Fix for 'Paths -1', added 'stock()'

1.8.1

Submitted v1.8.1 to CRAN

Support for `remotes` tags for installing specific package versions

Headline changes

Librarian 1.7.0 provides more ways of providing package names (as bare names, as strings, as a mix of the two, or as a character vector). This opens up support for some of the fancier installation features of remotes. Namely:

# Install a branch, commit, or tag, in this case tag v1.6.8
shelf("user/[email protected]")

# Install the newest release
shelf("user/package@*release")

# Install pull request #212
shelf("user/package#212")

Other changes

• Added check_attached() and check_installed(), which lets you check the status of packages. If you run the functions with no packages named, they will return a list of all packages that are attached and installed.
• You can now detach everything except R's default packages by using safe = FALSE in unshelf(). If safe = TRUE, the packages that you've set as default ones in your .RProfile (via lib_startup() for example) will not be detached. Fixes #17.
• Improved unit testing so that more aspects of Librarian get tested in more stringent ways. This will help keep things stable.

See NEWS.md entries 1.6.1–1.7.0 for a full account.

Bioconductor, startup packages, CRAN package discovery

Headline changes

• Added Bioconductor package installation.
  shelf(phyloseq)
  If you have the Biobase packaged installed and a package was not found on CRAN, Librarian will try to install it from Bioconductor.

• Added lib_startup().
  lib_startup(librarian, magrittr, lib = "C:/Dropbox/My R Library", global = TRUE)
  Tells R to load selected packages and library folders at the start of every session (or on a per-project basis).

• Added browse_cran().
  browse_cran("zero-inf.*?(abundance|count)")
  Lets you search for relevant CRAN packages by keyword or regular expression.

Other changes

• Added a vignette to introduce people to Librarian more smoothly.
• Fixed handling of package names with punctuation characters in them.
• More informative warning and error messages.
• Many speed improvements and fewer dependencies.

See NEWS.md entries 1.3.0–1.6.0 for a full account.

Notes

• The required R version is now R 3.5.0 and higher (changed from 3.4.0 and higher) because BiocManager does not have a 3.4.0 release. I previously supported this with biocLite, but Bioconductor is deprecating that method of installation. I am open to supporting the old release again, but only if there is demand for it.

Cran release 1

Accepted on CRAN, 2018-07-08.

• ADD - lib_paths() is a wrapper for .libPaths() with folder creation built-in. It
  lets you name and create folders where new packages will be installed, view the folders
  that are on the package search path, and reshuffle their order.
• ADD - lib argument for shelf() lets you specify the folder where new packages will
  be installed. The ask argument controls whether R asks for permission before creating
  this folder; set ask = FALSE to create the folder automatically.
  • If the packages are already installed, they will be loaded from their current
    location and not re-installed.
  • If you set update_all = TRUE, a new copy of the package will be installed to
    lib. This means that you can potentially have several copies of the same package
    across many folders on your machine, each a different version. I felt that this was
    reasonable so that you could maintain a different library folder for different
    projects, and updates that you made in Project B would not affect the package
    versions you rely on for Project A.
• FIX - The cran_repo warning raised by shelf() now shows the original string.
• FIX - Unexported functions are now properly documented.
• FIX - unshelf() raises an error when you haven't told it to detach anything.

Known issues

• On CRAN, the unexported functions (check_installed, check_attached, make_dirs, nse_dots, suppress_lib_message) are shown in the documentation PDF as if they were exported. I wonder if I can put them in a different section of the PDF?