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"))
oslerInstall
packageThe 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.
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)
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.
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).
For learning R, there are many resources such as Try-R at codeschool and DataCamp.
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.
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