renv/library/R-4.0/x86_64-w64-mingw32/renv/NEWS.md

In tessaleejohnson/corclus: Simulate Data from the Correlated Cluster Multiple Membership Model

renv 0.12.5

• Fixed an issue where renv would fail to bootstrap. (#608)

renv 0.12.4

• renv now invalidates the available packages cache if the https_proxy environment variable changes. (#579)

• renv::install(<pkg>) will now install the latest-available version of that package from local sources, if that package is available and newer than any package available on the active package repositories. (#591)

• The configuration option startup.quiet has been added, allowing one to control whether renv will display the typical startup banner when a project is loaded.

• renv now better handles being unloaded and reloaded within the same R session. In particular, warnings related to a corrupted lazy-load database should no longer occur. (#600)

• renv no longer re-installs packages that are already installed and up-to-date in bare calls to renv::install().

• renv now uses the R temporary directory for staging, when performing transactional restores / installs. If you need to control the path used for staged installs, please set the RENV_PATHS_LIBRARY_STAGING environment variable.

• The install.verbose configuration option has been added. When set to TRUE, renv will stream the output generated by R when performing a package installation. This can be helpful in some cases when diagnosing a failed restore / install. (#330)

• Fixed an issue where renv could fail to parse R Markdown chunk headers with an empty label. (#598)

• The environment variable RENV_PATHS_LIBRARY_ROOT_ASIS can now be used to control whether the project name should be used as-is when forming the library path within the RENV_PATHS_LIBRARY_ROOT folder. Set this to "TRUE" if you would prefer renv did not append a unique identifier to your project's library path. (#593)

• Fixed an issue where GitLab references were not URL encoded. (#590)

• renv no longer emits warnings when parsing multi-mode R files that make use of re-used knitr chunks (those specified as <<label>>). (#586)

• The library used for staged installs can now be configured via the RENV_PATHS_LIBRARY_STAGING environment variable. (#584)

• Fixed an issue where bootstrapping an older version of renv could fail if the R repositories had not been appropriately set.

renv 0.12.3

• Fixed an issue where renv::dependencies() could give an error if called with a path argument of length > 1.

• renv::restore() gains the rebuild argument, allowing users to control whether packages should be rebuilt on restore() rather than installed via links or copies from the cache, or other sources providing already-installed packages.

• renv will now attempt to bootstrap itself from CRAN, in addition to any repositories declared via getOption("repos"). If you'd prefer to disable this behavior, you can set options(renv.bootstrap.repos = character()).

• The renv setting r.version has been added. This can be set if you'd like to associate a particular project with a specific version of R, independent of the version of R actually used when subsequent lockfiles are created via renv::snapshot(). For example, setting renv::settings$r.version("4.0") will ensure that R version "4.0" is encoded in the lockfile for future calls to renv::snapshot() in a project. (#254)

• renv::dependencies() now detects the usage of R packages within dotfiles; e.g. the project .Rprofile. (#569)

• renv::status() gains the cache argument, used to control whether renv::status() also performs diagnostics on the global package cache. (#570)

• Fixed an issue where renv::status() would make an un-necessary call to renv::dependencies(). (#570)

• Fixed an issue where renv::install("bioc::<package>", rebuild = TRUE) would fail to install the requested package. (#565)

• Fixed an issue where the repository name for a package installed from an R package repository was sometimes incorrect. (#402)

• When RENV_PATHS_LIBRARY_ROOT is set, renv will now disambiguate library paths based on a hash of the project's path. (#564)

renv 0.12.2

• renv no longer errs when running tests with _R_CHECK_SUGGESTS_ONLY_=false.

renv 0.12.1

• renv now ensures all of its dependencies are loaded eagerly when running tests, to avoid issues with missing + lazily-loaded packages.

• renv::snapshot() now accepts library paths specified with a relative path. (#562)

• renv::snapshot() no longer excludes the project itself, for R package projects that use golem. (#538)

• The renv configuration option cache.symlinks can now be used to control whether renv used symlinks into the cache, as opposed to full package copies. Please see ?renv::config for more details. (#556)

• renv::snapshot() gains the packages argument, to be used when creating a lockfile that captures a specific set of packages and their dependencies. renv will use the currently-installed versions of those packages when determining the package records to be written to the lockfile. (#554)

• renv::dependencies() now accepts an R function as the first argument, for finding the packages used by a particular function. Currently, package usages must be prefixed with :: to be detected. (#554)

• renv::record(<package>) now ensures that the latest-available version of that package is recorded in the lockfile. Previously, a package record without any specified version was added instead. For existing records without a recorded version, the latest-available version on the package repositories will be used during restore() instead. (#540)

• renv now reads the default branch tagged for repositories created on GitHub, ensuring that calls of the form renv::install("<user>/<repo>") resolve to the declared default branch, rather than always defaulting to "master". (#557)

• renv now only installs packages from sources if it detects that build tools are available. This determination is done by checking whether make is available on the PATH. (#552)

• Warnings related to unknown sources can now be suppressed by setting options(renv.warnings.unknown_sources = FALSE). (#546)

• renv now ignores chunks with the parameter exercise=TRUE set, under the assumption that such chunks might contain errors and so otherwise be un-parsable.

• renv now warns if sandbox generation takes a long time (> 30 seconds).

• renv now provides an optional locking mechanism, to help minimize the chance of interprocess conflicts when multiple R processes need to use the same renv project. The option is currently disabled by default; it can be enabled by setting options(renv.config.locking.enabled = TRUE) in an appropriate R startup file. (#525)

renv 0.12.0

• renv now uses R's internal tar implementation by default on Windows. This is done to avoid issues that may occur when a version of tar.exe on the PATH exists, but does not accept Windows-style paths. The TAR environment variable can be set if one needs to explicitly force the use of a particular tar.exe executable. (#521)

• renv now prepends renv (<version>) to the user agent string. This should help ensure that package binaries are located when installing packages from RSPM outside of RStudio. (#520)

• renv now uses a task callback to detect mutations to the project library when the auto.snapshot configuration option is enabled. This will help ensure that automatic snapshots occur when packages are installed via a mechanism not explicitly understood by renv. (#501)

• renv now treats the user + site libraries as package sources during a restore. If renv sees that a package already installed in one of these libraries is compatible with the record requested via renv::install() or renv::restore(), that copy of the package will be copied and used. (#492)

• renv now performs a lighter-weight check as to whether the project lockfile is synchronized with the project library on load. The default value for the synchronized.check config option has been changed back to TRUE. (#496)

• renv now handles the remotes syntax for installing packages lying within the sub-directory of a GitHub repository; that is, renv::install("user/repo/subdir") should work as expected. (#497)

• Fixed an issue where renv did not construct the correct URL for packages to be installed from Bitbucket remotes. (#494)

• Fixed an issue where the RENV_PATHS_PREFIX environment variable was inappropriately normalized when renv was loaded. (#465)

renv 0.11.0

• Fixed an issue where renv::install(..., type = "binary") would still attempt to install packages from sources in some cases. (#461)

• renv now always writes renv/.gitignore, to ensure that the appropriate directories are ignored for projects which initialize git after renv itself is initialized. (#462)

• R Markdown documents with the .Rmarkdown file extension are now parsed for dependencies.

• Fixed an issue where setting the external.libraries configuration option would trigger a warning. (#452)

• Improved handling of unicode paths on Windows. (#451)

• renv::snapshot(project = <path>) now properly respects .gitignore / .renvignore files, even when that project has not yet been explicitly initialized yet. (#439)

• The default value of the synchronized.check option has been changed from TRUE to FALSE.

• Fixed an issue where packages downloaded from Bitbucket and GitLab did not record the associated commit hash.

• Fixed an issue where attempting to install packages from GitLab could fail to install the correct version of the package. (#436)

• renv::snapshot() now preserves records in a lockfile that are only available for a different operating system. This should make it easier to share lockfiles that make use of platform-specific packages. (#419)

• renv better handles files that are removed during an invocation to renv::dependencies(). (#429)

• The configuration option install.staged has been renamed to install.transactional, to better reflect its purpose. install.staged remains supported as a deprecated alias.

• Fixed an issue where renv could fail to parse non-ASCII content on Windows. (#421)

• renv::update() gains the exclude argument, useful in cases where one would like to update all packages used in a project, except for a small subset of excluded packages. (#425)

• renv::update() now respects the project ignored.packages setting. (#425)

• Fixed an issue where RSPM binary URL transformations could fail for Ubuntu Trusty. (#423)

• renv now records the OS_type reported in a package's DESCRIPTION file (if any), and ignores packages incompatible with the current operating system during restore. (#394)

renv 0.10.0

• renv::install() gains the type argument, used to control whether renv should attempt to install packages from sources ("source") or using binaries ("binary").

• renv now knows how to find and activate Rtools40, for R 4.0.0 installations on Windows.

• The RENV_PATHS_PREFIX environment variable can now be used to prepend an optional path component to the project library and global cache paths. This is primarily useful for users who want to share the renv cache across multiple operating systems on Linux, but need to disambigutate these paths according to the operating system in use. See ?renv::paths for more details.

• Fixed an issue where renv::install() could fail for packages from GitHub whose DESCRIPTION files contained Windows-style line endings. (#408)

• renv::update() now also checks and updates any Bioconductor packages used within a project. (#392)

• renv now properly parses negated entries within a .gitignore; e.g. !script.R will indicate that renv should include script.R when parsing dependencies. (#403)

• Fixed an issue where packages which had only binaries available on a package repository were not detected as being from a package repository. (#402)

• Fixed an issue where calls of the form p_load(char = <vctr>) caused a failure when enumerating dependencies. (#401)

• Fixed an issue where renv::install() could fail when multiple versions of a package are available from a single repository, but some versions of those packages are incompatible with the current version of R. (#252)

• Fixed an issue where downloads could fail when the associated pre-flight HEAD request failed as well. (#390)

• Fixed an issue where empty records within a DESCRIPTION file could cause renv::dependencies() to fail. (#382)

• renv will now download binaries of older packages from MRAN when possible.

• renv will now attempt to re-generate the system library sandbox if it is deleted while a session is active. (#361)

• Fixed an issue where Python packages referenced using reticulate::import() were incorrectly tagged as R package dependencies. Similarly, renv now only considers calls to modules::import() if those calls occur within a call to modules::module(). (#359)

• renv::scaffold() now also generates a lockfile when invoked. (#351)

• The argument confirm has been renamed to prompt in all places where it is used. confirm remains supported for backwards compatibility, but is no longer explicitly documented. (#347)

• The continuous integration renv vignette now also contains a template for using renv together with GitLab CI. (#348, @artemklevtsov)

• renv now properly resets the session library paths when calling renv::deactivate() from within RStudio. (#219)

• renv::init() now restores the associated project library when called in a project containing a lockfile but no project library nor any pre-existing project infrastructure.

• Fixed an issue on Windows where attempts to download packages from package repositories referenced with a file:// scheme could fail.

• The configuration option dependency.errors has been added, controlling how errors are handled during dependency enumeration. This is used, for example, when enumerating dependencies during a call to renv::snapshot(). By default, errors are reported, and (for interactive sessions) the user is prompted to continue. (#342)

• renv::dependencies() gains two new arguments: the progress argument controls whether renv reports progress while enumerating dependencies, and errors controls how renv handles and reports errors encountered during dependency discovery. The quiet argument is now soft-deprecated, but continues to be supported for backwards compatibility. Specifying quiet = TRUE is equivalent to specifying progress = FALSE and errors = "ignored". Please see the documentation in ?dependencies for more details. (#342)

• The environment variable RENV_PATHS_LIBRARY_ROOT can now be set, to instruct renv to use a particular directory as a host for any project libraries that are used by renv. This can be useful for certain cases where it is cumbersome to include the project library within the project itself; for example, when developing an R package. (#345)

• The code used to bootstrap renv (that is, the code used to install renv into a project) has been overhauled. (#344)

• renv no longer unsets an error handler set within the user profile when loading a project. (#343)

• renv gains the "explicit" snapshot type, wherein only packages explicitly listed as dependencies within the project DESCRIPTION file (and those package's transitive dependencies) will enter the lockfile when renv::snapshot() is called. (#338)

• renv will now transform RSPM source URLs into binary URLs as appropriate, allowing renv to use RSPM's binary repositories during restore. See ?config for more details. (#124)

• renv will now infer a dependency on hexbin in projects that make use of the ggplot2::geom_hex() function.

• renv now tries to place Rtools on the PATH when a package is installed with the install.packages() hook active. (#335)

renv 0.9.3

• Fixed an issue where attempts to specify RENV_PATHS_RTOOLS would be ignored by renv. (#335)

• Fixed an issue where downloads could fail when using the wininet downloader, typically with a message of the form "InternetOpenUrl failed: 'The requested header was not found'".

• renv better handles projects containing special characters on Windows. (#334)

• renv better handles unnamed repositories. (#333)

• renv gains the config option hydrate.libpaths, allowing one to control the library paths used by default for renv::hydrate(). (#329)

• renv::hydrate() gains the sources argument, used to control the library paths used by renv when hydrating a project. (#329)

• renv now sandboxes the system library by default on Windows.

• renv now validates that the Xcode license has been accepted before attempting to install R packages from sources. (#296)

• The R option renv.download.override can now be used to override the machinery used by renv when downloading files. For example, setting options(renv.download.override = utils::download.file) would instruct renv to use R's own downloader when downloading files from the internet. This can be useful when configuration of curl is challenging or intractable in your environment, or you've already configured the base R downloader suitably.

• renv::use_python("~/path/to/python") now works as expected.

• renv now properly expands R_LIBS_SITE and R_LIBS_USER when set within a startup .Renviron file. (#318)

• The renv.download.headers option can now be used to provide arbitrary HTTP headers when downloading files. See the Authentication section in vignette("renv") for more details. (#307)

• renv gains the project setting package.dependency.fields, for controlling which fields in an R package's DESCRIPTION file are examined when discovering recursive package dependencies. This can be useful when you'd like to instruct renv to track, for example, the Suggests dependencies of the packages used in your project. (#315)

• renv now better handles repositories referenced using file URIs.

• Packages installed from GitHub using renv::install() will now also have Github* fields added, in addition to the default Remote* fields. This should help fix issues when attempting to deploy projects to RStudio Connect requiring packages installed by renv. (#397)

• renv now prefers using a RemoteType field (if any) when attempting to determine a package's source. (#306)

• renv gains a new function renv::scaffold(), for generating renv project infrastructure without explicitly loading the project. (#303)

• renv now updates its local .gitignore file, when part of a git repository whose git root lives in a parent directory. (#300)

renv 0.9.2

• Fixed an issue in invoking find on Solaris.

renv 0.9.1

• Fixed an issue in invoking cp on Solaris.

renv 0.9.0

• renv gains a new function renv::record(), for recording new packages within an existing lockfile. This can be useful when one or more of the recorded packages need to be modified for some reason.

• An empty .renvignore no longer erroneously ignores all files within a directory. (#286)

• renv now warns if the version of renv loaded within a project does not match the version declared within the renv autoloader. (#285)

• renv gains a new function renv::run(), for running R scripts within a particular project's context inside an R subprocess. (#126)

• The algorithm used by renv for hashing packages has changed. Consider using renv::rehash() to migrate packages from the old renv cache to the new renv cache.

• renv::status() now reports packages which are referenced in your project code, but are not currently installed. (#271)

• renv is now able to restore packages with a recorded URL remote. (#272)

• renv::dependencies() can now parse R package dependencies used as custom site generator in an Rmd yaml header. (#269, @cderv)

• renv now properly respects a downloader requested by the environment variable RENV_DOWNLOAD_FILE_METHOD.

• renv no longer sources the user profile (normally located at ~/.Rprofile) by default. If you desire this behavior, you can opt-in by setting RENV_CONFIG_USER_PROFILE = TRUE; e.g. within your project or user .Renviron file. (#261)

• renv::restore() gains the packages argument, to be used to restore a subset of packages recorded within the lockfile. (#260)

• renv now tries harder to preserve the existing structure in infrastructure files (e.g. the project .Rprofile) that it modifies. (#259)

• renv now warns if any Bioconductor packages used in the project appear to be from a different Bioconductor release than the one currently active and stored in the lockfile. (#244)

• renv now normalizes any paths set in the RENV_PATHS_* family of environment variables when renv is loaded.

• Fixed an issue where renv would not properly clean up after a failed attempt to call Sys.junction(). (#251)

• Fixed an issue where renv would, in some cases, copy rather than link from the package cache when the library path had been customized with the RENV_PATHS_LIBRARY environment variable. (#245)

• The method renv uses when copying directories can now be customized. When copying directories, renv now by default uses robocopy on Windows, and cp on Unix. This should improve robustness when attempting to copy files in some contexts; e.g. when copying across network shares.

• renv now tracks the version of Bioconductor used within a project (if applicable), and uses that when retrieving the set of repositories to be used during renv::restore().

• renv::dependencies() can now parse R package dependencies declared and used by the modules package. (#238, @labriola)

• Fixed an issue where renv::restore() could fail in Docker environments, usually with an error message like 'Invalid cross-device link'. (#243)

• renv::install() disables staged package install when running with the Windows Subsystem for Linux. (#239)

renv 0.8.3

• renv::dependencies() gains a new argument dev, indicating whether development dependencies should also be included in the set of discovered package dependencies. By default, only runtime dependencies will be reported.

• renv has gained the function renv::diagnostics(), which can occasionally be useful in understanding and diagnosing renv (mis)behaviors.

• renv::equip() can now be used on macOS to install the R LLVM toolchain normally used when compiling packages from source. renv will also use this toolchain as appropriate when building packages from source.

• renv::install() now provides a custom Makevars when building packages on macOS with Apple Clang, to avoid issues due to the use of '-fopenmp' during compilation.

• renv::install() now respects explicit version requests when discovered in a project's DESCRIPTION file. (#233)

• Fixed an issue where renv:::actions() would fail to report any actions if the project lockfile was empty. (#232)

• When using renv for R package development, renv will no longer attempt to write the package being developed to the lockfile. (#231)

• Fixes for checks run on CRAN.

• renv will now search for Rtools in more locations. (#225)

• renv::load() now ensures that the version of renv associated with the loaded project is loaded when possible. In addition, experimental support for switching between projects with renv::load() has been implemented. (#229)

• renv::dependencies() no longer treats folders named with the extension .Rmd as though they were regular files. (#228)

• It is now possible to install source packages contained within .zip archives using renv::install().

• Fixed an issue where attempts to call renv::restore() with the path to the lockfile explicitly provided would fail. (#227)

renv 0.8.2

• Further fixes for checks run on CRAN.

renv 0.8.1

• Fixes for checks run on CRAN.

renv 0.8.0

• Initial CRAN release.

tessaleejohnson/corclus documentation built on Oct. 11, 2022, 3:46 a.m.