CVS commit: pkgsrc/devel/R-renv

["Makoto Fujiwara" <mef%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   mef
Date:           Mon Jan 22 13:50:34 UTC 2024

Modified Files:
        pkgsrc/devel/R-renv: Makefile distinfo

Log Message:
(devel/R-renv) Updated 0.17.3 to 1.0.3

# renv 1.0.3

* Fixed an issue where `renv` could warn the project appeared to be out-of-sync
  when using packages installed without an explicit source recorded. (#1683)

* `renv::install()` gains the `exclude` argument, which can be useful when
  installing a subset of project dependencies.

* Fixed an issue where PPM repositories were not appropriately transformed
  into the correct binary repository in `renv::restore()` when using pak.

* `renv::init()` no longer prompts the user for the intended action for
  projects containing a library with only renv installed. (#1668)

* Fixed an issue where non-interactive usages of `renv::init()` could fail
  with projects containing a DESCRIPTION file. (#1663)

* Fixed an issue that could cause code within a project `.Rprofile` to execute
  before the project had been loaded in RStudio. (#1650)

* `renv::snapshot()` and `renv::status()` gain the `dev` argument. This
  can be used when you'd like to capture package dependencies from
  the *Suggests* field of your package's DESCRIPTION file. (#1019)

# renv 1.0.2

* renv now parses package `NAMESPACE` files for imported dependencies. (#1637)

* renv no longer locks the sandbox by default.

* Fixed an issue where renv used the wrong library paths when attempting
  to activate the watchdog. This could cause a 10 second delay when activating
  the sandbox.

# renv 1.0.1

* Fixed an issue where authentication headers could be duplicated when
  using the `libcurl` download method. (#1605)

* `renv::use()` now defaults to setting `isolate = TRUE` when `sandbox = TRUE`.

* Fixed an issue where the renv watchdog could fail to load, leading to slowness
  in activating the sandbox on startup. (#1617)

* Fixed an issue where renv did not display warnings / errors from `renv::snapshot()`
  when `options(renv.verbose = FALSE)` was set. The display of these messages
  is now controlled via the `renv.caution.verbose` R option. (#1607, #1608)

* `renv::load()` now notifies the user if the synchronization check took an
  excessive amount of time due to the number of files being scanned in the
  project. (#1573)

* `renv::init()` gains the `load` argument, making it possible to initialize
  a project without explicitly loading it. (#1583)

* renv now uses a lock when synchronizing installed packages with the cache.
  This should help alleviate issues that can arise when multiple R processes
  are installing and caching packages concurrently. (#1571)

* Fixed a regression in parsing expressions within R Markdown chunk options. (#1558)

* Fixed an issue that prevented `renv::install()` from functioning
  when source-only repositories were included. (#1578)

* Fixed a logic error in reading `RENV_AUTOLOAD_ENABLED`. (#1580)

* `renv::restore()` no longer runs without prompting on load if the
  library is empty. (#1543)

* `renv::repair()` now checks for installed packages which lack a known
  remote source, and updates their `DESCRIPTION` files if it can infer an
  appropriate remote source. This typically occurs when a package is installed
  from local sources, but appears to be maintained or published on a remote
  repository (e.g. GitHub). This was previously done in `renv::snapshot()`, but
  we've rolled back that change as the prompting was over-aggressive. (#1574)

* `renv::status()` now first reports on uninstalled packages, before reporting on
  used <-> installed mismatches. (#1538)

* When the `RENV_STARTUP_DIAGNOSTICS` environment variable is set to `TRUE`,
  renv now displays a short diagnostics report after a project's autoloader
  has been run. This can be useful when diagnosing why renv is slow to load
  in certain projects. (#1557)

* renv now ensures the sandbox is activated on load, for R processes which
  are launched with the renv sandbox on the library paths. (#1565)

* `renv::restore()` no longer erroneously prompts when determining the packages
  which need to be installed. (#1544)

* `renv::update()` now ensures the `prompt` parameter is properly respected
  during package installation. (#1540)

* `renv::activate()` no longer erroneously preserves the previous library
  paths after restarting the session within RStudio. (#1530)

* Use correct spelling of IRkernel package (#1528).

* Honor `R_LIBCURL_SSL_REVOKE_BEST_EFFORT` when using an external `curl.exe`
  binary to download files. (#1624)

# renv 1.0.0

## New features

* New `renv::checkout()` installings the latest-available packages from a
  repository. For example, `renv::checkout(date = "2023-02-08")` will install
  the packages available on 2023-02-08 from the Posit
  [Package Manager](https://packagemanager.rstudio.com/) repository.
  The `actions` argument allows you choose whether a lockfile is generated from
  the provided repositories ("snapshot"), or whether packages are installed
  from the provided repositories ("restore").

* `renv::deactivate()` gains a `clean` argument: when `TRUE` it will delete
  all renv files/directories, leaving the project the way it was found.

* `renv::init()` now uses [Posit Public Package Manager](https://packagemanager.posit.co)
  by default, for new projects where the repositories have not already been
  configured externally. See the options `renv.config.ppm.enabled`,
  `renv.config.ppm.default`, and `renv.config.ppm.url` in `?config` for more
  details (#430).

* `renv::lockfile_create()`, `renv::lockfile_read()`, `renv::lockfile_write()`
  and `renv::lockfile_modify()` provide a small family of functions for
  interacting with renv lockfiles programmatically (#1438).

* Handling of development dependencies has been refined. `renv::snapshot()`
  and `renv::status()` no longer track development dependencies, while
  `install()` continues to install them (#1019). `Suggested` packages listed in
  `DESCRIPTION` files are declared as development dependencies regardless of
  whether or not they're a "package" project.

* MRAN integration is now disabled by default, pending the upcoming shutdown
  of Microsoft's MRAN service. Users who require binaries of older R packages
  on Windows + macOS can consider using the instance of CRAN mirrored by the
  [Posit Public Package Manager](https://packagemanager.posit.co) (#1343).

## Bug fixes and minor improvements

* Development versions of renv are now tracked using the Git SHA of the
  current commit, rather than a version number that's incremented on every
  change (#1327). This shouldn't have any user facing impact, but makes
  renv maintenance a little easier.

* Fixed an issue causing "restarting interrupted promise evaluation" warnings
  to be displayed when querying available packages failed. (#1260)

* `renv::activate()` uses a three option menu that hopefully make your choices
  more clear (#1372).

* `renv::dependencies()` now discovers R package dependencies inside Jupyter
  notebooks (#929).

* `renv::dependencies()` includes packages used by user profile (`~/.Rprofile`)
  if `renv::config$user.profile()` is `TRUE`. They are set as development
  dependencies, which means that they will be installed by `install()` but not
  recorded in the snapshot.

* `renv::dependencies()` only extracts dependencies from text in YAML
  headers that looks like valid R code (#1288).

* `renv::dependencies()` no longer treats `box::use(module/file)` as using
  package `module` (#1377).

* `renv::init()` now prompts the user to select a snapshot type if the project
  contains a top-level DESCRIPTION file (#1485).

* `renv::install(type = "source")` now ensures source repositories are used
  in projects using [PPM](https://packagemanager.posit.co/). (#927)

* `renv::install()` activates Bioconductor repositories when installing a
  package from a remote (e.g. GitHub) which declares a Bioconductor dependency
  (via a non-empty 'biocViews' field) (#934).

* `renv::install()` respects the project snapshot type, if set.

* `renv::install()` now keeps source when installing packages from source (#522).

* `renv::install()` now validates that binary packages can be loaded after
  installation, in a manner similar to source packages (#1275).

* `renv::install()` now supports Bioconductor remotes of the form
  `bioc::<BiocVersion>/<Package>`, for installing packages from
  a particular version of Bioconductor. Aliases like 'release' and
  'devel' are also supported (#1195).

* `renv::install()` now requires interactive confirmation that you want to
  install packages (#587).

* `renv::load()` gives a more informative message if a lockfile is present but
  no packages are installed (#353).

* `renv::load()` no longer attempts to query package repositories when checking
  if a project is synchronized (#812).

* `renv::load()` no longer duplicates entries on the `PATH` environment variable
  (#1095).

* `renv::restore()` can now use `pak::pkg_install()` to install packages
  when `pak` integration is enabled. Set `RENV_CONFIG_PAK_ENABLED = TRUE`
  in your project's `.Renviron` if you'd like to opt-in to this behavior.
  Note that this requires a nightly build of `pak` (>= 0.4.0-9000);
  see https://pak.r-lib.org/dev/reference/install.html for more details.

* `renv::restore()` now emits an error if called within a project that
  does not contain a lockfile (#1474).

* `renv::restore()` correctly restores packages downloaded and installed
  from [r-universe](https://r-universe.dev/) (#1359).

* `renv::snapshot()` now standardises pak metadata so CRAN packages installed via
  pak look the same as CRAN packages installed with renv or `install.packages()`
  (#1239).

* If `renv::snapshot()` finds missing packages, a new prompt allows you to
  install them before continuing (#1198).

* `renv::snapshot()` no longer requires confirmation when writing the first
  snapshot, since that's an action that can easily be undone (by deleting
  `renv.lock`) (#1281).

* `renv::snapshot()` reports if the R version changes, even if no packages
  change (#962).

* `renv::snapshot(exclude = <...>)` no longer warns when attempting to exclude
  a package that is not installed (#1396).

* `renv::status()` now uses a more compact display when packages have some
  inconsistent combination of being installed, used, and recorded.

* `renv::status()` now works more like `renv::restore()` when package versions
  are different (#675).

* `renv::update()` can now update packages installed from GitLab (#136) and
  BitBucket (#1194).

* `renv::settings$package.dependency.fields()` now only affects packages
  installed directly by the user, not downstream dependencies of those packages.

* renv functions give a clearer error if `renv.lock` has somehow become
  corrupted (#1027).


To generate a diff of this commit:
cvs rdiff -u -r1.3 -r1.4 pkgsrc/devel/R-renv/Makefile
cvs rdiff -u -r1.5 -r1.6 pkgsrc/devel/R-renv/distinfo

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Modified files:

Index: pkgsrc/devel/R-renv/Makefile
diff -u pkgsrc/devel/R-renv/Makefile:1.3 pkgsrc/devel/R-renv/Makefile:1.4
--- pkgsrc/devel/R-renv/Makefile:1.3    Sun Jun 18 14:10:23 2023
+++ pkgsrc/devel/R-renv/Makefile        Mon Jan 22 13:50:34 2024
@@ -1,7 +1,7 @@
-# $NetBSD: Makefile,v 1.3 2023/06/18 14:10:23 mef Exp $
+# $NetBSD: Makefile,v 1.4 2024/01/22 13:50:34 mef Exp $
 
 R_PKGNAME=     renv
-R_PKGVER=      0.17.3
+R_PKGVER=      1.0.3
 CATEGORIES=    devel
 
 MAINTAINER=    pkgsrc-users%NetBSD.org@localhost
@@ -12,7 +12,7 @@ USE_LANGUAGES=        # none
 REPLACE_SH=    inst/bin/renv inst/resources/scripts-git-askpass.sh
 
 # Packages suggested but not available:
-#   'BiocManager', 'packrat', 'reticulate'
+#  'BiocManager', 'packrat', 'reticulate', 'webfakes'
 
 TEST_DEPENDS+= R-covr-[0-9]*:../../devel/R-covr
 TEST_DEPENDS+= R-devtools-[0-9]*:../../devel/R-devtools

Index: pkgsrc/devel/R-renv/distinfo
diff -u pkgsrc/devel/R-renv/distinfo:1.5 pkgsrc/devel/R-renv/distinfo:1.6
--- pkgsrc/devel/R-renv/distinfo:1.5    Sun Jun 18 14:10:23 2023
+++ pkgsrc/devel/R-renv/distinfo        Mon Jan 22 13:50:34 2024
@@ -1,5 +1,5 @@
-$NetBSD: distinfo,v 1.5 2023/06/18 14:10:23 mef Exp $
+$NetBSD: distinfo,v 1.6 2024/01/22 13:50:34 mef Exp $
 
-BLAKE2s (R/renv_0.17.3.tar.gz) = 7ed8342a87bcdbb320ea4e9da3e05c3bdbaf4d344e19824aedcf42b73cf8e517
-SHA512 (R/renv_0.17.3.tar.gz) = 8f94bb5d3942ea0264fb205b51498a47ea677c7533bfc7b3a818de5df5ac7c9ebe36af5587d3153be85120ddf395394acffafe068ae4fd74dd88a8835a4caedf
-Size (R/renv_0.17.3.tar.gz) = 1063877 bytes
+BLAKE2s (R/renv_1.0.3.tar.gz) = 127ba31993d108803d0157c4cc8b1d350c61b939917853e9ed852c4ae29dc16f
+SHA512 (R/renv_1.0.3.tar.gz) = e4172aa09acf2e44ed2293dfd2156ba37b4c9443ce97c4d9ce4a764eb04b32c600025bdc017d98c971646b83595f5c219e3fcb0019739d4f16e2fa79ccf9fc6c
+Size (R/renv_1.0.3.tar.gz) = 1140033 bytes