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