BiocDevel |
BiocDevel |
BiocRelease |
BiocRelease |
biocReposForVers |
biocReposForVers |
BiocSource-class |
PkgSource An object representing the source location of a package. This is a virtual used exlusively through its subclasses, which are used to differentiate the different types of package source locations. |
BiocSVNManifest |
Create a manifest of Bioc SVN locations |
BiocVers |
BiocVers A constructor for creating a RepoSubset object for a specified release of Bioconductor, which includes only the BiocInstaller package. |
branch |
Get or set the branch associated with a Package Source |
branch,PkgSource |
Get or set the branch associated with a Package Source |
branch-method |
Get or set the branch associated with a Package Source |
branch<- |
Get or set the branch associated with a Package Source |
branch<-,PkgSource |
Get or set the branch associated with a Package Source |
branch<--method |
Get or set the branch associated with a Package Source |
c,PkgManifest |
cmethods Combine 2 or more manifests of the same type (PkgManifest or SessionManifest) |
c-method |
cmethods Combine 2 or more manifests of the same type (PkgManifest or SessionManifest) |
checkIsPkgDir |
Check if a directory contains package sources |
cranPkgVersManifest |
cranPkgVersManifest Create a Pkg manifest which points to tarballs representing a particular version of a CRAN package and versions of its (recursive) dependencies that were contemporary on the first or last day the specified package version resided on CRAN |
CRANSource-class |
PkgSource An object representing the source location of a package. This is a virtual used exlusively through its subclasses, which are used to differentiate the different types of package source locations. |
currentCompEnv |
currentCompEnv |
CVSSource-class |
PkgSource An object representing the source location of a package. This is a virtual used exlusively through its subclasses, which are used to differentiate the different types of package source locations. |
getPkgDir |
Construct pockage directory path |
GithubManifest |
GithubManifest |
GithubSource-class |
PkgSource An object representing the source location of a package. This is a virtual used exlusively through its subclasses, which are used to differentiate the different types of package source locations. |
GitSource-class |
PkgSource An object representing the source location of a package. This is a virtual used exlusively through its subclasses, which are used to differentiate the different types of package source locations. |
gotoVersCommit |
gotoVersCommit This is a low-level function not intended for direct use by the end user. |
gotoVersCommit,character,BiocSource |
gotoVersCommit This is a low-level function not intended for direct use by the end user. |
gotoVersCommit,character,CRANSource |
gotoVersCommit This is a low-level function not intended for direct use by the end user. |
gotoVersCommit,character,GitSource |
gotoVersCommit This is a low-level function not intended for direct use by the end user. |
gotoVersCommit,character,SVNSource |
gotoVersCommit This is a low-level function not intended for direct use by the end user. |
gotoVersCommit-method |
gotoVersCommit This is a low-level function not intended for direct use by the end user. |
lazyRepo |
lazyRepo |
lazyRepo,character,PkgManifest |
lazyRepo |
lazyRepo,character,SessionManifest |
lazyRepo |
lazyRepo,PkgManifest,ANY |
lazyRepo |
lazyRepo,SessionManifest,ANY |
lazyRepo |
lazyRepo-method |
lazyRepo |
libManifest |
libManifest Create a Session- or PkgManifest for the contents of a switchr library. |
libManifest,character |
libManifest Create a Session- or PkgManifest for the contents of a switchr library. |
libManifest,missing |
libManifest Create a Session- or PkgManifest for the contents of a switchr library. |
libManifest,SwitchrCtx |
libManifest Create a Session- or PkgManifest for the contents of a switchr library. |
libManifest-method |
libManifest Create a Session- or PkgManifest for the contents of a switchr library. |
LibraryProfile-class |
LibraryProfile (experimental) Currently unused/under heavy development. |
library_paths |
library_paths |
library_paths,SwitchrCtx |
library_paths |
library_paths-method |
library_paths |
loadGRAN |
Load a GRAN repo package |
loadManifest |
loadManifest |
LocalSource-class |
PkgSource An object representing the source location of a package. This is a virtual used exlusively through its subclasses, which are used to differentiate the different types of package source locations. |
locatePkgVersion |
locatePkgVersion |
location |
location generic Retreive the directory associated with an object |
location-method |
location generic Retreive the directory associated with an object |
logfun |
Get or set the logging function in an object associated with a SwitchrParam |
logfun,SwitchrParam |
Get or set the logging function in an object associated with a SwitchrParam |
logfun-method |
Get or set the logging function in an object associated with a SwitchrParam |
logfun<- |
Get or set the logging function in an object associated with a SwitchrParam |
logfun<-,SwitchrParam |
Get or set the logging function in an object associated with a SwitchrParam |
logfun<--method |
Get or set the logging function in an object associated with a SwitchrParam |
makeBiocSVNURL |
Make a Bioconductor SVN url for a package |
makeFileURL |
make file url |
makeLibraryCtx |
makeLibraryCtx |
makeManifest |
Manifest constructor Create a package manifest |
makePkgCheckout |
Create a checkout of a package and all it's dependencies from a manifest |
makePkgDir |
makePkgDir This is an internal function not intended to be called directly by end users |
makePkgDir,ANY,ANY |
makePkgDir This is an internal function not intended to be called directly by end users |
makePkgDir,ANY,BiocSource |
makePkgDir This is an internal function not intended to be called directly by end users |
makePkgDir,ANY,CRANSource |
makePkgDir This is an internal function not intended to be called directly by end users |
makePkgDir,ANY,GithubSource |
makePkgDir This is an internal function not intended to be called directly by end users |
makePkgDir,ANY,GitSource |
makePkgDir This is an internal function not intended to be called directly by end users |
makePkgDir,ANY,LocalSource |
makePkgDir This is an internal function not intended to be called directly by end users |
makePkgDir,ANY,SVNSource |
makePkgDir This is an internal function not intended to be called directly by end users |
makePkgDir,ANY,TarballSource |
makePkgDir This is an internal function not intended to be called directly by end users |
makePkgDir-method |
makePkgDir This is an internal function not intended to be called directly by end users |
makeSeedMan |
makeSeedMan |
makeSeedMan,missing |
makeSeedMan |
makeSeedMan,parsedSessionInfo |
makeSeedMan |
makeSeedMan,sessionInfo |
makeSeedMan |
makeSeedMan-method |
makeSeedMan |
makeSource |
Create a PkgSource object for a package |
manifest |
Get or set the manifest associated with an object |
manifest,SessionManifest |
Get or set the manifest associated with an object |
manifest-method |
Get or set the manifest associated with an object |
manifest<- |
Get or set the manifest associated with an object |
manifest<-,SessionManifest |
Get or set the manifest associated with an object |
manifest<--method |
Get or set the manifest associated with an object |
ManifestRow |
ManifestRow |
manifest_df |
manifest_df |
manifest_df,PkgManifest |
manifest_df |
manifest_df,SessionManifest |
manifest_df |
manifest_df-method |
manifest_df |
manifest_df<- |
manifest_df |
manifest_df<-,PkgManifest |
manifest_df |
manifest_df<-,SessionManifest |
manifest_df |
manifest_df<--method |
manifest_df |
packages |
List the packages installed in a switchr context (library) |
packages,SwitchrCtx |
List the packages installed in a switchr context (library) |
packages-method |
List the packages installed in a switchr context (library) |
parsedSessionInfo-class |
Parsed sessionInfo output |
parseSessionInfoString |
Parse text output from printing SessionInfo objects |
PkgManifest |
PkgManifest |
PkgManifest-class |
PkgManifest |
pkgname |
Get or set the package name associated with a Package Source |
pkgname,PkgSource |
Get or set the package name associated with a Package Source |
pkgname-method |
Get or set the package name associated with a Package Source |
pkgname<- |
Get or set the package name associated with a Package Source |
pkgname<-,PkgSource |
Get or set the package name associated with a Package Source |
pkgname<--method |
Get or set the package name associated with a Package Source |
PkgSource-class |
PkgSource An object representing the source location of a package. This is a virtual used exlusively through its subclasses, which are used to differentiate the different types of package source locations. |
publishManifest |
publishManifest |
publishManifest,missing,ANY |
publishManifest |
publishManifest,PkgManifest,character |
publishManifest |
publishManifest,SessionManifest,character |
publishManifest |
publishManifest,SwitchrCtx,ANY |
publishManifest |
publishManifest-method |
publishManifest |
SessionManifest |
SessionManifest |
SessionManifest-class |
SessionManifest |
shell_timing |
Get or set the number of seconds to wait between successive shell commands |
shell_timing,SwitchrParam |
Get or set the number of seconds to wait between successive shell commands |
shell_timing-method |
Get or set the number of seconds to wait between successive shell commands |
shell_timing<- |
Get or set the number of seconds to wait between successive shell commands |
shell_timing<-,SwitchrParam |
Get or set the number of seconds to wait between successive shell commands |
shell_timing<--method |
Get or set the number of seconds to wait between successive shell commands |
sh_init_script |
Set or Retrieve the shell initialization script for an object |
sh_init_script,SwitchrParam |
Set or Retrieve the shell initialization script for an object |
sh_init_script-method |
Set or Retrieve the shell initialization script for an object |
sh_init_script<- |
Set or Retrieve the shell initialization script for an object |
sh_init_script<-,SwitchrParam,ANY |
Set or Retrieve the shell initialization script for an object |
sh_init_script<--method |
Set or Retrieve the shell initialization script for an object |
subdir |
subdir |
subdir,PkgSource |
subdir |
subdir-method |
subdir |
subdir<- |
subdir |
subdir<-,PkgSource |
subdir |
subdir<--method |
subdir |
SVNSource-class |
PkgSource An object representing the source location of a package. This is a virtual used exlusively through its subclasses, which are used to differentiate the different types of package source locations. |
switchBack |
switchBack |
switchDeps |
switchrDeps The base packages, as well as switchr and its dependencies. |
switchrBaseDir |
Get or set the base directory for switchr libraries |
SwitchrCtx |
SwitchrCtx |
SwitchrCtx-class |
SwitchrCtx |
switchrDontUnload |
Get or set the packages to not unload when flushing the system |
switchrManifest |
switchrManifest |
switchrNoUnload |
Skip unloading of packages in session |
SwitchrParam |
SwitchrParam A contstructor for a SwitchrParam object representing a number of common parameters understood by the switchr framework |
SwitchrParam-class |
SwitchrParam A contstructor for a SwitchrParam object representing a number of common parameters understood by the switchr framework |
switchTo |
switchTo |
switchTo,character,character |
switchTo |
switchTo,character,missing |
switchTo |
switchTo,character,PkgManifest |
switchTo |
switchTo,character,RepoSubset |
switchTo |
switchTo,character,SessionManifest |
switchTo |
switchTo,character,SwitchrCtx |
switchTo |
switchTo,SwitchrCtx,ANY |
switchTo |
switchTo-method |
switchTo |
system_w_init |
system_w_init |