Changes in version 0.11.4.2 Bugfixes o Fix bug that doesn't look for the DESCRIPTION file in a complex git repo Miscellaneous o Corrected typos in vignette Changes in version 0.10.7 Minor API changes o Rename Rcmd function to Rcmd2 to avoid conflict in R 3.3.* Miscellaneous o Gracefully handle expected failures of BiocSVNManifest test, on systems which choke on https svn urls. o No longer evaluate libManifest chunk in vignette due to problems on CRAN build system. Changes in version 0.10.0 API changes o addPkgs generic now has replace argument controlling behavior in case that the package already appears in the manifest. o New nrow generic and methods for PkgManifest and SessionManifest. o makeBiocSVNUrl now takes pkgtype argument and supports both software and experimental data packages. Bugfixes o Fix major bug which broke versioned package installation from CRAN archive. o download.packages2 utility function now has necessary type argument. o BiocSVNManifest now grabs the correct branch of the data repository when software_only is FALSE. o Reordered NEWS to be most-recent-first Changes in version 0.9.27 Minor API changes o export .libPaths2 Changes in version 0.9.26 Bugfixes o fix bug in updateSVN when user/password are not specified Changes in version 0.9.25 Bugfixes o Switch R system call to Rcmd in findPkgVersionInBioc o Fix code which determines bioconductor branch to search for exact bioc version. o Make download method defaults more robust (on systems without wget) Changes in version 0.9.23 Bugfixes o Fix svn update code by initializing args variable so function is not hit o Fix code in findSVNRev to use new system_w_init api Changes in version 0.9.21 API Changes o system_w_init not accepts args and env arguments a la system2, though ... still accepts system() based arguments, as that is called underneath o BiocSVNManifest now uses 'svn ls' rather than available.packages to populate the manifest. not_in_repo argument removed. Bugfixes o Updated Bioc devel and Bioc release version numbers o Fixed system calls which were failing on Windows o annotateDESC now protects against packages appearing in more than one place in the provided manifest Miscellaneous o Added basic testing for svn-based ops, including makePkgSource and BiocSVNManifest Changes in version 0.9.19 (2015-09-17) API changes o makeManifest() constructor now normalizes path for local packages in manifest Miscellaneous o disable git-based tests on build systems that don't have git installed Changes in version 0.9.18 (2015-09-02) Bugfixes o fix dependencies test. o fix documentation Changes in version 0.9.17 Bugfixes o fix problems related to git checkouts that were breaking tests (and functionality) in Windows API Changes o Add mustWork argument to normalizePath2, passthrough on Windows Changes in version 0.9.16 API Changes o Add shell_timing slot to SwitchrParam, and add accessor o Use shell_timing to split git commands o add experimental makePkgCheckout function Bugfixes o fix typo in git command o findPkgDir no longer takes a repo argument, which was unused. Changes in version 0.9.14 Bugfixes o further iteration on how git checkouts are updated. Changes in version 0.9.13 Bugfixes o refine how git existing git checkouts are updated. o Add testing of git-based makePkgDir and updateGit functions Changes in version 0.9.12 Bugfixes o Fix regression in publishManifest resulting in files which contain only the header comments Miscellaneous o Remove unnecessary usage of globalVariable to increase compatability with old R versions o Add requireNamespace2 for backwards compatability with old Rs, switch to using that throughout package o Add alternative definition of paste0 for backwards compatability with Rs old enough not to have it. Changes in version 0.9.11 Miscellaneous o We no longer use tools::package_dependencies to determine depedencies because it is relatively new and prevents switchr from installing in older Rs. Changes in version 0.9.10 (2015-07-02) Bugfixes o Fix regression(?) where specifying a SessionManifest seed for an existing library would force it to rebuild and reinstall everything in the seed. o Calling switchTo with a seed for library that already exists now invokes a message rather than a warning o We now import symbols from base packages (other than base) as per new R CMD check requirements. Changes in version 0.9.8 API changes o SessionManifest now defaults to defining a cohort of 0 specified package versions on top of the specified package manifest o Added head and tail methods for PkgManifest and SessionManifest objects o makeBiocSVNURL and related functions will now accept "devel" or "trunk" to indicate the current devel version. Default is now "devel" New features o Added BiocSVNManifest function which creates a manifest of all svn locations for Bioc packages for a specific release (or the current devel trunk). Bugfixes o Fix extraneous warning from dir.create call within lazyRepo when dir already exists o When specifying a package in switchrDontUnload, its (recursive) dependencies are now included also. o libManifest will no longer list base packages, as they are not installable in the normal sense. o lazyRepo ignores base packages o install_packages no longer builds a lazy repo when passed urls for existing repositories o empty calls to ManifestRow now correctly return an empty (0 row) manifest df, rather than a df with 1 row filled with NAs o crandb related methods (rVersionManifest and cranPkgVersManifest) now return SessionManifests rather than PkgManifests with tarball sources. o install_packages no longer prompts the user to select a CRAN mirror unnecessarily (bypass bug when avail is specified in install.packages) o Switched to dynamic determination of Bioc devel version using yaml across the whole package Changes in version 0.9.6 (2015-06-17) API changes o Installation will no longer fail if bioconductor.com/config.yaml is unreachable. In this case the package will attempt to read it when the package is loaded, and throw a warning if this fails as well. o makeFileURL and fileFromFileURL are now exported. Bugfixes o Fix transformation to and from file URLs in Windows (added regression test) Changes in version 0.9.4 (2015-06-06) Minor new features o Add a lazyRepo,PkgManifest,ANY convenience method for building a lazy repo of an entire manifest Bugfixes o Fix test for whether a url points to a repository to handle gist urls correctly o Fix handling of package checkout directories for Git branches o Fix typo strSplit -> strsplit o Fix gist-based manifest (url) support