update_all = TRUE. Closes #27.LazyData from DESCRIPTION for CRAN
resubmission.stock() lets you install packages from a list
without attaching them, unlike shelf() which does both.
Closes #26.shelf() was refactored to pull package
installation into the new stock() function.testthat has changed since the last
librarian version c. 2019. Updated the list.stock() and shelf() are
now reported in the same order as the user gave them in
....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.lib_paths() doesn’t call itself as an argument in
shelf(). Thanks, Miles Smith!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.unshelf() only acts on dependencies that are
actually attached. It previously also acted on packages that were only
namespaced but not attached. Closes #20.make_dirs() no longer validates filenames that
contain dots as if they were filenames,
e.g. C:/MyPath/R/3.5.lib_paths() shows names of non-writeable paths,
instead of the result -1.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.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.shelf(), unshelf(),
reshelf(), check_attached(), and
check_installed() can now accept four different input
methods:
shelf(package, name, here)shelf("package", "name", "here")shelf("package", name, "here")....
shelf(c("package", "name", "here"))remotes. They also make it possible to use these functions
inside scripts, like passing package lists around.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.biocLite has been replaced with
BiocManager for installing BioConductor packages.
BiocManager has been added as a dependency.browse_cran() for searching CRAN package titles
and descriptions by keyword or regular expression.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.remotes replaces devtools. Closes #11.backports package is no longer needed.librarian:::check_installed() failed if the package name
had a . inside it, so those packages were installable but
not attachable with librarian. Closes #12.cran_repo argument in shelf()
contains the default R value @CRAN@. Closes Issue
#10. Thanks, Jim Hunter!lib_startup() uses to mark
the lines it edited previously indicated an old function name.check_installed() now works much faster, so
librarian in general should work much faster because
check_installed() was called in every function.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.shelf() now supports installing Bioconductor
packages via biocLite(). Bioconductor’s
Biobase package needs to be installed before
librarian will attempt to install Bioconductor packages.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.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.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.
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.cran_repo warning raised by
shelf() now shows the original string.unshelf() raises an error when you haven’t told
it to detach anything.shelf() now sets a default CRAN repo properly on
the command line.
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.shelf(), unshelf(), and
reshelf() now invisibly return named vectors describing the
packages that were operated on and whether they were successfully
attached or detached.unshelf(everything = TRUE) argument detaches all
packages except for the default ones.unshelf(safe = TRUE) argument checks if packages
are still needed by others before detaching them.unshelf(warn = TRUE) argument will print a
Message if packages were not detached (because safe = TRUE
and the packages were still needed).unshelf(..., also_depends = TRUE) argument
detaches packages named in ... as well as their
dependencies.
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.tools
package, but it’s distributed with R.reshelf() for refreshing a package. Useful for
loading new builds of your personal package.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.shelf() and unshelf() check for
duplicates in the package list you provide.utils (a default package) for base R’s
package-handling functions. Omitting this caused warnings in R CMD
CHECK.unshelf() that made it try to unload
packages even if they were not loaded.custom_repo argument for shelf(),
which defaults to R’s default behaviour.rlang. Only imports
devtools now.shelf() now returns
devtools::session_info() invisibly so that you can print
it.NEWS.md file to track changes to the
package.shelf() and
unshelf() in feature-complete form.
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