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Introduction
Managing libraries
Installation of packages
Installation of packages in RStudio
Dealing with proxy when accccesing CRAN

Introduction

R functions and datasets can be organized into a package. Package is essentially a library of functions for specific domain and helps to accomplish a specific for this domain set of tasks. For example ggplot2 is the package for plotting result of computations in graphical form.

Typically packages that have high quality are available from CRAN. Some of them are well maintained. Other lost key developer and gradually sliding into abandonware status. Most package are written by statisticians and as such provides functionality that might be different then a programmer coming to R from other scripting language such as Perl of Python would expect.

R package is a essentially a folder of folders, each containing specific types of files. For example, the root of package TTR on Windows can be located in

C:\Users\username\Documents\R\R-3.2.0\library\TTR

Within this folder there are several subfolders that constitute the package. Some of then are obligatory some of them are optional. minimum is two (R and man) and typical number is six:

Folder /R contains functions that can be called from the package. For most packages they are precompiled and you need to download the package source separately to see the code.
Folder./man contains documentation files.
Folder ./data can contain data tat are sometimes included with the package.
Folder scr contains compiled Fortran or C++ code used by the package. This is somewhat paradoxical as the name suggests source files, not binaries.
Folder inst contain files that need to be installed for the end user
Folder test contain code that tests functions in the package.

Root folder contains two mandatory files DESCRIPTION file and NAMESPACE as well as can contain several other (recommended) files such as NEWS, LICENSE, and README.

06/14/2015 01:03 AM <DIR> .
06/14/2015 01:03 AM <DIR> ..
06/14/2015 01:03 AM <DIR> data
06/14/2015 01:03 AM 562 DESCRIPTION
06/14/2015 01:03 AM <DIR> help
06/14/2015 01:03 AM <DIR> html
06/14/2015 01:03 AM 2,193 INDEX
06/14/2015 01:03 AM <DIR> libs
06/14/2015 01:03 AM 1,177 MD5
06/14/2015 01:03 AM <DIR> Meta
06/14/2015 01:03 AM 965 NAMESPACE
06/14/2015 01:03 AM <DIR> R

For each subject domain there is a set of most popular packages. For example for technical analysis the following package are commonly used:

Only when a package is loaded functions and datasets provided by the package became available. This is done both for efficiency (the full list would take more memory and would take longer to search than a subset), and to aid package developers, who are protected from name clashes with other code. The process of developing packages is described in Creating R packages in Writing R Extensions.

Managing libraries

User can inquire which packages are installed and load the necessary from the command line:

library()                       # list all available packages
library(lib.loc = .Library)     # list all packages in the default library
library(help = quantmod)        # documentation on package 'quantmod'
library(quantmod)               # load package 'quantmod'
require(quantmod)               # the same
search()                        #  
detach("package:quantmod")      # detach package

Getting the list of installed libraries

To see which packages are installed on your desktop or server, issue the command

> library()

with no arguments. On just installed RStudio you will get something like:

Packages in library ‘C:/Users/user/Documents/R/R-3.2.0/library’:

base               The R Base Package. 
boot               Bootstrap Functions (Originally by
                   Angelo Canty for S)
class              Functions for Classification
cluster            Cluster Analysis Extended Rousseeuw et
                   al.
codetools          Code Analysis Tools for R
compiler           The R Compiler Package
datasets           The R Datasets Package
foreign            Read Data Stored by Minitab, S, SAS,
                   SPSS, Stata, Systat, Weka, dBase, ...
graphics           The R Graphics Package
grDevices          The R Graphics Devices and Support for
                   Colours and Fonts
grid               The Grid Graphics Package
KernSmooth         Functions for Kernel Smoothing
                   Supporting Wand & Jones (1995)
lattice            Lattice Graphics
manipulate         Interactive Plots for RStudio
MASS               Support Functions and Datasets for
                   Venables and Ripley's MASS
Matrix             Sparse and Dense Matrix Classes and
                   Methods
methods            Formal Methods and Classes
mgcv               Mixed GAM Computation Vehicle with
                   GCV/AIC/REML Smoothness Estimation
nlme               Linear and Nonlinear Mixed Effects
                   Models
nnet               Feed-Forward Neural Networks and
                   Multinomial Log-Linear Models
parallel           Support for Parallel computation in R
rpart              Recursive Partitioning and Regression
                   Trees
rstudio            Tools and Utilities for RStudio
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
tcltk              Tcl/Tk Interface
tools              Tools for Package Development
translations       The R Translations Package
utils              The R Utils Package

The base package contains the basic functions which let R function as a language: arithmetic, input/output, basic programming support, etc. For a complete list of functions, use library(help = "base").

Loading a library

To load a particular package (e.g., Quantmod package) use need to use a command:

> library(quantmod)

After that you can use functions provided by the package. This statement works only when package is installed. If it is not you need to install it.

library(package) and require(package) both load the package with name package and put it on the search list. require is designed for use inside other functions; it returns FALSE and gives a warning (rather than an error as library() does by default) if the package does not exist. Both functions check and update the list of currently loaded packages and do not reload a package which is already loaded. (If you want to reload such a package, call detach(unload = TRUE) or unloadNamespace first.) If you want to load a package without putting it on the search list, use requireNamespace.

The set of libraries which are loaded by default

Not each and every library needs to be loaded. There is a set of packages loaded on startup is by default

> getOption("defaultPackages")
[1] "datasets"  "utils"     "grDevices" "graphics"  "stats"    
[6] "methods"

(plus, of course, base) and this can be changed by setting the option in startup code (e.g. in ~/.Rprofile).

It is initially set to the value of the environment variable R_DEFAULT_PACKAGES if set (as a comma-separated list).

Setting R_DEFAULT_PACKAGES=NULL ensures that only package base is loaded.

Installation of packages

Users connected to the Internet can use the install.packages() and update.packages() functions.

In Rstudio you can use GUI to achieve the same result (see below). See Installing packages in R Installation and Administration) on more information about to install and update packages.

To see which packages are currently loaded, use

> search()

to display the search list.

> search() 
 [1] ".GlobalEnv"        "tools:rstudio"     "package:stats"    
 [4] "package:graphics"  "package:grDevices" "package:utils"    
 [7] "package:datasets"  "package:methods"   "Autoloads"        
[10] "package:base"

Some packages may be loaded but not available on the search list (see Namespaces): these will be included in the list given by

> loadedNamespaces()

To see a list of all available help topics in an installed package, use

> help.start()

to start the HTML help system, and then navigate to the package listing in the Reference section.

R packages are installed into libraries, which are directories in the file system containing a subdirectory for each package installed there.

R comes with a single library, R_HOME/library which is the value of the R object ‘.Library’ containing the standard and recommended packages.

Both sites and users can create others and load them in an R session. At the lowest level ‘.libPaths()’ can be used to add paths to the collection of libraries or to report the current collection.

R will automatically make use of a site-specific library R_HOME/site-library if this exists (it does not in a vanilla R installation). This location can be overridden by setting¹³ ‘.Library.site’ in R_HOME/etc/Rprofile.site, or (not recommended) by setting the environment variable R_LIBS_SITE. Like ‘.Library’, the site libraries are always included by ‘.libPaths()’.

Users can have one or more libraries, normally specified by the environment variable R_LIBS_USER. This has a default value (to see it, use ‘Sys.getenv("R_LIBS_USER")’ within an R session), but that is only used if the corresponding directory actually exists (which by default it will not).

Both R_LIBS_USER and R_LIBS_SITE can specify multiple library paths, separated by colons (semicolons on Windows).

Installation of packages in RStudio

Access to the package page can be done using shortcut Ctrl+7. From this dialog you can search packages in CRAN and install those that you found.

Selecting "install dependencies" checkbox allow you to install all the necessary dependencies for the package.

Sometimes there is a need to install package from a zip file downloaded to the local filesystem. In this case you need to chose Package Archive File (zip) in "Install From" dialog.

Dealing with proxy when accccesing CRAN

The best way to avoid troubles with proxy, if your proxy requires authentication is to submit ticket to make one of CRAN mirror accessible without authentication. For the USA it might be

http://watson.nci.nih.gov/cran_mirror/

Then you can put this mirror in Rstudio (Configuring R to Use an HTTP Proxy – RStudio Support)

...The R documentation for the download.file method explains how to configure R to use an HTTP proxy. In short this requires adding one or more environment variables to your installation to point to the proxy.

To set the required environment variables you should add them to the R environment file (which is read by R at startup). On RStudio Server this file is found at R_HOME/etc/Renviron.site. On RStudio Desktop this file is found in the user home directory at ~/.Renviron.

You can easily access your .Renviron file by running the command file.edit('~/.Rprofile') within RStudio

Note that these files might not exist in the default installation of R so you may need to create them if they aren't already present.

Example environment file entries for proxy configuration might be:
http_proxy=http://proxy.dom.com/
http_proxy_user=user:passwd
Note that the http_proxy_user entry need only be supplied if the proxy requires authentication. There is also an ftp_proxy entry which can be specified for FTP transfers. You can consult the download.file documentation for detailed information on all available proxy options.

These environment variables are read once during the first call to download.file so if you have running R sessions you'll need to quit and restart them for the proxy behavior to take effect.

To see diagnostic information for HTTP transfers you can set the internet.info option to 0 or 1 (the default is 2, which only shows diagnostics for failure cases). For example:
options(internet.info = 0)

alternative to modifying the config file is to use the following command from the command line:

Sys.setenv(http_proxy="http://MyLoGiN:MyPaSs@1ncproxy1:80")

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NEWS CONTENTS

20150625 : Packages in R for Everyone by Jared Lander ( Packages in R for Everyone by Jared Lander, Jun 25, 2015 )
20150620 : R help - How to set proxy settings for R ( R help - How to set proxy settings for R, Jun 20, 2015 )
20150620 : Proxy setting for R ( Stack Overflow )
20150620 : r - Setting up the proxy for rstudio ( Ask Ubuntu )

Old News ;-)

[Jun 25, 2015] Packages in R for Everyone by Jared Lander

This is way too many packages for the introductory (actually basic level) book. But that reflects problem with R in general, not only the problem with the particular book.

Package URL

Amelia http://cran.r-project.org/web/packages/Amelia/index.html

BH http://cran.r-project.org/web/packages/BH/index.html

GGally http://cran.r-project.org/web/packages/GGally/index.html

RODBC http://cran.r-project.org/web/packages/RODBC/index.html

RXKCD http://cran.r-project.org/web/packages/RXKCD/index.html

Rcpp http://cran.r-project.org/web/packages/Rcpp/index.html

RcppArmadillo http://cran.r-project.org/web/packages/RcppArmadillo/index.html

RevoScaleR http://cran.r-project.org/web/packages/RevoScaleR/index.html

Sweave http://cran.r-project.org/web/packages/Sweave/index.html

UsingR http://cran.r-project.org/web/packages/UsingR/index.html

WDI http://cran.r-project.org/web/packages/WDI/index.html

XLConnect http://cran.r-project.org/web/packages/XLConnect/index.html

XML http://cran.r-project.org/web/packages/XML/index.html

arm http://cran.r-project.org/web/packages/arm/index.html

bayesGARCH http://cran.r-project.org/web/packages/bayesGARCH/index.html

bigmemory http://cran.r-project.org/web/packages/bigmemory/index.html

boot http://cran.r-project.org/web/packages/boot/index.html

chron http://cran.r-project.org/web/packages/chron/index.html

cluster http://cran.r-project.org/web/packages/cluster/index.html

coefplot http://cran.r-project.org/web/packages/coefplot/index.html

data.table http://cran.r-project.org/web/packages/data.table/index.html

devtools http://cran.r-project.org/web/packages/devtools/index.html

doParallel http://cran.r-project.org/web/packages/doParallel/index.html

fGarch http://cran.r-project.org/web/packages/fGarch/index.html

fastcluster http://cran.r-project.org/web/packages/fastcluster/index.html

foreach http://cran.r-project.org/web/packages/foreach/index.html

forecast http://cran.r-project.org/web/packages/forecast/index.html

foreign http://cran.r-project.org/web/packages/foreign/index.html

gdata http://cran.r-project.org/web/packages/gdata/index.html

ggplot2 http://cran.r-project.org/web/packages/ggplot2/index.html

ggthemes http://cran.r-project.org/web/packages/ggthemes/index.html

glmnet http://cran.r-project.org/web/packages/glmnet/index.html

knitr http://cran.r-project.org/web/packages/knitr/index.html

lars http://cran.r-project.org/web/packages/lars/index.html

lattice http://cran.r-project.org/web/packages/lattice/index.html

lubridate http://cran.r-project.org/web/packages/lubridate/index.html

maptools http://cran.r-project.org/web/packages/maptools/index.html

mgcv http://cran.r-project.org/web/packages/mgcv/index.html

mi http://cran.r-project.org/web/packages/mi/index.html

mice http://cran.r-project.org/web/packages/mice/index.html

nnet http://cran.r-project.org/web/packages/nnet/index.html

pam http://cran.r-project.org/web/packages/pam/index.html

parallel http://cran.r-project.org/web/packages/parallel/index.html

plyr http://cran.r-project.org/web/packages/plyr/index.html

proto http://cran.r-project.org/web/packages/proto/index.html

quantmod http://cran.r-project.org/web/packages/quantmod/index.html

randomForest http://cran.r-project.org/web/packages/randomForest/index.html

reshape http://cran.r-project.org/web/packages/reshape/index.html

reshape2 http://cran.r-project.org/web/packages/reshape2/index.html

rgeos http://cran.r-project.org/web/packages/rgeos/index.html

roxygen2 http://cran.r-project.org/web/packages/roxygen2/index.html

rpart http://cran.r-project.org/web/packages/rpart/index.html

rpart.plot http://cran.r-project.org/web/packages/rpart.plot/index.html

rugarch http://cran.r-project.org/web/packages/rugarch/index.html

scales http://cran.r-project.org/web/packages/scales/index.html

slidify http://cran.r-project.org/web/packages/slidify/index.html

sp http://cran.r-project.org/web/packages/sp/index.html

splines http://cran.r-project.org/web/packages/splines/index.html

stringr http://cran.r-project.org/web/packages/stringr/index.html

survival http://cran.r-project.org/web/packages/survival/index.html

tseries http://cran.r-project.org/web/packages/tseries/index.html

useful http://cran.r-project.org/web/packages/useful/index.html

vars http://cran.r-project.org/web/packages/vars/index.html

xlsReadWrite http://cran.r-project.org/web/packages/xlsReadWrite/index.html

xts http://cran.r-project.org/web/packages/xts/index.html

Package	URL
Amelia	http://cran.r-project.org/web/packages/Amelia/index.html
BH	http://cran.r-project.org/web/packages/BH/index.html
GGally	http://cran.r-project.org/web/packages/GGally/index.html
RODBC	http://cran.r-project.org/web/packages/RODBC/index.html
RXKCD	http://cran.r-project.org/web/packages/RXKCD/index.html
Rcpp	http://cran.r-project.org/web/packages/Rcpp/index.html
RcppArmadillo	http://cran.r-project.org/web/packages/RcppArmadillo/index.html
RevoScaleR	http://cran.r-project.org/web/packages/RevoScaleR/index.html
Sweave	http://cran.r-project.org/web/packages/Sweave/index.html
UsingR	http://cran.r-project.org/web/packages/UsingR/index.html
WDI	http://cran.r-project.org/web/packages/WDI/index.html
XLConnect	http://cran.r-project.org/web/packages/XLConnect/index.html
XML	http://cran.r-project.org/web/packages/XML/index.html
arm	http://cran.r-project.org/web/packages/arm/index.html
bayesGARCH	http://cran.r-project.org/web/packages/bayesGARCH/index.html
bigmemory	http://cran.r-project.org/web/packages/bigmemory/index.html
boot	http://cran.r-project.org/web/packages/boot/index.html
chron	http://cran.r-project.org/web/packages/chron/index.html
cluster	http://cran.r-project.org/web/packages/cluster/index.html
coefplot	http://cran.r-project.org/web/packages/coefplot/index.html
data.table	http://cran.r-project.org/web/packages/data.table/index.html
devtools	http://cran.r-project.org/web/packages/devtools/index.html
doParallel	http://cran.r-project.org/web/packages/doParallel/index.html
fGarch	http://cran.r-project.org/web/packages/fGarch/index.html
fastcluster	http://cran.r-project.org/web/packages/fastcluster/index.html
foreach	http://cran.r-project.org/web/packages/foreach/index.html
forecast	http://cran.r-project.org/web/packages/forecast/index.html
foreign	http://cran.r-project.org/web/packages/foreign/index.html
gdata	http://cran.r-project.org/web/packages/gdata/index.html
ggplot2	http://cran.r-project.org/web/packages/ggplot2/index.html
ggthemes	http://cran.r-project.org/web/packages/ggthemes/index.html
glmnet	http://cran.r-project.org/web/packages/glmnet/index.html
knitr	http://cran.r-project.org/web/packages/knitr/index.html
lars	http://cran.r-project.org/web/packages/lars/index.html
lattice	http://cran.r-project.org/web/packages/lattice/index.html
lubridate	http://cran.r-project.org/web/packages/lubridate/index.html
maptools	http://cran.r-project.org/web/packages/maptools/index.html
mgcv	http://cran.r-project.org/web/packages/mgcv/index.html
mi	http://cran.r-project.org/web/packages/mi/index.html
mice	http://cran.r-project.org/web/packages/mice/index.html
nnet	http://cran.r-project.org/web/packages/nnet/index.html
pam	http://cran.r-project.org/web/packages/pam/index.html
parallel	http://cran.r-project.org/web/packages/parallel/index.html
plyr	http://cran.r-project.org/web/packages/plyr/index.html
proto	http://cran.r-project.org/web/packages/proto/index.html
quantmod	http://cran.r-project.org/web/packages/quantmod/index.html
randomForest	http://cran.r-project.org/web/packages/randomForest/index.html
reshape	http://cran.r-project.org/web/packages/reshape/index.html
reshape2	http://cran.r-project.org/web/packages/reshape2/index.html
rgeos	http://cran.r-project.org/web/packages/rgeos/index.html
roxygen2	http://cran.r-project.org/web/packages/roxygen2/index.html
rpart	http://cran.r-project.org/web/packages/rpart/index.html
rpart.plot	http://cran.r-project.org/web/packages/rpart.plot/index.html
rugarch	http://cran.r-project.org/web/packages/rugarch/index.html
scales	http://cran.r-project.org/web/packages/scales/index.html
slidify	http://cran.r-project.org/web/packages/slidify/index.html
sp	http://cran.r-project.org/web/packages/sp/index.html
splines	http://cran.r-project.org/web/packages/splines/index.html
stringr	http://cran.r-project.org/web/packages/stringr/index.html
survival	http://cran.r-project.org/web/packages/survival/index.html
tseries	http://cran.r-project.org/web/packages/tseries/index.html
useful	http://cran.r-project.org/web/packages/useful/index.html
vars	http://cran.r-project.org/web/packages/vars/index.html
xlsReadWrite	http://cran.r-project.org/web/packages/xlsReadWrite/index.html
xts	http://cran.r-project.org/web/packages/xts/index.html

[Jun 20, 2015] R help - How to set proxy settings for R

Apr 19, 2010; 12:00pm How to set proxy settings for R

dandaonline

I would like to run R on my computer (with win xp on it) at work bu the proxy restrictions of the university don't let me download the packages or to connect to a cran mirror, I usually get this message:

> chooseCRANmirror()

Warning message:

In open.connection(con, "r") :
unable to connect to 'cran.r-project.org' on port 80.

Do you know if there is a way to set proxy settings for using R normally?
Thanks a lot

Henrique Dallazuanna, Selected post Apr 19, 2010; 2:12pm
Try this:
setInternet2() 
chooseCRANmirror()
Pete Brecknock, Apr 19, 2010; 4:29pm
Re: How to set proxy settings for R

In reply to this post by danda

Also, the FAQ suggests using the alternative internet2.dll by starting R with the flag --internet2

If you start R from a desktop icon, you can add the --internet flag to the target line (right click, properties) e.g.
"C:\Program Files\R\R-3.2.1\bin\Rgui.exe" --internet2
see http://cran.r-project.org/bin/windows/rw-FAQ.html#The-Internet-download-functions-fail_002e

HTH

Pete
djmuseR, Apr 19, 2010; 9:32pm

In reply to this post by danda

Hi:

One alternative to sneaking around the proxy restrictions is to load R onto a jump drive and run it off of that. I know of several instructors
who are using that approach with their students for similar reasons.

Unless you have a compelling reason to install every single package, you should be able to fit R comfortably on a 4Gb memory stick.

Just wanted to provide a different possible solution to your problem :)

Dennis

danda:

In reply to this post by Pete Brecknock

Dear Pete,

Thanks, it works now!

I did as you suggested:

--internet flag to the target line (right click, properties) e.g. "C:\Program Files\R\R-2.8.1\bin\Rgui.exe" --internet2

Strangely enough, I can now easly download packages but I still get these messages:

chooseCRANmirror()

Warning message:
In open.connection(con, "r") :
cannot open: HTTP status was '407 Proxy Authentication Required'

> utils:::menuInstallPkgs()
Warning: unable to access index for repository http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.10

..but eventually it does install what I want...any clue?

Alessandra

Pete Brecknock

Hi Alessandra

Did you restart R?

You should be able to download packages using the Packages> Install Package(s) … from the menu bar in the GUI.

Once the package has been downloaded select Packages> Load Package … you should see what you just downloaded in a list of available packages

Proxy setting for R

Stack Overflow
I am facing problem while connecting R with internet in my office. May be this due to LAN settings. I tried the almost all possible ways I come across in the web (see below) but still in vain.

Method1: Invoking R using --internet2

Method2: Invoking R by setting "~/Rgui.exe" http_proxy=http:/999.99.99.99:8080/ http_proxy_user=ask

Method3: Setting Setinternet2=TRUE

Method4:
curl <- getCurlHandle()

curlSetOpt(.opts = list(proxy = '999.99.99.99:8080'), curl = curl)

Res <- getURL('http://www.cricinfo.com', curl = curl)

In above all methods I can able to load packages directly from CRAN also able to download files using download.file command

But using getURL(RCurl), readHTMLTable(XML), htmlTreeParse(XML) commands I am unable to extract web data. I am getting ~<HEAD>\n<TITLE>Access Denied</TITLE>\n</HEAD>~ error.

How to set LAN proxy settings for XML package in R?

user813966

If you've tried everything and it still doesn't work, then speak to your network administrator; they may need to set up a firewall exception to allow traffic through from your machine. – Richie Cotton Jun 28 '11 at 13:39

Geek On Acid
On Mac OS, I found the best solution here. Quoting the author, two simple steps are:

1) Open Terminal and do the following:
export http_proxy=http://staff-proxy.ul.ie:8080
export HTTP_PROXY=http://staff-proxy.ul.ie:8080
2) Run R and do the following:
Sys.setenv(http_proxy="http://staff-proxy.ul.ie:8080")
double-check this with:
Sys.getenv("http_proxy")
I am behind university proxy, and this solution worked perfectly. The major issue is to export the items in Terminal before running R, both in upper- and lower-case.
Richie Cotton
The problem is with your curl options – the RCurl package doesn't seem to use internet2.dll. You need to specify the port separately, and will probably need to give your user login details as network credentials, e.g.,
opts <- list(
  proxy         = "999.999.999.999", 
  proxyusername = "mydomain\\myusername", 
  proxypassword = "mypassword", 
  proxyport     = 8080
)
getURL("http://stackoverflow.com", .opts = opts)
Remember to escape any backslashes in your password. You may also need to wrap the URL in a call to curlEscape.
if the options specified are globally set with curlSetOpt(.opts=opts) are these also used for other connections such as with connections from XML package e.g.: htmlTreeParse() or how do I force them to use the proxy? thanks! – Seb Nov 20 '12 at 13:23
I had the same problem at my office and I solved it adding the proxy in the destination of the R shortcut; clik on right button of the R icon, preferences, and in the destination field add
"C:\Program Files\R\your_R_version\bin\Rgui.exe" http_proxy=http://user_id:passwod@your_proxy:your_port/
Be sure to put the directory where you have the R program installed. That works for me. Hope this help.

If you start R from a desktop icon, you can add the --internet flag to the target line (right click, properties) e.g. "C:\Program Files\R\R-2.8.1\bin\Rgui.exe" --internet2

On Windows 7 I solved this by going into my environment settings (try this link for how) and adding user variables http_proxy and https_proxy with my proxy details.
Tried all of these and also the solutions using netsh, winhttp etc. Geek On Acid's answer helped me download packages from the server but none of these solutions worked for using the package I wanted to run (twitteR package).
The best solution is to use a software that let's you configure system-wide proxy.

FreeCap (free) and Proxifier (trial) worked perfectly for me at my company.

Please note that you need to remove proxy settings from your browser and any other apps that you have configured to use proxy as these tools provide system-wide proxy for all network traffic from your computer.

r - Setting up the proxy for rstudio

Ask Ubuntu

My machine is running on Ubuntu 14.04, and I have already tried looking at Configuring R to Use an HTTP Proxy in the FAQ section of Rstudio support.

This is what I did till now...

in my home directory, I created a file named .Renviron with the following contents
http_proxy = http:// ip_address : port_num/
http_proxy_user = username : password

then in the rstudio, I tried to install swirl package
> install.packages("swirl")
Warning in install.packages :
cannot open: HTTP status was '403 Forbidden'
Warning in install.packages :
cannot open: HTTP status was '403 Forbidden'
Warning in install.packages :
unable to access index for repository http://cran.rstudio.com/src/contrib
Installing package into '/home/dmacs/R/x86_64-pc-linux-gnu-library/3.1'
(as 'lib' is unspecified)
Warning in install.packages :
cannot open: HTTP status was '403 Forbidden'
Warning in install.packages :
cannot open: HTTP status was '403 Forbidden'
Warning in install.packages :
unable to access index for repository http://cran.rstudio.com/src/contrib
Warning in install.packages :
package 'swirl' is not available (for R version 3.1.2)

and there I see all this stuff, but I am able to access the link http://cran.rstudio.com/src/contrib from my browser.

I even tried setting up the proxy using GUI based rstudio, but I couldn't figure out where was the option to set the proxy.

enter image description here

Thanks in advance.

r

===

Swaroop

You should add proxy information to your Renviron.site file that is located 'R_HOME/etc/Renviron.site'. You can find your R_HOME by call bellow command on RStudio console.
> R.home()
[1] "/usr/lib/R"

Add you proxy server address in 'R_HOME/etc/Renviron.site'
http_proxy=http://<<your proxy server address>>/

and restart RStudio.

Good luck.

Ky Ryu

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