NEWS.md

In librarian: Install, Update, Load Packages from CRAN, 'GitHub', and 'Bioconductor' in One Step

librarian 1.8.1 (2021-07-12)

• FIX - There was an issue where brand new GitHub packages wouldn't be installed unless update_all = TRUE. Closes #27.
• FIX - Changed link to CONDUCT.md in README to an absolute link for CRAN resubmission.
• FIX - Removed LazyData from DESCRIPTION for CRAN resubmission.
• FIX - Cached data is no longer used when checking if a package is installed.

librarian 1.8.0 (2021-06-29)

• ADD - stock() lets you install packages from a list without attaching them, unlike shelf() which does both. Closes #26.
• MOD - shelf() was refactored to pull package installation into the new stock() function.
• FIX - An internal QA test was failing because the dependency list of the package testthat has changed since the last librarian version c. 2019. Updated the list.
• FIX - Results of stock() and shelf() are now reported in the same order as the user gave them in ....
• MOD - update_all = TRUE in shelf() and stock() now force reinstallation of a GitHub package even if the remote package's SHA1 matches the installed version. The reasoning is a) that 'forcing an update' should actually perform an update even if the files are identical, and b) in the event that some of the user's files have been changed, the stored SHA1 will not reflect this. Closes #24.
• FIX - The "paths '-1' are not writeable" error was apparently fixed in v1.7.2, but that version was never uploaded to CRAN. Uploading it to CRAN should hopefully solve this once and for all. Closes #21. Closes #23.

librarian 1.7.2 (2019-03-11)

• FIX - lib_paths() doesn't call itself as an argument in shelf(). Thanks, Miles Smith!
• FIX - shelf() now exits as soon as possible by trying to attach all packages right at the start of the function. Previously, package attachment was done only at the end, after all the other checks were done. If you set update_all = TRUE then the function will run package installation first and package attachment second. Closes #19.
• FIX - unshelf() only acts on dependencies that are actually attached. It previously also acted on packages that were only namespaced but not attached. Closes #20.
• FIX - make_dirs() no longer validates filenames that contain dots as if they were filenames, e.g. C:/MyPath/R/3.5.
• FIX - lib_paths() shows names of non-writeable paths, instead of the result -1.

librarian 1.7.0 (2019-03-13)

• FIX - 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.
• ADD - 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.
• MOD - shelf(), unshelf(), reshelf(), check_attached(), and check_installed() can now accept four different input methods:
• A comma-separated list of bare names. shelf(package, name, here)
• A comma-separated list of strings. shelf("package", "name", "here")
• A comma-separated list of names and strings. shelf("package", name, "here")
• A character vector of package names, as long as it is the only item passed in .... shelf(c("package", "name", "here"))
• These changes were made to accommodate the advanced input methods of remotes. They also make it possible to use these functions inside scripts, like passing package lists around.
• ADD - Many new unit tests, with more stringent testing methods.
• MOD - Major refactoring. The biggest change is that user-facing stuff like messages have been extracted from the functions so that the logic of the function is easier to maintain.

librarian 1.6.1 (2019-03-09)

• FIX - unshelf() with everything = TRUE arg now detaches all non-default packages if safe = FALSE is also set. In the past, it would leave behind the packages that you had added to your .Rprofile using lib_startup(). This is still the default behaviour.
• ADD - Various behind-the-scenes helper functions in preparation for a code refactor.

librarian 1.6.0 (2019-02-19)

• MOD - biocLite has been replaced with BiocManager for installing BioConductor packages. BiocManager has been added as a dependency.
• FIX - Various spelling errors in preparation for CRAN submission.
• ADD - Vignette for CRAN
• ADD - browse_cran() for searching CRAN package titles and descriptions by keyword or regular expression.

librarian 1.5.5 (2019-02-18)

• FIX - nse_dots() used to insert spaces in names that included - because it was formatting them nicely as if they were expressions with the minus operator. The function now removes any spaces that were created in the process of converting from a symbol to a string. Closes #13.
• MOD - remotes replaces devtools. Closes #11.
• REM - The backports package is no longer needed.

librarian 1.5.4 (2019-02-15)

• FIX - The regular expression used in librarian:::check_installed() failed if the package name had a . inside it, so those packages were installable but not attachable with librarian. Closes #12.

librarian 1.5.3 (2019-01-24)

• MOD - Less alarming and more informative message (not a warning) for when the cran_repo argument in shelf() contains the default R value @CRAN@. Closes Issue #10. Thanks, Jim Hunter!

librarian 1.5.2 (2018-11-19)

• FIX - The code comment that lib_startup() uses to mark the lines it edited previously indicated an old function name.

librarian 1.5.1 (2018-11-15)

• MOD - check_installed() now works much faster, so librarian in general should work much faster because check_installed() was called in every function.

librarian 1.5.0 (2018-11-02)

• ADD - lib_startup() lets you set library search paths and packages that will be loaded globally at the start of every R session, or on a per-project basis.

librarian 1.4.0

• ADD - shelf() now supports installing Bioconductor packages via biocLite(). Bioconductor's Biobase package needs to be installed before librarian will attempt to install Bioconductor packages.

librarian 1.3.2

• REVERT - R dependency back to => 3.4.0.

librarian 1.3.1

• FIX - librarian was written for R 3.5.0 but only asked for 3.4.0 as a dependency. The R dependency is now 3.5.0.
• MOD - I have added a dependency for backports so that users of R < 3.5.0 do not have to update their R installation for only one important function that librarian needs (...length()). Closes issue #4.
• FIX - Sometimes the CRAN URL check would return a vector of length >1, raising a warning message.

librarian 1.3.0

• 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.

librarian 1.2.0

• FIX - shelf() now sets a default CRAN repo properly on the command line.
  • REM - The custom_repo argument in shelf() has been renamed to cran_repo.
  • cran_repo arg checks that its value is a valid URL. I previously supported custom_repo = NULL because the base install.packages() uses NULL to signal installation from a local file, but the point of librarian is to install CRAN and GitHub packages from the net, so cran_repo does not keep this functionality.
• MOD - Improved the documentation following CRAN feedback.
• ADD - shelf(), unshelf(), and reshelf() now invisibly return named vectors describing the packages that were operated on and whether they were successfully attached or detached.
• ADD - Unit tests to make sure that my fixes don't break stuff.
• ADD - unshelf(everything = TRUE) argument detaches all packages except for the default ones.
• ADD - unshelf(safe = TRUE) argument checks if packages are still needed by others before detaching them.
• ADD - unshelf(warn = TRUE) argument will print a Message if packages were not detached (because safe = TRUE and the packages were still needed).
• ADD - unshelf(..., also_depends = TRUE) argument detaches packages named in ... as well as their dependencies.
  • With the safe and quiet arguments defaulting to TRUE, the default behaviour is to leave packages behind if other packages in the search path still need them, but not to interrupt the user with a message about it. unshelf() still invisibly returns the success/failure for each package it attempted to detached.
  • Looking through the search path is pretty slow, I don't recommend it for sessions with lots of packages!
• MOD - The new dependency-checking code needs the tools package, but it's distributed with R.

librarian 1.1.0

• ADD - reshelf() for refreshing a package. Useful for loading new builds of your personal package.

librarian 1.0.3

• ADD - unshelf() can handle the Github Username/packagename format now, instead of requiring the user to provide only the package name. The biggest effect of this change is that if you want to unload your packages, you can now just change your shelf() to unshelf() and run it.
• ADD - shelf() and unshelf() check for duplicates in the package list you provide.

librarian 1.0.2

• FIX - Many documentation changes for CRAN submission.
• FIX - Import utils (a default package) for base R's package-handling functions. Omitting this caused warnings in R CMD CHECK.
• FIX - Bug in unshelf() that made it try to unload packages even if they were not loaded.
• ADD - custom_repo argument for shelf(), which defaults to R's default behaviour.

librarian 1.0.1

• REM - No longer imports rlang. Only imports devtools now.
• ADD - shelf() now returns devtools::session_info() invisibly so that you can print it.
• ADD - NEWS.md file to track changes to the package.
• ADD - info re. updating package dependencies.

librarian 1.0.0

• Initial release. Includes shelf() and unshelf() in feature-complete form.

librarian documentation built on July 12, 2021, 5:07 p.m.