D4Science Infrastructure

I have tried to gather the offline and the online packages required for both the Statistical Manager and the WPS service.

At this link there is a set of packages to be installed offline (see instructions below), plus one test script to check if many of the packages work: http://goo.gl/tlG7QR

The required R version is 2.15.3

In the following, I report the non-R software, the packages, and the sequences of commands used to install the offline packages. The sequence is currently configured to take packages from a /root/download/ folder.

Please, correct this report should you find errors:

#Required software:
1 - 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
2 - JAGS:
http://mcmc-jags.sourceforge.net/

#Packages to install from CRAN
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

#Packages for ICES processes - Install sequence
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)

#Packages for FAO processes - Install sequence
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")

#Test
source("/root/download/interpolateTacsat.r")

Some notes:

• Almost all the R packages must be installed specifying the version and take them from the archives, because the latest versions do not install on R 2.15.3
• maptools was not installed on dataminer1-d-d4s.d4science.org that I'm using as a reference for the packages versions that were not specified here. The same is true for runjags.

This is the list of installed R packages with their versions:

           Package      Version
abind      "abind"      "1.4-3"
bayesmix   "bayesmix"   "0.7-4"
bitops     "bitops"     "1.0-6"
chron      "chron"      "2.3-47"
coda       "coda"       "0.18-1"
data.table "data.table" "1.9.6"
devtools   "devtools"   "1.4.1"
digest     "digest"     "0.6.8"
doBy       "doBy"       "4.5-3"
evaluate   "evaluate"   "0.5.5"
httr       "httr"       "0.2"
lme4       "lme4"       "1.0-5"
maptools   "maptools"   "0.8-37"
Matrix     "Matrix"     "1.1-4"
memoise    "memoise"    "0.1"
minqa      "minqa"      "1.2.3"
multcomp   "multcomp"   "1.3-3"
mvtnorm    "mvtnorm"    "1.0-3"
plyr       "plyr"       "1.8"
R2HTML     "R2HTML"     "2.2.1"
R2jags     "R2jags"     "0.03-08"
R2WinBUGS  "R2WinBUGS"  "2.1-21"
Rcpp       "Rcpp"       "0.9.10"
RcppEigen  "RcppEigen"  "0.3.2.0"
RCurl      "RCurl"      "1.95-4.3"
reshape2   "reshape2"   "1.2"
RFigisGeo  "RFigisGeo"  "0.3"
rgdal      "rgdal"      "0.9-1"
rgeos      "rgeos"      "0.3-8"
rjags      "rjags"      "3-10"
rsdmx      "rsdmx"      "0.5-1"
runjags    "runjags"    "1.2.1-0"
sandwich   "sandwich"   "2.3-0"
snow       "snow"       "0.3-13"
sp         "sp"         "1.0-15"
stringr    "stringr"    "0.6.2"
TH.data    "TH.data"    "1.0-6"
uuid       "uuid"       "0.1-2"
whisker    "whisker"    "0.3-2"
XML        "XML"        "3.98-1.3"
zoo        "zoo"        "1.7-11"
base       "base"       "2.15.3"
boot       "boot"       "1.3-3"
class      "class"      "7.3-3"
cluster    "cluster"    "1.14.1"
codetools  "codetools"  "0.2-8"
compiler   "compiler"   "2.15.3"
datasets   "datasets"   "2.15.3"
foreign    "foreign"    "0.8-48"
graphics   "graphics"   "2.15.3"
grDevices  "grDevices"  "2.15.3"
grid       "grid"       "2.15.3"
KernSmooth "KernSmooth" "2.23-7"
lattice    "lattice"    "0.20-13"
MASS       "MASS"       "7.3-16"
Matrix     "Matrix"     "1.0-2"
methods    "methods"    "2.15.3"
mgcv       "mgcv"       "1.7-12"
nlme       "nlme"       "3.1-102"
nnet       "nnet"       "7.3-1"
parallel   "parallel"   "2.15.3"
rpart      "rpart"      "3.1-50"
spatial    "spatial"    "7.3-3"
splines    "splines"    "2.15.3"
stats      "stats"      "2.15.3"
stats4     "stats4"     "2.15.3"
survival   "survival"   "2.36-10"
tcltk      "tcltk"      "2.15.3"
tools      "tools"      "2.15.3"
utils      "utils"      "2.15.3"