---
title: "A.0 -- Installation"
author:
  Martin Morgan <Martin.Morgan@RoswellPark.org><br/>
date: "8 - 9 May 2017"
output:
  BiocStyle::html_document2:
    toc: true
    toc_depth: 2
vignette: >
  % \VignetteIndexEntry{A.0 -- Installation}
  % \VignetteEngine{knitr::rmarkdown}
---

```{r style, echo = FALSE, results = 'asis'}
knitr::opts_chunk$set(
    eval=as.logical(Sys.getenv("KNITR_EVAL", "TRUE")),
    cache=as.logical(Sys.getenv("KNITR_CACHE", "TRUE")))
```

# Easy installation

## Windows

NOTE: See [Windows installation instructions][Windows] for more
detail. Install _R_ and _RStudio_ as regular users.

To install _R_, visit the [Windows base][] distribution page. Click on
the `Download R-3.4.0 for Windows` link. Click on the installer and
make the default selection for each option.

To install _RStudio_, visit the [RStudio download][] page. Click on
the current RStudio release for Windows link. Click on the installer
and follow default instructions.

## Mac

NOTE: See [R for Mac OS X][MacOS] for more detail.

To install _R_, visit the [R for Mac OS X][MacOS]. Click on the the
`R-3.4.0.pkg` link. Click on the installer and follow default
instructions.

To install _RStudio_, visit the [RStudio download][] page. Click on
the current RStudio release for Windows link. Click on the installer
and follow default instructions.

## Linux

NOTE: See [distribution-specific instructions][Linux-distro] for
additional detail.

On debian-based systems, the easiest way to install _R_ is through a
package manager manager, run under an administrator account.  On Linux
one usually needs to install _R_ packages from source, and _R_ package
source often contains C, C++, or Fortran code requiring a compiler and
`-dev` versions of various system libraries. It is therefore
convenient to install the `-dev` version of R.

```
sudo apt-get install r-base r-base-dev
```

When installing source packages, it may be necessary to have access to
the `-dev` version of various system libraries. Many of these are
installed as dependencies of `r-base-dev`; other common examples
include the xml and curl libraries

```
sudo apt-get install libxml2-dev
sudo apt-get install libcurl-dev
```

Note in particular the use specification of libraries (the `lib`
prefix) and the use of the `-dev` version.

To install _RStudio_, visit the [RStudio download][] page. Download
the appropriate archive for your OS. On Ubuntu, install the `.deb`
installer with

```
sudo dpkg -i rstudio-1.0.136-amd64.deb
```

[Windows]: https://cran.r-project.org/bin/windows/
[Windows base]: https://cran.r-project.org/bin/windows/base/
[MacOS]: https://cran.r-project.org/bin/macosx/
[RStudio download]: https://www.rstudio.com/products/rstudio/download/

[Rtools]: https://cran.r-project.org/bin/windows/Rtools/
[Linux-distro]: https://cran.r-project.org/bin/linux/
[R-admin]: https://cran.r-project.org/doc/manuals/r-release/R-admin.html)