Task #138: Automate the installation of the R suite and its packages - D4Science Infrastructure - D4science

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Task #138

closed

Task #131: Report the R Interpreter environment to reproduce on the Generic Worker nodes

Automate the installation of the R suite and its packages

Added by Andrea Dell'Amico about 10 years ago. Updated about 10 years ago.

Status:

Closed

Priority:

High

Assignee:

Andrea Dell'Amico

Category:

System Application

Target version:

System Configuration

Start date:

May 22, 2015

Due date:

% Done:

100%

Estimated time:

Infrastructure:

Production

Description

Create an ansible playbook that installs R and the listed packages on Ubuntu precise

Related issues

Related to D4Science Infrastructure - Task #140: 36 new smartgears VMs are needed

Closed

Andrea Dell'Amico

May 23, 2015

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Updated by Andrea Dell'Amico about 10 years ago

The result is the following:

Package Version
abind "abind" "1.4-3"
bayesmix "bayesmix" "0.7-3"
coda "coda" "0.17-1"
R2jags "R2jags" "0.5-6"
R2WinBUGS "R2WinBUGS" "2.1-19"
rjags "rjags" "3-15"
runjags "runjags" "2.0.1-4"
abind "abind" "1.4-0"
coda "coda" "0.14-5"
maptools "maptools" "0.7-38"
rjags "rjags" "3-3"
sp "sp" "0.9-81"
base "base" "2.14.1"
boot "boot" "1.3-3"
class "class" "7.3-3"
cluster "cluster" "1.14.1"
codetools "codetools" "0.2-8"
compiler "compiler" "2.14.1"
datasets "datasets" "2.14.1"
foreign "foreign" "0.8-48"
graphics "graphics" "2.14.1"
grDevices "grDevices" "2.14.1"
grid "grid" "2.14.1"
KernSmooth "KernSmooth" "2.23-7"
lattice "lattice" "0.20-0"
MASS "MASS" "7.3-16"
Matrix "Matrix" "1.0-2"
methods "methods" "2.14.1"
mgcv "mgcv" "1.7-12"
nlme "nlme" "3.1-102"
nnet "nnet" "7.3-1"
parallel "parallel" "2.14.1"
rpart "rpart" "3.1-50"
spatial "spatial" "7.3-3"
splines "splines" "2.14.1"
stats "stats" "2.14.1"
stats4 "stats4" "2.14.1"
survival "survival" "2.36-10"
tcltk "tcltk" "2.14.1"
tools "tools" "2.14.1"
utils "utils" "2.14.1"

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Updated by Andrea Dell'Amico about 10 years ago

Status changed from New to In Progress
% Done changed from 0 to 90

There's now a library playbook called 'R' that installs the base R packages and even additional packages.
The additional packages can be installed in two ways:

From the linux distribution repository
From the CRAN repository as binary files.

The default packages are the ones listed by Gianpaolo.

The ones installed as debian packages are:
r-cran-rjags,r-cran-abind,r-cran-boot,r-cran-class,r-cran-cluster,r-cran-coda,r-cran-codetools,r-cran-foreign,r-cran-lattice,r-cran-maptools,r-cran-mass,r-cran-matrix,r-cran-mgcv,r-cran-nlme,r-cran-nnet,r-cran-rpart,r-cran-sp,r-cran-spatial,r-cran-survival

The ones installed directly from CRAN are: R2WinBUGS, R2jags, bayesmix, runjags

All the other packages in the Gianpaolo's list are part of the base R distribution.

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