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wiki:installpkage [2017/12/05 22:53] (current)
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 +====== Installing a new package ======
 +
 +Start R as superuser to have rights to install new packages:
 +
 +  sudo R 
 +
 +To verify which packages you have installed and where the library directories are type:
 +  library()
 +
 +You will see the list of your available library as follows:
 +
 +  class                   ​Functions for Classification
 +  colorspace ​             Color Space Manipulation
 +  gdata                   ​Various R programming tools for data
 +                          manipulation
 +  gtools ​                 Various R programming tools
 +  maptools ​               Tools for reading and handling spatial objects
 +  MASS                    Main Package of Venables and Ripleys MASS
 +  mda                     ​Mixture and flexible discriminant analysis
 +  nnet                    Feed-forward Neural Networks and Multinomial
 +                          Log-Linear Models
 +  randomForest ​           Breiman and Cutlers random forests for
 +                          classification and regression
 +  rgdal                   ​Bindings for the Geospatial Data Abstraction
 +                          Library
 +  sp                      classes and methods for spatial data
 +  spatial ​                ​Functions for Kriging and Point Pattern
 +                          Analysis
 +  vcd                     ​Visualizing Categorical Data
 +  xtable ​                 Export tables to LaTeX or HTML
 +  Packages in library '/​usr/​lib/​R/​site-library':​
 +  base                    The R Base Package
 +  boot                    Bootstrap R (S-Plus) Functions (Canty)
 +  class                   ​Functions for Classification
 +  grid                    The Grid Graphics Package
 +  KernSmooth ​             Functions for kernel smoothing for Wand & Jones
 +                          (1995)
 +  lattice ​                ​Lattice Graphics
 +  MASS                    Main Package of Venables and Ripleys MASS
 +  Matrix ​                 Sparse and Dense Matrix Classes and Methods
 +  methods ​                ​Formal Methods and Classes
 +  mgcv                    GAMs with GCV/​AIC/​REML smoothness estimation
 +                          and GAMMs by PQL
 +  nlme                    Linear and Nonlinear Mixed Effects Models
 +  nnet                    Feed-forward Neural Networks and Multinomial
 +                          Log-Linear Models
 +  rpart                   ​Recursive Partitioning
 +  spatial ​                ​Functions for Kriging and Point Pattern
 +                          Analysis
 +  splines ​                ​Regression Spline Functions and Classes
 +  stats                   The R Stats Package
 +  stats4 ​                 Statistical Functions using S4 Classes
 +   ​survival ​               Survival analysis, including penalised
 +                          likelihood.
 +  tcltk                   ​Tcl/​Tk Interface
 +  tools                   Tools for Package Development
 +  utils                   The R Utils Package
 +  (END)
 +
 +
 +<note important>​
 +To exit the library mode list, type q
 +  q
 +</​note>​
 +
 +
 +
 +  libPaths()
 +  update.packages
 + 
 +  library(splines)
 +  >
 +
 + ** > ** this means that the splines package is now loaded
 +
 +  library(spgrass6)
 +  ​
 +If you see 
 +  Error in library(spgrass6) : there is no package called '​spgrass6'​
 +This means that spgrass6 is not loaded and ypou need to download it and installing it
 +
 +So you need to install the package:
 +install.packages(pkgs="​PACKAGE NAME", lib= "​library directories where to install the packages",​ dependencies=TRUE)
 +
 +To know more:
 + ? install.packages
 +
 +<code r>
 +  install.packages(pkgs="​randomForest",​ lib= "/​usr/​lib/​R/​site-library",​ dependencies=TRUE)
 + </​code>​
 +
 +You will see:
 +  install.packages(pkgs="​spgrass6",​lib= "/​usr/​lib/​R/​site-library"​),​dependencies=TRUE)
 +  install.packages(pkgs="​rgdal",​lib= "/​usr/​lib/​R/​site-library",​dependencies=TRUE)
 +   --- Please select a CRAN mirror for use in this session ---
 +  Loading Tcl/Tk interface ... done
 +  also installing the dependencies ‚Äòsp‚Äô,​ ‚Äòrgdal‚Äô,​ ‚ÄòXML‚Äô
 +  trying URL '​http://​cran.ch.r-project.org/​src/​contrib/​sp_0.9-36.tar.gz'​
 +  Content type '​application/​x-gzip'​ length 412739 bytes (403 Kb)
 +  opened URL
 +    ===============================================
 +  downloaded 403 Kb
 +  trying URL '​http://​cran.ch.r-project.org/​src/​contrib/​rgdal_0.6-8.tar.gz'​
 +  Content type '​application/​x-gzip'​ length 1389205 bytes (1.3 Mb)
 +  opened URL
 +  ==================================================
 +  downloaded 1.3 Mb
 +  trying URL '​http://​cran.ch.r-project.org/​src/​contrib/​XML_2.3-0.tar.gz'​
 +  Content type '​application/​x-gzip'​ length 659797 bytes (644 Kb)
 +  opened URL
 +  ==================================================
 +  downloaded 644 Kb
 +
 +Check :
 +  available.packages()
 +  ​
 +===== Install a new package from source =====
 +
 +From the bash terminal browse https://​cran.r-project.org/​src/​contrib/​ repository and find the pakage yopu like to wownload and it's web link
 +    wget https://​cran.r-project.org/​src/​contrib/​dismo_1.0-15.tar.gz
 +    sudo R CMD INSTALL dismo_1.0-15.tar.gz
 +
 +Done
 +
  
wiki/installpkage.txt · Last modified: 2017/12/05 22:53 (external edit)