 
 tools 
 utils
 withr

##ICES processes##
 install.packages("/root/download/Rcpp_0.9.10.tar.gz", repos = NULL, type="source")
 install.packages("/root/download/plyr_1.8.tar.gz", repos = NULL, type="source")
 install.packages("stringr")
 install.packages("/root/download/reshape2_1.2.tar.gz", repos = NULL, type="source")
 install.packages("/root/download/data.table_1.9.2.tar.gz", repos = NULL, type="source")
 install.packages("R2HTML")
 install.packages("multcomp")
 install.packages("Matrix")
 install.packages("lattice")
 install.packages("snow")
 install.packages("/root/download/RcppEigen_0.3.2.0.tar.gz", repos = NULL, type="source")
 install.packages("minqa")
 install.packages("/root/download/lme4_1.0-5.tar.gz", repos = NULL, type="source")
 install.packages("/root/download/doBy_4.5-3.tar.gz", repos = NULL, type="source")
 install.packages("mvtnorm")
 install.packages("survival")
 install.packages("data.table")
 help(package=splines)
 help(package=TH.data)
 help(package=MASS)

##FAO processes##
 install.packages("RCurl")
 install.packages("digest")
 install.packages("/root/download/httr_0.2.tar.gz", repos = NULL, type="source")
 install.packages("memoise")
 install.packages("whisker")
 install.packages("evaluate")
 install.packages("/root/download/devtools_1.4.1.tar.gz", repos = NULL, type="source")
 require(devtools)
 install_github("rsdmx", "opensdmx")
 apt-get update
 apt-get install libgdal1-dev
 apt-get install libgeos-dev
 apt-get install libspatialite-dev
 install.packages("rgdal")
 install.packages("rgeos")
 require(devtools)
 install_github("RFigisGeo", "openfigis")

##Knitr##
install.packages('knitr', repos = c('http://yihui.name/xran', 'http://cran.rstudio.org'))
devtools::install_github('HenrikBengtsson/R.methodsS3')
devtools::install_github('HenrikBengtsson/R.oo')
devtools::install_github('eddelbuettel/digest')
devtools::install_github('HenrikBengtsson/R.utils')
devtools::install_github('HenrikBengtsson/R.cache')
devtools::install_github('christophergandrud/repmis')
->Install utf8x latex packages
install.packages("rworldmap", repos="http://R-Forge.R-project.org")
wget https://cran.r-project.org/src/contrib/spam_1.3-0.tar.gz
install.packages('./spam_1.3-0.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/maps_3.0.1.tar.gz
install.packages('./maps_3.0.1.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/fields_8.3-5.tar.gz
install.packages('./fields_8.3-5.tar.gz', repos = NULL, type="source")
wget http://download.r-forge.r-project.org/src/contrib/rworldmap_1.3-4.tar.gz
install.packages('./rworldmap_1.3-4.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/highlight_0.4.7.tar.gz
install.packages('./highlight_0.4.7.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/Rcpp_0.12.2.tar.gz
install.packages('./Rcpp_0.12.2.tar.gz', repos = NULL, type="source")
devtools::install_github('hadley/pryr')
devtools::install_github('cran/RColorBrewer')
wget http://cran.jellyfish.lol/src/contrib/dichromat_2.0-0.tar.gz
install.packages('./dichromat_2.0-0.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/colorspace_1.2-6.tar.gz
install.packages('./colorspace_1.2-6.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/munsell_0.4.2.tar.gz
install.packages('./munsell_0.4.2.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/labeling_0.3.tar.gz
install.packages('./labeling_0.3.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/scales_0.3.0.tar.gz
install.packages('./scales_0.3.0.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/gtable_0.1.2.tar.gz
install.packages('./gtable_0.1.2.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/ggplot2_2.0.0.tar.gz
install.packages('./ggplot2_2.0.0.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/jsonlite_0.9.19.tar.gz
install.packages('./jsonlite_0.9.19.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/magrittr_1.5.tar.gz
install.packages('./magrittr_1.5.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/gridExtra_2.0.0.tar.gz
install.packages('./gridExtra_2.0.0.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/viridis_0.3.1.tar.gz
install.packages('./viridis_0.3.1.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/base64enc_0.1-3.tar.gz
install.packages('./base64enc_0.1-3.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/htmltools_0.2.6.tar.gz
install.packages('./htmltools_0.2.6.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/htmlwidgets_0.5.tar.gz
install.packages('./htmlwidgets_0.5.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/plotly_2.0.16.tar.gz
install.packages('./plotly_2.0.16.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/mapdata_2.2-5.tar.gz
install.packages('./mapdata_2.2-5.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/mapplots_1.5.tar.gz
install.packages('./mapplots_1.5.tar.gz', repos = NULL, type="source")
->install the netcdf-bin linux package
wget https://cran.r-project.org/src/contrib/ncdf_1.6.9.tar.gz
install.packages('./ncdf_1.6.9.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/mnormt_1.5-3.tar.gz
install.packages('./mnormt_1.5-3.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/numDeriv_2014.2-1.tar.gz
install.packages('./numDeriv_2014.2-1.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/sn_1.3-0.tar.gz
install.packages('./sn_1.3-0.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/mclust_5.1.tar.gz
install.packages('./mclust_5.1.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/tclust_1.2-3.tar.gz
install.packages('./tclust_1.2-3.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/modeltools_0.2-21.tar.gz
install.packages('./modeltools_0.2-21.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/flexmix_2.3-13.tar.gz
install.packages('./flexmix_2.3-13.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/prabclus_2.2-6.tar.gz
install.packages('./prabclus_2.2-6.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/diptest_0.75-7.tar.gz
install.packages('./diptest_0.75-7.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/DEoptimR_1.0-4.tar.gz
install.packages('./DEoptimR_1.0-4.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/robustbase_0.92-5.tar.gz
install.packages('./robustbase_0.92-5.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/kernlab_0.9-22.tar.gz
install.packages('./kernlab_0.9-22.tar.gz', repos = NULL, type="source")
wget http://cran.jellyfish.lol/src/contrib/trimcluster_0.1-2.tar.gz
install.packages('./trimcluster_0.1-2.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/fpc_2.1-10.tar.gz
install.packages('./fpc_2.1-10.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/RJSONIO_1.3-0.tar.gz
install.packages('./RJSONIO_1.3-0.tar.gz', repos = NULL, type="source")
require(devtools)
install_github('rCharts', 'ramnathv')
wget https://cran.r-project.org/src/contrib/cowplot_0.6.0.tar.gz
install.packages('./cowplot_0.6.0.tar.gz', repos = NULL, type="source")
require(devtools)
install_github("IRDTunaAtlas", "juldebar")
wget https://cran.r-project.org/src/contrib/DBI_0.3.1.tar.gz
install.packages('./DBI_0.3.1.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/RPostgreSQL_0.4.tar.gz
install.packages('./RPostgreSQL_0.4.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/maptools_0.8-37.tar.gz
install.packages('./maptools_0.8-37.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/sp_1.2-1.tar.gz
install.packages('./sp_1.2-1.tar.gz', repos = NULL, type="source")
install.packages("raster", repos="http://R-Forge.R-project.org")

I can start working on it tomorrow morning, is it OK?

rstudio.d4science.org now runs R version 3.2.3. All the packages listed by Gianpaolo have been installed.