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

Provides an abstraction for managing, installing, and switching between sets of installed R packages. This allows users to maintain multiple package libraries simultaneously, e.g. to maintain strict, package-version-specific reproducibility of many analyses, or work within a development/production release paradigm. Introduces a generalized package installation process which supports multiple repository and non-repository sources and tracks package provenance.

Install the latest version of this package by entering the following in R:
install.packages("switchr")
AuthorGabriel Becker[aut, cre]
Date of publication2017-01-12 23:53:28
MaintainerGabriel Becker <becker.gabriel@gene.com>
LicenseArtistic-2.0
Version0.11.2
https://github.com/gmbecker/switchr

View on CRAN

Man pages

addPkg: addPkg

archive_retries: archive_retries

archive_timing: archive_timing

BiocDevel: BiocDevel

BiocRelease: BiocRelease

biocReposForVers: biocReposForVers

BiocSVNManifest: Create a manifest of Bioc SVN locations

BiocVers: BiocVers

branch: branch

checkIsPkgDir: Check if a directory contains package sources

cmethods: cmethods

cranPkgVersManifest: cranPkgVersManifest

currentCompEnv: currentCompEnv

defaultRepos: defaultRepos

dep_repos: dep_repos

dl_method: dl_method

errorOrNonZero: Identify error states from R or external programs

fileFromFileURL: Get path from file URL

findPkgDir: Find a package directory within an SCM checkout

findPkgVersionInRepo: findPkgVersionInRepo

flushSession: flushSession

full_libpaths: full_libpaths

getPkgDir: Construct pockage directory path

GithubManifest: GithubManifest

gotoVersCommit: gotoVersCommit

headtail: Head and tail operations on manifests

install: install_packages

lazyRepo: lazyRepo

libManifest: libManifest

librarypath: .libpaths2

library_paths: library_paths

LibraryProfile-class: LibraryProfile (experimental)

loadGRAN: Load a GRAN repo package

loadManifest: loadManifest

locatePkgVersion: locatePkgVersion

location-methods: location

logfun: logfun

makeBiocSVNURL: Make a Bioconductor SVN url for a package

makeFileURL: make file url

makeLibraryCtx: makeLibraryCtx

makeManifest: Manifest constructor

makePkgCheckout: Create a checkout of a package and all it's dependencies from...

makePkgDir: makePkgDir

makeSeedMan: makeSeedMan

makeSource: Create a PkgSource object for a package

manifest_df: manifest_df

manifest_methods: Get or set the manifest associated with an object

ManifestRow: ManifestRow

normalizePath2: normalizePath2

notrack: Notrack directory

nrow: Number of rows

packages: packages

parsedSessionInfo-class: Parsed sessionInfo output

parseSessionInfoString: Parse text output from printing SessionInfo objects

PkgManifest: PkgManifest

pkgname: pkgname

PkgSource-class: PkgSource

publishManifest: publishManifest

removeLib: removeLib

RepoSubset: RepoSubset

rVersionManifest: rVersionManifest

SessionManifest: SessionManifest

shell_timing: Get or set the number of seconds to wait between successive...

sh_init: shell init

subdir: subdir

switchBack: switchBack

switchDeps: switchrDeps

switchrBaseDir: Get or set the base directory for switchr libraries

SwitchrCtx: SwitchrCtx

switchrDontUnload: Get or set packages to not unload when flushing the system

switchrManifest: switchrManifest

switchrNoUnload: Skip unloading of packages in session

SwitchrParam: SwitchrParam

switchTo: switchTo

system_w_init: system_w_init

updateManifest: updateManifest

versions: versions_df

Functions

addPkg Man page
addPkg,PkgManifest Man page
addPkg,PkgManifest-method Man page
addPkg,SessionManifest Man page
addPkg,SessionManifest-method Man page
archive_retries Man page
archive_retries<- Man page
archive_retries<-,SwitchrParam Man page
archive_retries,SwitchrParam Man page
archive_retries<-,SwitchrParam-method Man page
archive_retries,SwitchrParam-method Man page
archive_timing Man page
archive_timing<- Man page
archive_timing<-,SwitchrParam Man page
archive_timing,SwitchrParam Man page
archive_timing<-,SwitchrParam-method Man page
archive_timing,SwitchrParam-method Man page
BiocDevel Man page
BiocRelease Man page
biocReposForVers Man page
BiocSource-class Man page
BiocSVNManifest Man page
BiocVers Man page
branch Man page
branch<- Man page
branch<-,PkgSource Man page
branch,PkgSource Man page
branch<-,PkgSource-method Man page
branch,PkgSource-method Man page
checkIsPkgDir Man page
c,PkgManifest-method Man page
cranPkgVersManifest Man page
CRANSource-class Man page
c,SessionManifest-method Man page
currentCompEnv Man page
CVSSource-class Man page
defaultRepos Man page
dep_repos Man page
dep_repos<- Man page
dep_repos<-,PkgManifest Man page
dep_repos,PkgManifest Man page
dep_repos<-,PkgManifest-method Man page
dep_repos,PkgManifest-method Man page
dep_repos<-,SessionManifest Man page
dep_repos,SessionManifest Man page
dep_repos<-,SessionManifest-method Man page
dep_repos,SessionManifest-method Man page
dl_method Man page
dl_method<- Man page
dl_method<-,SwitchrParam Man page
dl_method,SwitchrParam Man page
dl_method<-,SwitchrParam-method Man page
dl_method,SwitchrParam-method Man page
errorOrNonZero Man page
fileFromFileURL Man page
findPkgDir Man page
findPkgVersionInRepo Man page
findPkgVersionInRepo,character Man page
findPkgVersionInRepo,character-method Man page
findPkgVersionInRepo,NULL Man page
findPkgVersionInRepo,NULL-method Man page
flushSession Man page
full_libpaths Man page
full_libpaths,SwitchrCtx Man page
full_libpaths,SwitchrCtx-method Man page
getPkgDir Man page
GithubManifest Man page
GithubSource-class Man page
GitSource-class Man page
gotoVersCommit Man page
gotoVersCommit,character,BiocSource Man page
gotoVersCommit,character,BiocSource-method Man page
gotoVersCommit,character,CRANSource Man page
gotoVersCommit,character,CRANSource-method Man page
gotoVersCommit,character,GitSource Man page
gotoVersCommit,character,GitSource-method Man page
gotoVersCommit,character,SVNSource Man page
gotoVersCommit,character,SVNSource-method Man page
head Man page
head,PkgManifest Man page
head,PkgManifest-method Man page
head,SessionManifest Man page
head,SessionManifest-method Man page
install_packages Man page
install_packages,character,character Man page
install_packages,character,character-method Man page
install_packages,character,missing Man page
install_packages,character,missing-method Man page
install_packages,character,PkgManifest Man page
install_packages,character,PkgManifest-method Man page
install_packages,character,SessionManifest Man page
install_packages,character,SessionManifest-method Man page
install_packages,SessionManifest,ANY Man page
install_packages,SessionManifest,ANY-method Man page
lazyRepo Man page
lazyRepo,character,PkgManifest Man page
lazyRepo,character,PkgManifest-method Man page
lazyRepo,character,SessionManifest Man page
lazyRepo,character,SessionManifest-method Man page
lazyRepo,PkgManifest,ANY Man page
lazyRepo,PkgManifest,ANY-method Man page
lazyRepo,SessionManifest,ANY Man page
lazyRepo,SessionManifest,ANY-method Man page
libManifest Man page
libManifest,character Man page
libManifest,character-method Man page
libManifest,missing Man page
libManifest,missing-method Man page
libManifest,SwitchrCtx Man page
libManifest,SwitchrCtx-method Man page
.libPaths2 Man page
library_paths Man page
library_paths,SwitchrCtx Man page
library_paths,SwitchrCtx-method Man page
LibraryProfile-class Man page
loadGRAN Man page
loadManifest Man page
LocalSource-class Man page
locatePkgVersion Man page
location Man page
location,PkgSource-method Man page
logfun Man page
logfun<- Man page
logfun<-,SwitchrParam Man page
logfun,SwitchrParam Man page
logfun<-,SwitchrParam-method Man page
logfun,SwitchrParam-method Man page
makeBiocSVNURL Man page
makeFileURL Man page
makeLibraryCtx Man page
makeManifest Man page
makePkgCheckout Man page
makePkgDir Man page
makePkgDir,ANY,ANY Man page
makePkgDir,ANY,ANY-method Man page
makePkgDir,ANY,BiocSource Man page
makePkgDir,ANY,BiocSource-method Man page
makePkgDir,ANY,CRANSource Man page
makePkgDir,ANY,CRANSource-method Man page
makePkgDir,ANY,GithubSource Man page
makePkgDir,ANY,GithubSource-method Man page
makePkgDir,ANY,GitSource Man page
makePkgDir,ANY,GitSource-method Man page
makePkgDir,ANY,LocalSource Man page
makePkgDir,ANY,LocalSource-method Man page
makePkgDir,ANY,SVNSource Man page
makePkgDir,ANY,SVNSource-method Man page
makePkgDir,ANY,TarballSource Man page
makePkgDir,ANY,TarballSource-method Man page
makeSeedMan Man page
makeSeedMan,missing Man page
makeSeedMan,missing-method Man page
makeSeedMan,parsedSessionInfo Man page
makeSeedMan,parsedSessionInfo-method Man page
makeSeedMan,sessionInfo Man page
makeSeedMan,sessionInfo-method Man page
makeSource Man page
manifest Man page
manifest<- Man page
manifest_df Man page
manifest_df<- Man page
manifest_df<-,PkgManifest Man page
manifest_df,PkgManifest Man page
manifest_df<-,PkgManifest-method Man page
manifest_df,PkgManifest-method Man page
manifest_df<-,SessionManifest Man page
manifest_df,SessionManifest Man page
manifest_df<-,SessionManifest-method Man page
manifest_df,SessionManifest-method Man page
ManifestRow Man page
manifest<-,SessionManifest Man page
manifest,SessionManifest Man page
manifest<-,SessionManifest-method Man page
manifest,SessionManifest-method Man page
normalizePath2 Man page
notrack Man page
notrack,NULL Man page
notrack,NULL-method Man page
nrow Man page
nrow,PkgManifest Man page
nrow,PkgManifest-method Man page
nrow,SessionManifest Man page
nrow,SessionManifest-method Man page
packages Man page
packages,SwitchrCtx Man page
packages,SwitchrCtx-method Man page
parsedSessionInfo-class Man page
parseSessionInfoString Man page
PkgManifest Man page
PkgManifest-class Man page
pkgname Man page
pkgname<- Man page
pkgname<-,PkgSource Man page
pkgname,PkgSource Man page
pkgname<-,PkgSource-method Man page
pkgname,PkgSource-method Man page
PkgSource-class Man page
publishManifest Man page
publishManifest,missing,ANY Man page
publishManifest,missing,ANY-method Man page
publishManifest,PkgManifest,character Man page
publishManifest,PkgManifest,character-method Man page
publishManifest,SessionManifest,character Man page
publishManifest,SessionManifest,character-method Man page
publishManifest,SwitchrCtx,ANY Man page
publishManifest,SwitchrCtx,ANY-method Man page
removeLib Man page
RepoSubset Man page
RepoSubset-class Man page
rVersionManifest Man page
SessionManifest Man page
SessionManifest-class Man page
shell_timing Man page
shell_timing<- Man page
shell_timing<-,SwitchrParam Man page
shell_timing,SwitchrParam Man page
shell_timing<-,SwitchrParam-method Man page
shell_timing,SwitchrParam-method Man page
sh_init_script Man page
sh_init_script<- Man page
sh_init_script,SwitchrParam Man page
sh_init_script<-,SwitchrParam,ANY Man page
sh_init_script<-,SwitchrParam-method Man page
sh_init_script,SwitchrParam-method Man page
subdir Man page
subdir<- Man page
subdir<-,PkgSource Man page
subdir,PkgSource Man page
subdir<-,PkgSource-method Man page
subdir,PkgSource-method Man page
SVNSource-class Man page
switchBack Man page
switchDeps Man page
switchrBaseDir Man page
SwitchrCtx Man page
SwitchrCtx-class Man page
switchrDontUnload Man page
switchrManifest Man page
switchrNoUnload Man page
SwitchrParam Man page
SwitchrParam-class Man page
switchTo Man page
switchTo,character,character Man page
switchTo,character,character-method Man page
switchTo,character,missing Man page
switchTo,character,missing-method Man page
switchTo,character,PkgManifest Man page
switchTo,character,PkgManifest-method Man page
switchTo,character,RepoSubset Man page
switchTo,character,RepoSubset-method Man page
switchTo,character,SessionManifest Man page
switchTo,character,SessionManifest-method Man page
switchTo,character,SwitchrCtx Man page
switchTo,character,SwitchrCtx-method Man page
switchTo,SwitchrCtx,ANY Man page
switchTo,SwitchrCtx,ANY-method Man page
system_w_init Man page
tail Man page
tail,PkgManifest Man page
tail,PkgManifest-method Man page
tail,SessionManifest Man page
tail,SessionManifest-method Man page
TarballSource-class Man page
updateManifest Man page
versions_df Man page
versions_df<- Man page
versions_df<-,SessionManifest Man page
versions_df,SessionManifest Man page
versions_df<-,SessionManifest-method Man page
versions_df,SessionManifest-method Man page

Files

inst
inst/examples
inst/examples/lazyRepo.R inst/examples/crandb.R inst/examples/sessionInfo.R inst/localcheckoutest.R
inst/talks
inst/talks/BarugLightning.org
inst/talks/JSM2015.pdf
inst/talks/JSM2015.org
inst/ropensciman.R inst/testlimma.R
inst/doc
inst/doc/switchrvign.Rnw
inst/doc/switchrvign.R
inst/doc/switchrvign.pdf
inst/xtable.R
tests
tests/winpath.R
NAMESPACE
NEWS
R
R/AllClasses.R R/lazyRepo.R R/Utilities.R R/show-methods.R R/accessors.R R/removeLibrary.R R/saveManifest.R R/SwitchrParam.R R/findCtx.R R/loadManifest.R R/biocversion.R R/conditionalCode.R R/profile.R R/SVNFunctions.R R/head-methods.R R/loadGRAN.R R/methods.R R/crandbtmp.R R/retrievePkgVersion.R R/allGenerics.R R/dodeps.R R/makeLibraryCtx.R R/makePkgSourceDir-methods.R R/GitFunctions.R R/cmethods.R R/sessionInfo.R R/Install.R R/manifestFromLib.R R/makeCheckout.R R/biocManifest.R R/manifest.R R/zzz.R R/makeBiocVersions.R R/flushSession.R R/annotateDESCs.R
vignettes
vignettes/switchrvign.Rnw
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/switchrBaseDir.Rd man/archive_timing.Rd man/pkgname.Rd man/lazyRepo.Rd man/RepoSubset.Rd man/install.Rd man/biocReposForVers.Rd man/versions.Rd man/fileFromFileURL.Rd man/ManifestRow.Rd man/subdir.Rd man/PkgSource-class.Rd man/checkIsPkgDir.Rd man/makeManifest.Rd man/dl_method.Rd man/makeSource.Rd man/makePkgDir.Rd man/getPkgDir.Rd man/switchrDontUnload.Rd man/notrack.Rd man/system_w_init.Rd man/manifest_methods.Rd man/addPkg.Rd man/makeFileURL.Rd man/SwitchrParam.Rd man/logfun.Rd man/currentCompEnv.Rd man/loadGRAN.Rd man/BiocDevel.Rd man/findPkgDir.Rd man/library_paths.Rd man/parseSessionInfoString.Rd man/cranPkgVersManifest.Rd man/nrow.Rd man/BiocSVNManifest.Rd man/GithubManifest.Rd man/switchTo.Rd man/switchrManifest.Rd man/removeLib.Rd man/libManifest.Rd man/normalizePath2.Rd man/locatePkgVersion.Rd man/makePkgCheckout.Rd man/BiocRelease.Rd man/cmethods.Rd man/headtail.Rd man/makeLibraryCtx.Rd man/defaultRepos.Rd man/LibraryProfile-class.Rd man/manifest_df.Rd man/loadManifest.Rd man/PkgManifest.Rd man/full_libpaths.Rd man/switchBack.Rd man/BiocVers.Rd man/packages.Rd man/branch.Rd man/updateManifest.Rd man/location-methods.Rd man/archive_retries.Rd man/parsedSessionInfo-class.Rd man/dep_repos.Rd man/switchrNoUnload.Rd man/errorOrNonZero.Rd man/SwitchrCtx.Rd man/gotoVersCommit.Rd man/shell_timing.Rd man/rVersionManifest.Rd man/makeSeedMan.Rd man/sh_init.Rd man/SessionManifest.Rd man/flushSession.Rd man/findPkgVersionInRepo.Rd man/publishManifest.Rd man/switchDeps.Rd man/makeBiocSVNURL.Rd man/librarypath.Rd

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All documentation is copyright its authors; we didn't write any of that.