In muschellij2/oslerInstall: OSLER Installer

Installing OSLER Packages

Install and start the latest release version of R. Although the installer will try to download and install devtools, there may be some system requirements for devtools that you may need before going forward.

Then, you can install a package using the following command:

## try http:// if https:// URLs are supported
source("https://oslerinhealth.org/oslerLite.R")
osler_install("PACKAGE")

where PACKAGE is the name of the package you'd like to install, such as fslr. For example, if we want to install oslerhcp and fslr we can run:

source("https://oslerinhealth.org/oslerLite.R")
osler_install(c("spotgear"))

oslerLite: an alias for osler_install

As Bioconductor uses the biocLite function to install packages, we have created a duplicate of osler_install, called oslerLite, for ease of use for those users accustomed to Bioconductor. The same command could have been executed as follows:

source("https://oslerinhealth.org/oslerLite.R")
oslerLite(c("spotgear"))

Installing the oslerInstall package

The oslerInstall package contains the oslerLite/osler_install functions, as well as others relevant for OSLER. You can install the package as follows:

source("https://oslerinhealth.org/oslerLite.R")
osler_install("oslerInstall")

After installation, you can use oslerInstall::osler_install() to install packages without source-ing the URL above.

Installing OSLER Packages without upgrading dependencies

The oslerLite/osler_install functions depend on devtools::install_github, which will upgrade dependencies by default, which is recommended. If you would like to install a package, but not upgrade the dependencies (missing dependencies will still be installed), you can set the upgrade_dependencies argument to FALSE:

oslerLite(c("spotgear"), upgrade_dependencies = FALSE)

Installing and starting R

1. Download the most recent version of R from https://cran.r-project.org/. There are detailed instructions on the R website as well as the specific R installation for the platform you are using, typically Linux, OSX, and Windows.

2. Start R; we recommend using R through RStudio. You can start R using RStudio (Windows, OSX, Linux), typing "R" at in a terminal (Linux or OSX), or using the R application either by double-clicking on the R application (Windows and OSX).

3. For learning R, there are many resources such as Try-R at codeschool and DataCamp.

Packages not available on OSLER

If a package is not in the OSLER list of packages , then it is not located on the OSLER Github. Therefore, when installing, you'll get the following error:

Error in osler_install(...) : 
  Package(s) PACKAGE_TRIED_TO_INSTALL are not in OSLER

Once a package is located on the list of packages, then it will be available to install.

muschellij2/oslerInstall documentation built on May 30, 2019, 7:17 p.m.