NEWS

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switchr 0.11.4.2

Bugfixes

• Fix bug that doesn't look for the DESCRIPTION file in a complex git repo

Miscellaneous

• Corrected typos in vignette

switchr 0.10.7

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.

switchr 0.10.0

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

switchr 0.9.27

Minor API changes

• export .libPaths2

switchr 0.9.26

Bugfixes

• fix bug in updateSVN when user/password are not specified

switchr 0.9.25

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)

switchr 0.9.23

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

switchr 0.9.21

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

switchr 0.9.19 (2015-09-17)

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

switchr 0.9.18 (2015-09-02)

Bugfixes

• fix dependencies test.
• fix documentation

switchr 0.9.17

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

switchr 0.9.16

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.

switchr 0.9.14

Bugfixes

• further iteration on how git checkouts are updated.

switchr 0.9.13

Bugfixes

• refine how git existing git checkouts are updated.
• Add testing of git-based makePkgDir and updateGit functions

switchr 0.9.12

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.

switchr 0.9.11

Miscellaneous

• We no longer use tools::package_dependencies to determine depedencies because it is relatively new and prevents switchr from installing in older Rs.

switchr 0.9.10 (2015-07-02)

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.

switchr 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

switchr 0.9.6 (2015-06-17)

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)

switchr 0.9.4 (2015-06-06)

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