Installing, Managing, and Switching Between Distinct Sets of Installed Packages


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Documentation for package ‘switchr’ version 0.9.19

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A B C D E F G H I L M N P R S T U V

-- A --

addPkg Add a package to an object associated with a manifest
addPkg,PkgManifest Add a package to an object associated with a manifest
addPkg,SessionManifest Add a package to an object associated with a manifest
addPkg-method Add a package to an object associated with a manifest
archive_retries archive_retries
archive_retries,SwitchrParam archive_retries
archive_retries-method archive_retries
archive_retries<- archive_retries
archive_retries<-,SwitchrParam archive_retries
archive_retries<--method archive_retries
archive_timing Get or set the number of seconds to wait after trying to retrieve a file from the CRAN Archive.
archive_timing,SwitchrParam Get or set the number of seconds to wait after trying to retrieve a file from the CRAN Archive.
archive_timing-method Get or set the number of seconds to wait after trying to retrieve a file from the CRAN Archive.
archive_timing<- Get or set the number of seconds to wait after trying to retrieve a file from the CRAN Archive.
archive_timing<-,SwitchrParam Get or set the number of seconds to wait after trying to retrieve a file from the CRAN Archive.
archive_timing<--method Get or set the number of seconds to wait after trying to retrieve a file from the CRAN Archive.

-- B --

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 --

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.

-- D --

defaultRepos defaultRepos
dep_repos dep_repos
dep_repos,PkgManifest dep_repos
dep_repos,SessionManifest dep_repos
dep_repos-method dep_repos
dep_repos<- dep_repos
dep_repos<-,PkgManifest dep_repos
dep_repos<-,SessionManifest dep_repos
dep_repos<--method dep_repos
dl_method Get or set the download method for retreiving files.
dl_method,SwitchrParam Get or set the download method for retreiving files.
dl_method-method Get or set the download method for retreiving files.
dl_method<- Get or set the download method for retreiving files.
dl_method<-,SwitchrParam Get or set the download method for retreiving files.
dl_method<--method Get or set the download method for retreiving files.

-- E --

errorOrNonZero Identify error states from R or external programs

-- F --

fileFromFileURL Get path from file URL
findPkgDir Find a package directory within an SCM checkout
findPkgVersionInRepo findPkgVersionInRepo
findPkgVersionInRepo,character findPkgVersionInRepo
findPkgVersionInRepo,NULL findPkgVersionInRepo
findPkgVersionInRepo-method findPkgVersionInRepo
flushSession flushSession Unload currently loaded packages from the current R session
full_libpaths full_libpaths
full_libpaths,SwitchrCtx full_libpaths
full_libpaths-method full_libpaths

-- G --

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.

-- H --

head Head and tail operations on manifests
head,PkgManifest Head and tail operations on manifests
head,SessionManifest Head and tail operations on manifests
head-method Head and tail operations on manifests

-- I --

install_packages install_packages
install_packages,character,character install_packages
install_packages,character,missing install_packages
install_packages,character,PkgManifest install_packages
install_packages,character,SessionManifest install_packages
install_packages,SessionManifest,ANY install_packages
install_packages-method install_packages

-- L --

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

-- M --

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

-- N --

normalizePath2 normalizePath2
notrack Notrack directory
notrack,NULL Notrack directory
notrack-method Notrack directory

-- P --

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

-- R --

Rcmd R executable
removeLib removeLib Remove a switchr library and update the manifest of existing libraries
RepoSubset RepoSubset
RepoSubset-class RepoSubset
rVersionManifest rVersionManifest Create a Pkg manifest which points to tarballs representing the cohort of packages associated with a particular release of R

-- S --

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

-- T --

tail Head and tail operations on manifests
tail,PkgManifest Head and tail operations on manifests
tail,SessionManifest Head and tail operations on manifests
tail-method Head and tail operations on manifests
TarballSource-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.

-- U --

updateManifest updateManifest

-- V --

versions_df versions_df
versions_df,SessionManifest versions_df
versions_df-method versions_df
versions_df<- versions_df
versions_df<-,SessionManifest versions_df
versions_df<--method versions_df