Changelog 0.2

bb8 0.2.0 (2019-10-20)

  • Added install, which wraps BiocManager::install with some improved defaults for Mike’s usage.
  • Added updatePackages, which wraps BiocManager::install and remotes::update_packages with some improved defaults.
  • Rexporting additional useful functions that get loaded by default in an interactive R session. See Mike’s corresponding Rprofile dotfile.
  • Package doesn’t load any other additional packages as dependencies, to keep loading super fast in a new R session.

bb8 0.2.1 (2019-10-23)

  • Added killAll function, which calls pkill rsession internally.
  • updateDeps: Now attempts to update “Enhances”, “LinkingTo”, and “Suggests” by default.
  • Consistently using system2 instead of system internally.
  • Added getPackageVersion, which gets current version of a GitHub package.
  • Added isInstalled, which checks against installed.packages return.

bb8 0.2.2 (2019-10-30)

  • Added more useful interactive reexports, including pipes.

bb8 0.2.3 (2019-11-19)

  • Updated package documentation to support roxygen2 7.0 update.
  • Added useful gh, locate, and remotes reexports.

bb8 0.2.4 (2019-12-04)

bb8 0.2.5 (2020-01-07)

  • Removed lookup package from reexports, to avoid accidental installation of GitHub versions that cause BiocManager::valid() check to fail.

bb8 0.2.6 (2020-01-18)

  • Updated BiocCheck reexport to not require biocViews in DESCRIPTION by default. This makes CI checks on non-Bioconductor packages destined for CRAN not error.

bb8 0.2.7 (2020-01-31)

  • rcmdcheck now uses --as-cran flag automatically.
  • Updated import to use pipette instead of brio.

bb8 0.2.8 (2020-04-12)

New functions

  • installGitHub: Install function that allows for versioned package installs without requiring GITHUB_PAT variable to be set. Intended for use inside Docker images. Otherwise, use remotes::install_github for interactive installs.

Major changes

  • Attempted to rework and simplify internal code, using acidbase and goalie as dependnecies. May revert back to no import approach.

bb8 0.2.9 (2020-04-12)

Major changes

  • Revert back to approach where package doesn’t import any dependencies via Imports, instead only using Suggests. This allows for package update calls inside Travis CI checks and Docker images to work more consistently.

bb8 0.2.10 (2020-04-12)

Minor changes

  • installGitHub: Bug fix for JSON parsing compability across Linux and macOS.

bb8 0.2.11 (2020-04-13)

Minor changes

  • install: Bug fix for systems lacking BiocManager or remotes packages. These dependencies are now installed in the fly if missing.

bb8 0.2.12 (2020-04-13)

Minor changes

  • install: Another bug fix. Switching from vapply to lapply internally to capture return from BiocManager, as this output can vary.

bb8 0.2.13 (2020-05-12)

Minor changes

  • printComment: Added width parameter. This allows for improved automatic return of comments at a desired width. Currently defaults to 80 characters.

bb8 0.2.14 (2020-06-21)

bb8 0.2.15 (2020-07-01)

Minor changes

  • Renamed getCurrentVersion function to getCurrentGitHubVersion.

bb8 0.2.16 (2020-07-22)

Major changes

  • install and installGitHub now default to reinstall = TRUE.

bb8 0.2.17 (2020-07-23)

Minor changes

bb8 0.2.18 (2020-07-28)

Minor changes

  • Removed internal references to patrick package, which provides parameterized unit testing. Now falling back to simply using for or mapply loops instead inside of packages.

bb8 0.2.19 (2020-08-03)

Minor changes

  • Removed reexport of export and import from pipette package. The export function doesn’t detect sym class correctly.
  • Switched magrittr from Depends to Imports.

bb8 0.2.20 (2020-08-05)

Minor changes

  • install now internally treats all warnings as errors.

bb8 0.2.21 (2020-08-05)

Minor changes

  • install now supports direct installation of package tarballs from URLs.

bb8 0.2.22 (2020-08-11)

Minor changes

  • install: Bug fix for skipping install from tarball URLs if the package is already installed. Can override with reinstall = TRUE.

bb8 0.2.23 (2020-08-11)

Minor changes

  • Renamed cleanSystemLibrary to isCleanSystemLibrary.

bb8 0.2.24 (2020-08-11)

  • updatePackages: Migrated automatic CRAN and GitHub removals here from code previously defined in koopa.
  • Migrated isCleanSystemLibrary to goalie package.

bb8 0.2.25 (2020-08-17)

  • install: Don’t attempt to update old packages by default.

bb8 0.2.26 (2020-08-18)

  • installedPackages: Improved detection of Acid Genomics packages installed from r.acidgenomics.com instead of GitHub.

bb8 0.2.27 (2020-08-18)

  • Bug fix for Bioconductor and CRAN/RSPM package detection.

bb8 0.2.28 (2020-08-25)

  • updatePackages: Don’t attempt to remove brio, as it’s now on CRAN.

bb8 0.2.29 (2020-10-07)

  • Renamed acidbase package to AcidBase, and updated import here.
  • Removed GitHub remotes to Acid Genomics packages.

bb8 0.2.30 (2020-10-12)

  • updatePackages: Only attempt to update GitHub packages if GITHUB_PAT environment variable is set.

bb8 0.2.31 (2020-10-20)

  • updateDeps: Hardened against missing packages.

bb8 0.2.32 (2020-10-23)

  • Draft update adding view as a reexport, from tibble package.

bb8 0.2.33 (2020-10-28)

  • Bug fix, ensuring tibble view is reexported.

bb8 0.2.34 (2020-10-29)

  • install: Added support for automatic installation from a Git repository. Calls remotes::install_git internally.

bb8 0.2.35 (2020-10-29)

  • install: Improve support for direct installation from a local file.

bb8 0.2.36 (2020-11-03)

Migrated some install functions from koopa R package:

  • installAcidverse: Install all Acid Genomics packages.
  • installBioconductor: Wrapper for BiocManager::install.
  • installDefaultPackages: Install default recommended R packages.

bb8 0.2.37 (2020-11-04)

  • install: Set dependencies argument to TRUE by default instead of NA, which will automatically install suggested packages.

bb8 0.2.38 (2020-11-04)

  • installBioconductor: Also include automatic installation of BiocCheck.

bb8 0.2.39 (2020-11-04)

  • Migrated installBioconductor code into koopa package.
  • Hardened uninstall and updatePackages against warnings.

bb8 0.2.40 (2020-11-05)

  • install: Attempt to improve internal repository handling.
  • updatePackages: Attempt to improve internal repository handling.

bb8 0.2.41 (2020-11-06)

  • Renamed installDefaultPackages to installRecommendedPackages.
  • Fixed internal Bioconductor installation code.

bb8 0.2.42 (2020-11-11)

  • Added currentBiocVersion, which checks for current Bioconductor release version.
  • updatePackages now automatically upgrades the Bioconductor release, when applicable.

bb8 0.2.43 (2020-11-24)

  • installRecommendedPackages: Install all packages by default.

bb8 0.2.44 (2020-11-25)

  • updatePackages: Improved error message handling when internal BiocManager validity checks fail. Wrapped using tryCatch call to better show which packages are responsible for the check failure.

bb8 0.2.45 (2020-12-03)

  • install: Improved automatic definition of type internally for manual local package installs.

bb8 0.2.46 (2020-12-07)

  • Fix for packages with dependency issues: Seurat and dendsort.

bb8 0.2.47 (2020-12-09)

  • check: Hardened against lintr check failure.

bb8 0.2.48 (2020-12-16)

  • Added pc alias for printComment, to reduce the amount of typing required during an interactive scripting session.

bb8 0.2.49 (2021-01-15)

  • check: Improved package name detection, which doesn’t always correspond to the directory name. Using desc package to harden this. Also a couple of bug fixes related to checking outside of package working directory.
  • printComment: Bug fix to better set the width.
  • Removed pc alias, which can get masked by Bioconductor.

bb8 0.2.50 (2021-01-31)

  • Added veloviz and liger to recommended packages.