Installing R packages from CRAN / Bioconductor / Omegahat / Github

CRAN

Comprehensive R Archive Network

online CRAN repositry
```
install.packages("timsac")
```

Offline (already downloaded pacakge - RSPython_0.7-1.tar.gz)
choose library path

.libPaths() # listing library paths

install.packages("/home/trendwise/Downloads/R packages/RSPython_0.7-1.tar.gz",repos=NULL,lib=.libPaths()[1])

Terminal / cmd
```
R CMD INSTALL RSPython_0.7-1.tar.gz
```

Bioconductor

installing biocLite
requires for downloading & installing pkg 4m Bioconductor

source("http://bioconductor.org/biocLite.R")
biocLite() # installs automatically 'Biobase' 'IRanges' 'AnnotationDbi' ‘BiocGenerics’ ‘RSQLite’

list of all packages in BioConductor
```
s=all_group()
print(s)
```
installing GenomicFeatures & AnnotationDbi packages
```
biocLite(c("GenomicFeatures", "AnnotationDbi"))
```

Omegahat

RCurl

install.packages("RCurl", repos = "http://www.omegahat.org/R")

For some packages, there are binaries for Windows.
For most others, you will need to specify to download the source package
```
install.packages(packageName, repos = "http://www.omegahat.org/R", type = "source")
```

Git-Hub

install devtools pkg
requires for downloading & installing GitHub packages
```
install.packages("devtools")
require(devtools)
```
package name:- rplos

repository name:- rOpenSci

install_github("rplos", "rOpenSci")
require(rplos)

build & install from git cloned

git clone https://github.com/yihui/knitr.git
R CMD build knitr
R CMD INSTALL knitr_*.tar.gz

RForge

audio & knitr pkg

install.packages("audio",repos="http://rforge.net")
install.packages('knitr', repos = c('http://rforge.net', 'http://cran.rstudio.org'),type = 'source')

Updating all existing packages

using update.packages

update.packages(ask = FALSE, repos = 'http://cran.rstudio.org')