CVS commit: pkgsrc/devel/R-renv

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

Module Name:    pkgsrc
Committed By:   mef
Date:           Sun Dec 18 04:18:29 UTC 2022

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

Log Message:
(devel/R-renv) Updated 0.14.0 to 0.16.0

# renv 0.16.0

* `renv` now supports installation of packages with remotes of the form
  `<package>=<remote>`. However, the provided package name is ignored
  and is instead parsed from the remote itself. (#1064)

* `renv` now passes along the headers produced by the `renv.download.headers`
  option when bootstrapping itself in the call to `utils::download.file()`.
  (#1084)

* `renv` now reports if `renv::snapshot()` will change or update the
  version of R recorded in the lockfile. (#1069)

* `renv` now supports the `install.packages.check.source` R option, which
  is used to allow R to query source repositories even if the option
  `options(pkgType = "binary")` is set. (#1074)

* `renv` better handles packages containing git submodules when installed
  from GitHub remotes. (#1075)

* `renv` now handles local sources within the current working directory. (#1079)

* The `renv` sandbox is once again enabled by default. On Unix, the sandbox
  is now created by default within the project's `renv/sandbox` library.
  On Windows, the sandbox is created within the R session's `tempdir()`.
  The path to the `renv` sandbox can be customized via the `RENV_PATHS_SANDBOX`
  environment variable if required.

* Fixed an issue where `renv::status()` could report spurious changes when
  comparing packages installed using `pak` in some cases. (#1070)

* `renv::restore()` now also ensures the project activate script is updated
  after a successful restore. (#1066)

* Fixed an issue where `renv` could attempt to install a package from the
  repository archives even when `type = "binary"` was set. (#1046)

* Fixed an issue where package installation could fail when the R session
  is configured to use multiple repositories, some of which do not provide
  any information on available packages for certain binary arms of the
  repository. (#1045)

* `renv` now uses `jsonlite` for reading lockfiles when loaded. This should
  help ensure useful errors are provided for manually-edited lockfiles
  which contain a JSON parsing error. If the `jsonlite` package is not loaded,
  `renv` will fall back to its own internal JSON parser. (#1027)

* Fixed an issue that would cause `renv` to fail to source the user
  `~/.Rprofile` if it attempted to register global calling handlers,
  e.g. as `prompt::set_prompt()` does. (#1036)

* (Linux only) `renv` now resets ACLs on packages copied to the cache, to
  avoid persisting default ACLs that might have been inherited on packages
  installed into a local project library. If desired, this behavior can be
  disabled by setting the `RENV_CACHE_ACLS` environment variable to `FALSE`.
  If you need finer control over ACLs set on packages moved into the cache,
  consider defining a custom callback via the `renv.cache.callback` R option.
  (#1025)

* Fixed an issue where `.gitignore` inclusion rules for sub-directories were
  not parsed correctly by `renv` for dependency discovery. (#403)

* Fixed an issue where `renv` could report spurious diffs within `renv::status()`
  when comparing package records installed from `pak` versus the default R
  package installer. (#998)

* Fixed an issue where `renv::use_python()` could cause the Requirements field
  for packages in the lockfile to be unintentionally dropped. (#974)

* The R option `renv.cache.callback` can now be set, to run a user-defined
  callback after a package has been copied into the cache. This can be useful
  if you'd like to take some action on the cached package's contents after
  the package has been moved into the cache.

* (Unix only) The `RENV_CACHE_MODE` environment variable can now be used to
  change the access permissions of packages copied into the cache. When set,
  after a package is copied into the cache, `renv` will use `chmod -Rf` to try
  and change the permissions of the cache entry to the requested permissions.

* (Unix only) The `RENV_CACHE_USER` environment variable can now be used to
  change the ownership of folders copied into the cache. When set, after a
  package is copied into the cache, `renv` will use `chown -Rf` to try and
  change the ownership of that cache entry to the requested user account.

* Fixed an issue where repositories containing multiple packages in
  sub-directories could fail to install. (#1016)

# renv 0.15.5

* Fixed an issue where indexing of packages in the package cellar could
  be slow. (#1014)

* Fixed an issue where installation of packages from Bioconductor's binary
  Linux package repositories could fail. (#1013)

* `renv::restore()` now supports restoration of packages installed from
  [R-Forge](https://r-forge.r-project.org/). (#671)

* Fixed an issue where `renv::init(bioconductor = TRUE)` would not update
  the version of Bioconductor used if a project setting had already been
  set.

* It is now possible to "update" an existing lockfile by using
  `renv::snapshot(update = TRUE)`. When set, any records existing in the
  old lockfile, but not the new lockfile, will be preserved. (#727)

* Fixed an issue where `renv` could fail to parse Git remotes for users
  whose username contains a number. (#1004)

* `renv` no longer infers a dependency on the "quarto" R package in projects
  containing a `_quarto.yml` file. (#995)

* Fixed an issue where `renv` could fail to download a package from MRAN if
  a compatible source package of the same version was available from the
  active R repositories. (#990)

* `renv` now reports permission errors during download more clearly. (#985)

* Fixed an issue where `RENV_PATHS_LIBRARY_ROOT_ASIS` was not interpreted
  correctly. (#976)

* `renv::modify()` gains the `changes` argument, which can be used to modify
  a project lockfile non-interactively.

* `renv::clean()` now returns the project directory, as documented. (#922)

* Fixed an issue where `renv` could fail to parse embedded YAML chunk options
  in R Markdown documents. (#963)

* `renv` now sets default placeholder names for the `repos` R option, for
  any repository URLs which happen to be unnamed. (#964)

* Fixed an issue where `renv` didn't respect the `PATH` ordering when
  discovering Python installations via `renv_python_discover()`. (#961)

* Fixed an issue where `renv` could fail to install packages containing
  multibyte unicode characters in their DESCRIPTION file. (#956)

* Fixed detection of Rtools 4.2 (#1002)

# renv 0.15.4

* Fixed an issue where package installation could fail when referencing the
  cache via a tilde-aliased path, e.g. `~/.local/share/renv`. (#953)

# renv 0.15.3

* A variety of fixes for R CMD check.

* `renv` gains an experimental function, `renv::autoload()`, to be used as a
  helper for automatically loading a project for R processes launched within a
  sub-directory of that project. See `?renv::autoload` for more details.

* `renv` will now print a warning message when attempting to read a lockfile
  containing merge conflict markers (as from e.g. a git merge). (#945)

* Fixed an issue where `renv::install()` could install into the wrong library
  path on Windows, if the R installation had a site-wide profile that mutated
  the library paths. (#941)

* Fixed an issue where `renv::install()` would fail to find a package within
  the cache when using an abbreviated commit hash for installation. (#943)

* Fixed an issue where `renv`'s automatic snapshot was not run after calls to
  `renv::install()` in some cases. (#939)

* Fixed an issue where `renv` would incorrectly copy a package from the cache,
  if the cached version of the package and the requested version of the package
  had the same package version, even if they were retrieved from different
  sources. (#938)

* The path to an `renv` tarball can now be set via the environment variable
  `RENV_BOOTSTRAP_TARBALL`, to be used to help `renv` bootstrap from local
  sources. This can either be the path to a directory containing `renv`
  source tarballs, or the path to the tarball itself.

* Fixed an issue where the R site library would not be appropriately masked
  for resumed RStudio sessions. (#936)

# renv 0.15.2

* Fixed issues encountered in R CMD check.

# renv 0.15.1

* Fixed an issue where `renv` inadvertently inserted extra newlines into
  a `DESCRIPTION` file when adding `Remotes` fields after install. (#914)

* Fixed an issue where packages installed from a remote sub-directory would
  fail to install when later re-installed from the cache. (#913)

* `renv` now recognizes YAML chunk options of the form `#| key: value` when
  used in R Markdown documents. (#912)

* Fixed an issue where the R site library was visible in `renv` projects with
  the system library sandbox disabled.

* Fixed an issue where `renv` could update the wrong `.gitignore` in R
  processes launched by `callr` (e.g. in `devtools::install`). (#910)

* Fixed an issue where `renv` could fail to read mis-encoded
  DESCRIPTION files. (#908)

* Fixed an issue where `config$cache.symlinks()` would report `NULL` when
  unset. (#906)

# renv 0.15.0

* The development branch for `renv` has moved from master to main.

* `renv` package records in the lockfile now include a `Requirements`
  entry, which gives a list of R packages this package depends on
  in some way. This is primarily for internal use by the `pak`
  package.

* Fixed an issue where packages containing DESCRIPTION files using
  a latin1 encoding would not be read correctly by `renv`.

* Fixed an issue that could cause `renv::dependencies()` to fail
  when a malformed `DESCRIPTION` file was encountered. (#892)

* The path to the project-local `renv` folder can now be configured
  via the `RENV_PATHS_RENV` environment variable. This can be useful
  if you'd prefer to store your project's `renv` resources within
  an alternate location in the project. (#472)

* `renv` now uses an external library by default for R package projects,
  with the library located within `tools::R_user_dir("renv", "cache")`.
  This directory can be configured via the `RENV_PATHS_LIBRARY_ROOT`
  environment variable if desired. See
  `vignette("packages", package = "renv")` for more details. (#384)

* `renv` now uses the repositories as defined within the project lockfile
  (if any) when attempting to bootstrap itself in a project. (#820)

* The `renv` sandbox is now disabled by default -- see #614 for more details.

* `renv` gains the function `repair()`, to be used to attempt to repair
  the project library when links into the global package cache appear to
  be broken. (#378)

* Fixed an issue where the staging library used during install could fail to
  inherit the same directory permissions as the target library itself. (#331)

* Fixed an regression which caused `renv::history()` to fail. (#886)

* `renv` gains experimental support for the [pak](https://pak.r-lib.org/)
  package. Set `RENV_CONFIG_PAK_ENABLED = TRUE` in an appropriate `.Renviron`
  file to enable `pak` integration. When enabled, calls to `renv::install()`
  will use `pak` to download and install packages.

* `renv::init()` gains the `bioconductor` argument, to be used to initialize
  a project with a particular Bioconductor release. You can also use
  `renv::init(bioconductor = TRUE)` to initialize with the latest-available
  release for the version of R being used.

* Project settings can now be overridden by setting an R option of the same
  name. For example, one could force a project to use Bioconductor 3.14 by
  setting `options(renv.settings.bioconductor.version = "3.14")` within
  the project `.Rprofile` (or similar startup R profile).

* The ad-hoc package repository called "local sources" has been renamed to
  the "package cellar". In addition, the path to the cellar is now
  controlled by the `RENV_PATHS_CELLAR` environment variable, rather than
  `RENV_PATHS_LOCAL`. This change was made to reduce confusion between
  "local sources" of packages located somewhere on the filesystem, as
  opposed to packages explicitly placed in this ad-hoc repository.
  `RENV_PATHS_LOCAL` remains supported for backwards compatibility.

* The `RENV_PATHS_CELLAR` environment variable can now be set to multiple
  paths. Use `;` as a separator between paths; for example,
  `RENV_PATHS_LOCAL=/path/to/sources/v1;/path/to/sources/v2`. (#550)

* Packages installed via e.g. `renv::install("./path/to/package")`
  will now retain the relative path to that package within the lockfile.
  (#873)

* Fixed an issue where invalid `config` option values were not properly
  reported. (#773)

* `renv` now supports restoration of packages installed via one of the
  [r-universe](https://r-universe.dev/) repositories.

* `renv` gains the `bioconductor.version` project setting, used to freeze
  the version of Bioconductor used in a particular project. When set, this
  will override any version that might be selected via the `BiocManager`
  package. (#864)

* `renv` now infers that parameterized R Markdown documents have a dependency
  on the `shiny` package. In addition, R code included within the `params:`
  list will be parsed for dependencies. (#859)

* `renv` now ignores hidden directories during dependency discovery by default.
  If you want to force a particular hidden directory to be included for
  discovery, you can use a `.renvignore` file with an explicit inclusion
  criteria; e.g. `!.hidden/`.

* `renv` now supports the `*release` remotes specifier for GitHub repositories,
  for requesting installation of the latest declared release of a package from
  GitHub. (#792)

* `renv` now handles packages stored within the sub-directory of a Git
  repository better. (#793)

* Fixed an issue where `renv::history()` would fail to resolve the correct
  lockfile path if the working directory was changed. (#834)

* Refined dependency discovery within `glue::glue()` expressions.

* `renv` now parses packages referenced via the `base_format` field within
  an R Markdown document's YAML header. (#854)

* Fixed an issue where `renv` would fail to produce the appropriate binary
  repository URL for RSPM repositories built using Red Hat Enterprise Linux.

* Fixed an issue where `renv::snapshot()` could cause the environment name
  and / or path associated with a Python environment to be omitted from the
  lockfile. (#843)

* Fixed an issue where `renv::restore()` could fail to restore packages which
  referred to their source via an explicit path in the `Source` field. (#849)

* `renv` no longer requires explicit user consent when used within Singularity
  containers. (#824, @kiwiroy)

* `renv` now respects the `R_PROFILE_USER` environment variable, in addition
  to the `user.profile` configuration option, when considering whether the
  user `.Rprofile` should be examined for package dependencies. (#821)

* The `renv` auto-loader can now be disabled by setting the environment
  variable `RENV_AUTOLOADER_ENABLED = FALSE`. This can be useful if you'd like
  to explicitly control how a project is loaded, e.g. by calling `renv::load()`
  explicitly.

* `renv::snapshot()` gains the `repos` argument, to be used to force
  the lockfile to be generated with the requested set of R repositories
  encoded within.

* `renv` now validates that the `repos` option, as used by `renv::snapshot()`,
  is a named vector. (#811)

* Fixed an issue where `renv`'s shims, e.g. for `install.packages()`, failed
  to pass along other optional arguments to the shimmed function correctly.
  (#808)


To generate a diff of this commit:
cvs rdiff -u -r1.1 -r1.2 pkgsrc/devel/R-renv/Makefile
cvs rdiff -u -r1.3 -r1.4 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:1.1 pkgsrc/devel/R-renv/Makefile:1.2
--- pkgsrc/devel/R-renv/Makefile:1.1    Tue Aug 17 14:01:02 2021
+++ pkgsrc/devel/R-renv/Makefile        Sun Dec 18 04:18:29 2022
@@ -1,7 +1,7 @@
-# $NetBSD: Makefile,v 1.1 2021/08/17 14:01:02 mef Exp $
+# $NetBSD: Makefile,v 1.2 2022/12/18 04:18:29 mef Exp $
 
 R_PKGNAME=     renv
-R_PKGVER=      0.14.0
+R_PKGVER=      0.16.0
 CATEGORIES=    devel
 
 MAINTAINER=    pkgsrc-users%NetBSD.org@localhost
@@ -16,6 +16,7 @@ REPLACE_SH=   inst/bin/renv inst/resources
 
 TEST_DEPENDS+= R-covr-[0-9]*:../../devel/R-covr
 TEST_DEPENDS+= R-devtools-[0-9]*:../../devel/R-devtools
+TEST_DEPENDS+= R-pak-[0-9]*:../../devel/R-pak
 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

Index: pkgsrc/devel/R-renv/distinfo
diff -u pkgsrc/devel/R-renv/distinfo:1.3 pkgsrc/devel/R-renv/distinfo:1.4
--- pkgsrc/devel/R-renv/distinfo:1.3    Tue Oct 26 10:14:08 2021
+++ pkgsrc/devel/R-renv/distinfo        Sun Dec 18 04:18:29 2022
@@ -1,5 +1,5 @@
-$NetBSD: distinfo,v 1.3 2021/10/26 10:14:08 nia Exp $
+$NetBSD: distinfo,v 1.4 2022/12/18 04:18:29 mef Exp $
 
-BLAKE2s (R/renv_0.14.0.tar.gz) = b01cff52fc73cec608806c2853aff9730e1295f1c59757372e4d20790930281f
-SHA512 (R/renv_0.14.0.tar.gz) = 75062bcd441b9e2925368c8f1d9c37521607048dd550dc0ac12a6323bc651a95e0521c804392f64e4c6e091d6758ea9262e600d6a02cf1f2903dc18c4e0194ba
-Size (R/renv_0.14.0.tar.gz) = 448230 bytes
+BLAKE2s (R/renv_0.16.0.tar.gz) = 35c2a399cac7584f3d94bdb0a6481f93146164f3a504cfc7981aa32225eb711e
+SHA512 (R/renv_0.16.0.tar.gz) = 3fab86f8cf7f1491f33ca0898b36211d01590efb5d4adfc410515731193722ca3f403c161af0ff043d691adfe3b4cc57e23c99d4280641a7d08eecd507e4083b
+Size (R/renv_0.16.0.tar.gz) = 1004572 bytes