Changes in version 0.11.4.2 (2017-05-24) ------------------------- Bugfixes * Fix bug that doesn't look for the DESCRIPTION file in a complex git repo Miscellaneous * Corrected typos in vignette Changes in version 0.10.7 (2016-05-10) ------------------------- Minor API changes * Rename Rcmd function to Rcmd2 to avoid conflict in R 3.3.* Miscellaneous * Gracefully handle expected failures of BiocSVNManifest test, on systems which choke on https svn urls. * No longer evaluate libManifest chunk in vignette due to problems on CRAN build system. Changes in version 0.10.0 (2016-05-04) ------------------------- API changes * addPkgs generic now has replace argument controlling behavior in case that the package already appears in the manifest. * New nrow generic and methods for PkgManifest and SessionManifest. * makeBiocSVNUrl now takes pkgtype argument and supports both software and experimental data packages. Bugfixes * Fix major bug which broke versioned package installation from CRAN archive. * download.packages2 utility function now has necessary type argument. * BiocSVNManifest now grabs the correct branch of the data repository when software_only is FALSE. * Reordered NEWS to be most-recent-first Changes in version 0.9.27 (2016-02-09) ------------------------- Minor API changes * export .libPaths2 Changes in version 0.9.26 (2016-02-09) ------------------------- Bugfixes * fix bug in updateSVN when user/password are not specified Changes in version 0.9.25 (2015-11-17) ------------------------- Bugfixes * Switch R system call to Rcmd in findPkgVersionInBioc * Fix code which determines bioconductor branch to search for exact bioc version. * Make download method defaults more robust (on systems without wget) Changes in version 0.9.23 (2015-11-17) ------------------------- Bugfixes * Fix svn update code by initializing args variable so function is not hit * Fix code in findSVNRev to use new system_w_init api Changes in version 0.9.21 (2015-10-20) ------------------------- API Changes * system_w_init not accepts args and env arguments a la system2, though ... still accepts system() based arguments, as that is called underneath * BiocSVNManifest now uses 'svn ls' rather than available.packages to populate the manifest. not_in_repo argument removed. Bugfixes * Updated Bioc devel and Bioc release version numbers * Fixed system calls which were failing on Windows * annotateDESC now protects against packages appearing in more than one place in the provided manifest Miscellaneous * Added basic testing for svn-based ops, including makePkgSource and BiocSVNManifest Changes in version 0.9.19 (2015-08-16) ------------------------- API changes * makeManifest() constructor now normalizes path for local packages in manifest Miscellaneous * disable git-based tests on build systems that don't have git installed Changes in version 0.9.18 (2015-04-08) ------------------------- Bugfixes * fix dependencies test. * fix documentation Changes in version 0.9.17 (2015-07-29) ------------------------- Bugfixes * fix problems related to git checkouts that were breaking tests (and functionality) in Windows API Changes * Add mustWork argument to normalizePath2, passthrough on Windows Changes in version 0.9.16 (2015-07-28) ------------------------- API Changes * Add shell_timing slot to SwitchrParam, and add accessor * Use shell_timing to split git commands * add experimental makePkgCheckout function Bugfixes * fix typo in git command * findPkgDir no longer takes a repo argument, which was unused. Changes in version 0.9.14 (2015-07-16) ------------------------- Bugfixes * further iteration on how git checkouts are updated. Changes in version 0.9.13 (2015-07-15) ------------------------- Bugfixes * refine how git existing git checkouts are updated. * Add testing of git-based makePkgDir and updateGit functions Changes in version 0.9.12 (2015-07-06) ------------------------- Bugfixes * Fix regression in publishManifest resulting in files which contain only the header comments Miscellaneous * Remove unnecessary usage of globalVariable to increase compatability with old R versions * Add requireNamespace2 for backwards compatability with old Rs, switch to using that throughout package * Add alternative definition of paste0 for backwards compatability with Rs old enough not to have it. Changes in version 0.9.11 (2015-07-06) ------------------------- Miscellaneous * 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 (2015-07-01) ------------------------- Bugfixes * Fix regression(?) where specifying a SessionManifest seed for an existing library would force it to rebuild and reinstall everything in the seed. * Calling switchTo with a seed for library that already exists now invokes a message rather than a warning * 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 * SessionManifest now defaults to defining a cohort of 0 specified package versions on top of the specified package manifest * Added head and tail methods for PkgManifest and SessionManifest objects * makeBiocSVNURL and related functions will now accept "devel" or "trunk" to indicate the current devel version. Default is now "devel" New features * Added BiocSVNManifest function which creates a manifest of all svn locations for Bioc packages for a specific release (or the current devel trunk). Bugfixes * Fix extraneous warning from dir.create call within lazyRepo when dir already exists * When specifying a package in switchrDontUnload, its (recursive) dependencies are now included also. * libManifest will no longer list base packages, as they are not installable in the normal sense. * lazyRepo ignores base packages * install_packages no longer builds a lazy repo when passed urls for existing repositories * empty calls to ManifestRow now correctly return an empty (0 row) manifest df, rather than a df with 1 row filled with NAs * crandb related methods (rVersionManifest and cranPkgVersManifest) now return SessionManifests rather than PkgManifests with tarball sources. * install_packages no longer prompts the user to select a CRAN mirror unnecessarily (bypass bug when avail is specified in install.packages) * Switched to dynamic determination of Bioc devel version using yaml across the whole package Changes in version 0.9.6 (2015-06-16) ------------------------ API changes * 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. * makeFileURL and fileFromFileURL are now exported. Bugfixes * Fix transformation to and from file URLs in Windows (added regression test) Changes in version 0.9.4 (2015-06-05) ------------------------ Minor new features * Add a lazyRepo,PkgManifest,ANY convenience method for building a lazy repo of an entire manifest Bugfixes * Fix test for whether a url points to a repository to handle gist urls correctly * Fix handling of package checkout directories for Git branches * Fix typo strSplit -> strsplit * Fix gist-based manifest (url) support