CVS commit: pkgsrc/devel/R-renv

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

Module Name:    pkgsrc
Committed By:   mef
Date:           Sat Oct 19 22:57:13 UTC 2024

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

Log Message:
(devel/R-renv) Updated 1.0.3 to 1.0.11

# renv 1.0.11

* Fixed an issue where headers were not properly passed to `available.packages()`
  during `renv` bootstrap. (#1942)

* `renv` now assumes that Artifactory package repositories will use a CRAN-like
  layout of packages for packages in the archive. (#1996)

* `renv` now includes compiled extensions on Linux + macOS. These
  extensions are primarily used to improve the performance of
  `renv::dependencies()` and other static analysis code.
  Support for Windows may come in a future release.

* Fixed an issue where `renv::snapshot()` could fail if the project
  contained a call to `module()` with no arguments. (#2007)

* On Linux, `renv` now emits a message on load if the R temporary directory
  is within a folder that has been mounted as 'noexec'. This message can be
  suppressed by setting the `RENV_TEMPDIR_NOEXEC_CHECK=FALSE` environment
  variable.

# renv 1.0.10

* Fixed a performance regression in `renv::dependencies()`. (#1999)

* Fixed an issue where `renv` tests could fail if the `parallel` package was
  loaded during test execution.

* `renv` now determines a package repository's type through the HTTP headers
  provided when accessing `src/contrib/PACKAGES`. This is mainly relevant
  when detecting Nexus and Artifactory repositories.

# renv 1.0.9

* Fixed an issue where repository URLs were inappropriately transformed into
  binary repository URLs on Linux. (#1991)

* Fixed an issue where code following `source("renv/activate.R")` in the project
  `.Rprofile` was not invoked for projects using RStudio. (#1990)

# renv 1.0.8

* `renv` now infers a dependency on the `ragg` package when the `ragg_png` device
  is used in R Markdown / Quarto documents, for documents using the code
  `knitr::opts_chunk$set(dev = "ragg_png")`. (#1985)

* `renv` now automatically generates a lockfile when loading a project containing
  a `manifest.json` file (typical for application bundles published to Posit Connect).
  (#1980, @toph-allen)

* `renv::install()` now errs if an incompatible `type` argument is provided.

* `renv::checkout()` now also checks out the version of `renv` available
  and associated with the requested snapshot date. (#1966)

* Fixed an issue where `renv::hydrate()` did not hydrate packages which
  were also listed as dependencies within a project's `DESCRIPTION` file.
  (#1970)

* Fixed an issue where `renv::checkout()` omitted some fields from lockfile
  records when using `actions = c("snapshot", "restore")`. (#1969)

* `renv` gains the function `renv::retrieve()`, which can be used to download
  packages without installing them. This is primarily useful in CI / CD scenarios,
  where you might want to download packages in a single stage before attempting
  to install / restore them. (#1965)

* `renv` now preserves `Remote` fields present on packages installed from
  public package repositories (e.g. <https://r-universe.dev/>). (#1961)

* Fixed an issue where `renv::load()` could fail to load an alternate project
  when `options(renv.config.autoloader.enabled = FALSE)` was set. (#1959)

* `renv` now emits clickable hyperlinks for runnable code snippets and help,
  for front-ends which support the `ide:run` and `ide:help` ANSI escapes.

* `renv::init(bioc = "<version>")` now prompts the user in interactive sessions
  when requesting a version of Bioconductor which is not compatible with the
  current version of R. (#1943)

* `renv::restore()` gains the `transactional` argument, which can be
  used to control whether `renv` will allow successfully-installed
  packages remain in the project library even if a package fails
  to install during a later step. (#1109)

* `renv` now infers a dependency on the `xml2` package for projects
  using the `testthat::JunitReporter` for tests. (#1936)

* Fixed an issue where `renv::dependencies()` could emit a warning
  when attempting to parse chunks using chunk options like
  `#| eval: c(1, 2)`. (#1906)

* `renv::install()` now properly delegates the `type` and `rebuild`
  arguments to `pak` when `options(renv.config.pak.enabled = TRUE)`
  is set. (#1924)

* `renv` now infers a dependency on the `svglite` package if it detects
  calls of the form `ggsave(filename = "path.svg")`. (#1930)

* `renv` now supports setting of GitHub authentication credentials via
  any of `GITHUB_TOKEN`, `GITHUB_PAT`, and `GH_TOKEN`. (#1937)

* `renv` now also passes any custom headers available to
  `utils::available.packages()` during bootstrap. (#1942)

* Fixed an issue where `renv` could fail during installation of packages
  stored within repository sub-directories, if that repository also
  contained a top-level DESCRIPTION file. (#1941)

* `renv` now normalizes lockfile entries for Bioconductor packages installed
  via `pak::pkg_install()`, to help prevent spurious diffs being produced
  via `renv::status()`. (#1920)

* `renv::install()` now respects the `prompt` parameter when `pak` is enabled,
  as via `options(renv.config.pak.enabled = TRUE)`. (#1907)

* Fixed an issue with `renv`'s `pak` integration where `renv` could install the
  wrong version of a GitHub package during restore if
  `options(renv.config.pak.enabled = TRUE)` was set. (#1883)

* `renv` no longer interacts with the user during autoloading, which coincides
  with R startup. If the IDE offers a session init hook (RStudio does),
  loading is deferred until startup is complete and interaction is possible.
  Otherwise, any suggested renv actions, such as `renv::restore()`, are emitted
  as a message for the user to act on. (#1879, #1915).

* Fixed an issue where installation of packages from local sources, as via
  `install("<package>", repos = NULL, type = "source")`, could fail. (#1880)

* A new function, `renv::lockfile_validate()`, can be used to validate your `renv.lock`
  against a default or custom schema. (#1889)

# renv 1.0.7

* Fixed an issue where `renv`'s activate script failed to report version
  conflict errors when starting up. (#1874)

# renv 1.0.6

* Fixed an issue where downloads could fail with curl >= 8.7.1. (#1869)

* Fixed an issue where `renv::snapshot()` did not properly normalize
  package records generated from packages installed using the `pak`
  package, e.g. via `pak::pkg_install("cran::<package>")`.

* Fixed an issue where `renv` could incorrectly prompt the user to record
  a version of `renv` installed from GitHub in some cases. (#1857)

* `renv::load()` now delegates to `base::load()` when it detects that the
  call was likely intended for `base::load()`, but `renv::load()` was used
  instead (e.g. because `base::load()` was masked by `renv::load()`).

* `renv::update()` gains the `lock` argument, which can be used to
  instruct `renv` to automatically update the lockfile after the requested
  packages have been updated. (#1849)

* Fixed an issue where `renv` could fail to update the project autoloader
  after calling `renv::upgrade()`. (#1837)

* Fixed an issue where attempts to install binary packages from older
  PPM snapshots could fail. (#1839)

* `renv` now uses a platform-specific prefix on Linux for library and
  cache paths by default with R (>= 4.4.0). This is equivalent to setting
  `RENV_PATHS_PREFIX_AUTO = TRUE`. If necessary, this behavior can be
  disabled by setting `RENV_PATHS_PREFIX_AUTO = FALSE` in an appropriate
  R startup file. (#1211)

# renv 1.0.5

* `renv` now only writes a `.renvignore` file into the cache directory
  if the cache appears to be part of the current project.

* `renv` now reports missing system libraries as part of its ABI
  checks in `renv::diagnostics()`.

* Fixed an issue where `renv::install(lock = TRUE)` produced lockfiles
  containing records with extraneous data. (#1828)

# renv 1.0.4

* `renv::install()` gains the `lock` argument. When `TRUE`, the project
  lockfile will be updated after the requested packages have been
  successfully installed. (#1811)

* `renv` now supports the use of GitHub Enterprise servers with the
  `gitcreds` package for authentication credentials. (#1814)

* `renv::dependencies()` now treats `#| eval: !expr <...>` chunk options
  as truthy by default, implying that such chunks are scanned for their
  R package dependencies. (#1816)

* `renv::dependencies()` now requires usages of the [import](https://cran.r-project.org/package=import)
  package to be namespace-qualified in order to be handled via static
  analysis; that is, `import::from(<pkg>)` is parsed for dependencies,
  but `from(pkg)` is not. (#1815)

* `renv::load()` gains the `profile` argument, allowing one to
  explicitly load a specific profile associated with an `renv` project.
  See `vignette("profiles", package = "renv")` or
  https://rstudio.github.io/renv/articles/profiles.html
  for more details.

* `renv::dependencies()` no longer includes `R` dependency versions
  declared from a `DESCRIPTION` file in its output. (#1806)

* Fixed an issue where `renv` could fail to infer dependencies from
  R Markdown code chunks using engine 'R' (upper-case) rather than
  'r' (lower-case). (#1803)

* Fixed an issue where `renv` did not report out-of-sync packages when
  one or more packages used in the project were not installed. (#1788)

* Fixed an issue where `renv` could over-aggressively activate P3M
  repositories when initializing a project. (#1782)

* `renv::status()` now notifies the user if the version of R recorded in
  the lockfile does not match the version of R currently in use. (#1779)

* Fixed an issue where packages could appear multiple times in the lockfile,
  if that package was installed into multiple library paths. (#1781)

* Installation of historical binaries of packages is once again enabled,
  now using the [Posit Public Package Manager (P3M)](https://packagemanager.posit.co)
  service instead of Microsoft's (now defunct) MRAN service.

* `renv::init()` now respects the `Remotes:` field declared in a project's
  `DESCRIPTION` file, if any. (#1522)

* `renv::embed()` now supports Quarto Markdown (`.qmd`) files. (#1700)

* renv now sets the `R_INSTALL_TAR` environment variable to match the default
  `tar` executable (if any) when installing packages. (#1724)

* renv now uses `--ssl-revoke-best-effort` by default when downloading files
  using `curl` on Windows. (#1739)

* Fixed an issue where `renv::install()` could fail to detect incompatible
  recursive package dependencies. (#1671)

* `renv::install()` now records remote information for packages installed from
  CRAN-like repositories, and uses that information when generating a lockfile
  and restoring those packages. This helps ensure that packages installed within
  an renv project via calls like `renv::install("<pkg>", repos = "<repos>")` can
  still be successfully restored in future sessions. (#1765)

* `renv::install()` now lazily resolves project remotes. (#1755)

* `renv::init()` now respects Remotes declared within a project's `DESCRIPTION`
  file, if any.

* Calling `renv::activate()` without explicitly providing the `profile` argument
  now preserves the current profile, if any. Use `renv::activate(profile = "default")`
  if you'd like to re-activate a project using the default profile. (#1217)

* Fixed an issue where `renv` would try to prompt for the installation of
  `BiocManager` when activating a project using Bioconductor. (#1754)

* Fixed an issue where directories containing a large number of files could
  cause `renv` to fail to activate a project. (#1733)

* Expanded the set of Linux distributions detected for automatic transformation
  of Posit Package Manager URLs to install binary packages. `renv` now correctly
  detects Red Hat Enterprise Linux 9, Rocky Linux 8 and 9, SLES 15 SP4 and SP5,
  Debian 11 and 12, AlmaLinux 8 and 9, and Amazon Linux 2. (#1720, #1721)


To generate a diff of this commit:
cvs rdiff -u -r1.4 -r1.5 pkgsrc/devel/R-renv/Makefile
cvs rdiff -u -r1.6 -r1.7 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:1.4 pkgsrc/devel/R-renv/Makefile:1.5
--- pkgsrc/devel/R-renv/Makefile:1.4    Mon Jan 22 13:50:34 2024
+++ pkgsrc/devel/R-renv/Makefile        Sat Oct 19 22:57:12 2024
@@ -1,7 +1,7 @@
-# $NetBSD: Makefile,v 1.4 2024/01/22 13:50:34 mef Exp $
+# $NetBSD: Makefile,v 1.5 2024/10/19 22:57:12 mef Exp $
 
 R_PKGNAME=     renv
-R_PKGVER=      1.0.3
+R_PKGVER=      1.0.11
 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', 'webfakes'
+#   'BiocManager', 'jsonvalidate', 'modules', 'packrat', 'reticulate',
 
 TEST_DEPENDS+= R-covr-[0-9]*:../../devel/R-covr
 TEST_DEPENDS+= R-devtools-[0-9]*:../../devel/R-devtools
@@ -20,6 +20,7 @@ TEST_DEPENDS+=        R-pak-[0-9]*:../../devel/
 TEST_DEPENDS+= R-shiny-[0-9]*:../../www/R-shiny
 TEST_DEPENDS+= R-testthat-[0-9]*:../../devel/R-testthat
 TEST_DEPENDS+= R-miniUI-[0-9]*:../../www/R-miniUI
+TEST_DEPENDS+= R-webfakes-[0-9]*:../../www/R-webfakes
 
 
 .include "../../math/R/Makefile.extension"

Index: pkgsrc/devel/R-renv/distinfo
diff -u pkgsrc/devel/R-renv/distinfo:1.6 pkgsrc/devel/R-renv/distinfo:1.7
--- pkgsrc/devel/R-renv/distinfo:1.6    Mon Jan 22 13:50:34 2024
+++ pkgsrc/devel/R-renv/distinfo        Sat Oct 19 22:57:12 2024
@@ -1,5 +1,5 @@
-$NetBSD: distinfo,v 1.6 2024/01/22 13:50:34 mef Exp $
+$NetBSD: distinfo,v 1.7 2024/10/19 22:57:12 mef Exp $
 
-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
+BLAKE2s (R/renv_1.0.11.tar.gz) = 306e0964dc1502925ec6a8050a745e770c42e305d3552b35a74d4ea874d01552
+SHA512 (R/renv_1.0.11.tar.gz) = ae993205b38b047f513ee1f2b0b0e71f4e780bfdd0accf6387006b4be022a172456bab747bf0d1eaefeb50b43e9d99843ade1590d9fd5669fdd3122633f79e67
+Size (R/renv_1.0.11.tar.gz) = 1220458 bytes