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Annexes : Installation Du Logiciel R Et Des Packages R

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Annexes : Installation Du Logiciel R Et Des Packages R Annexes : Installation du logiciel R et des packages R Pr´e-requis et objectif • Aucun pr´e-requis n’est n´ecessaire.La lecture du chapitre 1 pourrait tou- tefois se r´ev´eler int´eressante. • Ce chapitre d´ecritcomment installer le logiciel R, dans sa version x (rem- placer partout dans le reste de ce document x par le num´ero de la derni`ere version disponible), sous le syst`emed’exploitation Microsoft Windows et aussi comment ajouter des packages suppl´ementaires sous Windows ou sous Linux. SECTION C.1 Installation de R sous Microsoft Windows Commencez par t´el´echarger le logiciel R (fichier R-x-win.exe o`u x est le nu- m´ero de la derni`ereversion disponible) `a l’aide de votre navigateur web usuel `a l’adresse suivante : http://cran.r-project.org/bin/windows/base/ Enregistrez ensuite ce fichier ex´ecutable sur le bureau de Windows puis double- cliquez sur le fichier R-x-win.exe dont voici l’icˆone : . Le logiciel s’installe alors et vous n’avez plus qu’`a suivre les instructions qui s’affichent et `a conserver les options propos´ees par d´efaut. Lorsque l’icˆone est ajout´ee sur le bureau, l’installation peut ˆetre consi- d´er´ee comme termin´ee. 574 Le logiciel R SECTION C.2 Installation de packages suppl´ementaires De nombreux modules (packages ou librairies) suppl´ementaires sont dispo- nibles sur le site internet : http://cran.r-project.org/web/packages/available_packages_by_name. html, ou bien encore ici : http://cran.r-project.org/bin/windows/contrib/, dans le dossier corres- pondant au num´ero x de votre version de R. Ils ´etendent les fonctionnalit´es de R. Il existe plusieurs moyens pour installer un nouveau package, que nous pr´esentons ci-dessous. C.2.1 Installation `a partir d’un fichier situ´e sur le disque Vous pouvez par exemple t´el´echarger depuis le site mentionn´e ci-dessus le fichier : R2HTML numero.zip et l’enregistrer sur le bureau de Windows. Pour installer ce package, commencez par lancer le logiciel R en double- cliquant sur son icˆone . Ensuite, allez dans le menu Packages, puis dans le sous-menu Installer le(s) package(s) depuis des fichiers zip... S´electionnez alors le fichier R2HTML numero.zip situ´e sur le bureau de Win- dows, puis cliquez sur « Ouvrir ». Annexes. Installation de R et de ses packages 575 C.2.2 Installation directement depuis l’Internet Pour installer, par exemple, les packages car et Rcmdr, commencez par lan- cer le logiciel R en double-cliquant sur son icˆone situ´ee sur le bureau. Ensuite, allez dans le menu Packages, puis dans le sous-menu Installer le(s) package(s)... S´electionnez un miroir (CRAN mirror) proche de votre situation g´eographique et cliquez sur OK. Puis, `al’´etape suivante, s´electionnez les entr´ees « car » et « Rcmdr ». Pour cela, cliquez d’abord sur « car » puis glissez l’ascenseur vers le bas et cliquez sur « Rcmdr » tout en maintenant la touche CTRL enfonc´ee. Vous devez v´erifier que les deux entr´ees sont bien s´electionn´ees(surlign´ees en bleu). 576 Le logiciel R Puis cliquez sur « OK ». Vous devriez alors voir apparaˆıtre successivement les deux ´ecrans suivants, indiquant que les packages que vous avez s´electionn´es sont en cours d’installation. Attention Il se peut que cette proc´edure ´echoue, par exemple si votre adminis- trateur a bloqu´e l’acc`es `a certains sites internet par un pare-feu, a impos´e l’utilisation d’un proxy pour acc´eder `a l’Internet ou encore s’il a inter- dit l’´ecrituredans certains dossiers de Windows. Nous vous conseillons de le contacter en cas de probl`eme. Notez que vous pouvez forcer R `autili- ser un proxy et que vous pouvez aussi installer des packages localement dans votre propre compte utilisateur. N’h´esitezpas `aconsulter `acesu- jet les sections 2.15 (How do I set environment variables ?) ou 2.19 (The Internet download functions fail) de la FAQ de Windows disponible ici : http://cran.r-project.org/bin/windows/base/rw-FAQ.html C.2.3 Installation depuis la ligne de commande On peut se passer des menus de l’interface graphique de R. C’est par exemple utile sous Unix/Linux o`u le logiciel R ne poss`ede pas d’interface graphique. Pour cela, tapez directement dans la console de R les commandes suivantes : –pourdespackages dont les fichiers *.zip sont situ´es sur votre disque dur : install.packages(choose.files(),repos = NULL) Annexes. Installation de R et de ses packages 577 – pour un package (par exemple Rcmdr) dont le fichier est sur le site internet CRAN : install.packages("Rcmdr") Une autre possibilit´e est d’installer un package sans passer par R, c’est-`a-dire directement depuis une fenˆetrede commandes MS-DOS sous Microsoft, ou une fenˆetre de terminal sous Linux ou MacOS. Mais dans ce dernier cas, vous aurez besoin de nombreux outils de compilation. Si ces outils ne sont pas install´es sur votre ordinateur, reportez-vous au paragraphe sur la cr´eation de packages dans le chapitre 7. Si ces outils sont install´es sur votre ordinateur, vous pouvez essayer ceci : T´el´echargez par exemple le fichier (package source) Rcmdr_numero.tar.gz `a partir de cette adresse internet : http://cran.r-project.org/web/packages/ Rcmdr. Enregistrez-le (sur le bureau) et lancez une fenˆetre de commande MS-DOS (Menu D´emarrer/Ex´ecuter/cmd), puis tapez : cd Bureau R CMD INSTALL Rcmdr_numero.tar.gz (remplacez bien entendu numero par ce qu’il faut). C.2.4 Installation de packages sous Linux Notez que les commandes de la section pr´ec´edente fonctionnent ´egalement sous Linux. Mais leur utilisation n´ecessiteparfois d’ˆetre connect´e en tant que super-utilisateur root (commande su - `a taper dans une fenˆetre de terminal). Si vous ne disposez pas des droits d’acc`es root, vous pouvez choisir d’instal- ler des packages localement, c’est-`a-dire dans votre r´epertoire personnel (home directory). Par exemple, pour le package Rcmdr, tapez dans un terminal : R CMD INSTALL --library=/home/user/Rlibs Rcmdr_numero.tar.gz (o`u, apr`es que vous avez cr´e´e le dossier Rlibs au moyen de la commande mkdir Rlibs,lechemin/home/user/Rlibs devra ˆetreremplac´epar le chemin appropri´eetnumero devra ´egalement ˆetre remplac´epar ce qu’il faut). Ensuite, afin que R puisse savoir o`u chercher les packages que vous aurez install´es, il vous faut cr´eer un fichier nomm´e ∼/.Renviron qui devra contenir la ligne R_LIBS=/home/user/Rlibs 578 Le logiciel R Astuce Si votre ordinateur est situ´e derri`ere un pare-feu et que vous devez uti- liser un proxy pour acc´eder `a l’Internet, vous pouvez utiliser la commande suivante pour installer un package directement depuis R : Sys.setenv("http_proxy"="http://user:pass@url_vers_ le_proxy:num_port") install.packages("Rcmdr",method="wget") N’h´esitez pas `aconsulter l’aide en ligne de la fonction download.file() pour plus de d´etails. SECTION C.3 Chargement des packages install´es Attention Pour bien comprendre cette section, vous devez avoir une id´ee grossi`ere de la diff´erence entre la m´emoire volatile (RAM) de votre ordinateur et la m´emoire physique d’un disque dur. Installer un package signifie que les fichiers qu’il contient sont « ´ecrits » physiquement sur le disque dur. Lorsque l’on ´eteint puis rallume l’ordinateur, ces fichiers seront toujours pr´esents `a l’endroit o`u ils auront ´et´e copi´es. Vous n’aurez donc plus besoin de r´einstallerce package, sauf pour en avoir une ver- sion plus r´ecente. Au contraire, charger un package (en m´emoire) signifie qu’il est temporaire- ment mis `adisposition de l’utilisateur dans R. Mais si l’on ferme puis rouvre R,cepackage ne sera plus disponible depuis R. Il faudra donc le charger de nouveau. Pour r´esumer, une fois que les packages souhait´es ont ´et´e install´es sur le disque dur de votre ordinateur, il faut les charger dans la m´emoire de R pour pouvoir les utiliser. Par exemple, si vous tapez dans la console de R : Commander() vous devriez voir apparaˆıtre le message d’erreur suivant indiquant que le package dont cette fonction est issue n’est pas accessible depuis R : Erreur: impossible de trouver la fonction "Commander" Annexes. Installation de R et de ses packages 579 Il faut donc d’abord charger Rcmdr en m´emoire. Pour cela, on peut soit taper require("Rcmdr") dans la console, soit aller dans le menu Packages/Charger le package..., et charger le package Rcmdr `a l’aide de la souris. La fenˆetresuivante apparaˆıtalors. 580 Le logiciel R Fermez-la et tapez de nouveau dans la console de R : Commander() Notez maintenant que le package Rcmdr abien´et´e charg´e et donc que la com- mande pr´ec´edente ne renvoie plus de message d’erreur. Astuce Notez que le logiciel R vous offre la possibilit´e de charger automatique- ment certains packages au d´emarrage de la fa¸consuivante : .First <- function() { require("pkg1") # Remplacez pkg1 par le # nom du package souhaité require("pkg2") # etc. } En fait, les fonctions .First() et .Last() permettent respectivement d’ex´ecuter au d´emarrage et `a l’arrˆet de R les instructions que l’on aura pris le soin de sp´ecifier dans le corps de ces deux fonctions. Ces fonctions peuvent ˆetreplac´ees dans un fichier nomm´e .Renviron situ´edansler´epertoire cou- rant ou bien dans le r´epertoire de l’utilisateur donn´e par l’instruction R : Sys.getenv("R_USER").
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