Description Usage Arguments Details Value See Also Examples
biocLite
installs or updates Bioconductor and CRAN packages,
ensuring that packages from the appropriate version of Bioconductor
are installed, and that all packages remain up to date.
1 2 3 4 5 |
pkgs |
|
suppressUpdates |
|
suppressAutoUpdate |
|
siteRepos |
|
ask |
|
... |
Additional arguments. |
The biocLite()
function is generally used after sourcing the
file biocLite.R
. This will install the BiocInstaller
package
if it is not already installed. See example section for more information.
biocLite()
returns the pkgs
argument, invisibly.
biocinstallRepos
returns the Bioconductor and CRAN
repositories used by biocLite
.
install.packages
installs the packages themselves.
update.packages
updates all installed packages.
chooseBioCmirror
lets you choose from a list of all
public Bioconductor mirror URLs.
chooseCRANmirror
lets you choose from a list of all
public CRAN mirror URLs.
monograph_group
, RBioinf_group
and
biocases_group
return package names associated
with Bioconductor publications.
all_group
returns the names of all Bioconductor
software packages.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 | ## Not run:
## Change default Bioconductor and CRAN mirrors
chooseBioCmirror()
chooseCRANmirror()
## If you don't have the BiocInstaller package installed, you can
## quickly install and load it as follows:
source("http://bioconductor.org/biocLite.R")
## The most recent version of the BiocInstaller package is now loaded.
## No need to load it with library().
biocLite() # installs default packages
## Now install a CRAN package:
biocLite("survival")
## install a Bioconductor package, but don't update all installed
## packages as well:
biocLite("GenomicRanges", suppressUpdates=TRUE)
## Install default packages, but do not update any package whose name
## starts with "org." or "BSgenome."
biocLite(suppressUpdates=c("^org\.", "^BSgenome\."))
## install a package from source:
biocLite("IRanges", type="source")
## don't install any packages, but update installed packages
biocLite(character(0), ask=FALSE)
## install all Bioconductor software packages
biocLite(all_group())
## End(Not run)
## Show the Bioconductor and CRAN repositories that will be used to
## install/update packages.
biocinstallRepos()
|
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