| addPkg | addPkg |
| archive_retries | archive_retries |
| archive_timing | archive_timing |
| BiocDevel | BiocDevel |
| BiocRelease | BiocRelease |
| biocReposForVers | biocReposForVers |
| BiocSVNManifest | DEPCRECATED - 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 |
| findnewestpkg | Find newest packages in a package info data.frame |
| 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 |
| internal | Internal internet harness |
| lazyRepo | lazyRepo |
| libManifest | libManifest |
| librarypath | .libpaths2 |
| library_paths | library_paths |
| 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 |
| manifestFromCheckoutDir | Create Manifest from 'checkedout' directory containing many... |
| 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 |
| update_PACKAGES | update existing package repository |
| versions | versions_df |
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