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

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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.

Author
Gabriel Becker[aut, cre]
Date of publication
2016-10-25 00:18:35
Maintainer
Gabriel Becker <becker.gabriel@gene.com>
License
Artistic-2.0
Version
0.11.0
URLs

View on CRAN

Man pages

addPkg
Add a package to an object associated with a manifest
archive_retries
archive_retries
archive_timing
archive_timing
BiocDevel
BiocDevel
BiocRelease
BiocRelease
biocReposForVers
biocReposForVers
BiocSVNManifest
Create a manifest of Bioc SVN locations
BiocVers
BiocVers A constructor for creating a RepoSubset object for a...
branch
Get or set the branch associated with a Package Source
checkIsPkgDir
Check if a directory contains package sources
cmethods
cmethods Combine 2 or more manifests of the same type...
cranPkgVersManifest
cranPkgVersManifest Create a Pkg manifest which points to...
currentCompEnv
currentCompEnv
defaultRepos
defaultRepos
dep_repos
dep_repos
dl_method
Get or set the download method for retreiving files.
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 Unload currently loaded packages from the...
full_libpaths
full_libpaths
getPkgDir
Construct pockage directory path
GithubManifest
GithubManifest
gotoVersCommit
gotoVersCommit This is a low-level function not intended for...
headtail
Head and tail operations on manifests
install
install_packages
lazyRepo
lazyRepo
libManifest
libManifest Create a Session- or PkgManifest for the contents...
librarypath
.libpaths2
library_paths
library_paths
LibraryProfile-class
LibraryProfile (experimental) Currently unused/under heavy...
loadGRAN
Load a GRAN repo package
loadManifest
loadManifest
locatePkgVersion
locatePkgVersion
location-methods
location generic Retreive the directory associated with an...
logfun
Get or set the logging function in an object associated with...
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...
makePkgDir
makePkgDir This is an internal function not intended to be...
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
List the packages installed in a switchr context (library)
parsedSessionInfo-class
Parsed sessionInfo output
parseSessionInfoString
Parse text output from printing SessionInfo objects
PkgManifest
PkgManifest
pkgname
Get or set the package name associated with a Package Source
PkgSource-class
PkgSource An object representing the source location of a...
publishManifest
publishManifest
removeLib
removeLib Remove a switchr library and update the manifest of...
RepoSubset
RepoSubset
rVersionManifest
rVersionManifest Create a Pkg manifest which points to...
SessionManifest
SessionManifest
shell_timing
Get or set the number of seconds to wait between successive...
sh_init
Set or Retrieve the shell initialization script for an object
subdir
subdir
switchBack
switchBack
switchDeps
switchrDeps The base packages, as well as switchr and its...
switchrBaseDir
Get or set the base directory for switchr libraries
SwitchrCtx
SwitchrCtx
switchrDontUnload
Get or set the packages to not unload when flushing the...
switchrManifest
switchrManifest
switchrNoUnload
Skip unloading of packages in session
SwitchrParam
SwitchrParam A contstructor for a SwitchrParam object...
switchTo
switchTo
system_w_init
system_w_init
updateManifest
updateManifest
versions
versions_df

Files in this package

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