NEWS.md
startup() gained argument encoding, which controls the encoding used to parse the R startup files.
Now sysinfo() report also on Jupyter, Visual Studio Code (VSCode) webR via flags jupyter, vscode, and webr.
Now install() and uninstall() respect environment variable R_PROFILE_USER, if specified.
Now startup() ignores files and folders specific version control, e.g. .git, .gitignore, .hg, .hgignore, and .svn.
sysinfo() gained flag rapp, which is TRUE when running R from the R.app GUI on macOS. This flag equals sysinfo()$gui == "AQUA".
sysinfo() gained flag rgui, which is TRUE when running R from the Rgui GUI on MS Windows. This flag equals sysinfo()$gui == "Rgui".
startup::startup(debug = TRUE) now reports on any Rconsole configure file processed when running R via the Rgui graphical user interface (GUI) available on MS Windows.
startup::check() no longer warns when R sets environment variables R_LIBS_USER and R_LIBS_SITE to the default folders that do not exist by default.
startup::check() would report on an incorrect default value if R option encoding or stringsAsFactors was set during startup to an unsafe value.
An R script in environment variable R_STARTUP_FILE will be evaluated by startup::startup() after Renviron and Rprofile files have been processed, and after any R_STARTUP_INIT code. For example, R_STARTUP_FILE="setup.R" R launches R, processes all R startup files, and at the end parses and evaluates file ‘setup.R’.
sysinfo() gained field quiet, which is TRUE if R or Rscript was called with command-line options -q, --quiet, or --silent.
sysinfo() gained field save, which is TRUE if R or Rscript was called with command-line options --save, FALSE if called with --no-save, and otherwise NA.
Now startup::startup(debug = TRUE) reports on any environment variables, options, global variables, locale settings that were added, removed, and changed while processing an Rprofile file.
startup::startup(debug = TRUE) now reports on any changes to the current working directory and the R library path while processing an Rprofile file.
startup::startup(debug = TRUE) already reported on updates to the state of R’s random number generator (RNG). Now it also reports on updates to the RNG kind, including what the change was.
startup::startup() now searches for Renviron.d/ and Rprofile.d/ (note, without leading periods) in user’s configuration folder in a way that is compatible with tools::R_user_dir() of R (>= 4.0.0) and that follows operating-system standards. For example, for Linux ~/.config/R/startup/, for macOS ~/Library/Preferences/org.R-project.R/R/startup/, and for MS Windows %LOCALAPPDATA%/R/cache/R/startup/. If environment variable XDG_CONFIG_HOME is set, then ${XDG_CONFIG_HOME}/R/startup/ is used. For now, startup::install() will continue to create ~/.Renviron.d/ and ~/.Rprofile.d/ by default.
startup::install() gained argument make_dirs to control whether directories .Renviron.d/ and .Rprofile.d/ should be created, if missing.
Add on_session_enter() for registering R functions and expressions to be evaluated at the end of R’s startup process via a custom .First() that is added to the global environment. If there is a .First() function on the search path, including any preexisting one in the global environment, that is called at the end.
Add on_session_exit() for registering R functions and expressions to be called at the very end when the R session terminates.
Now startup() warns about non-standard, platform-specific capitalization of Renviron and Rprofile file names. For example, although ~/.RProfile works on MS Windows and macOS with non-case sensitive file systems, the officially supported file name is ~/.Rprofile.
Now startup(debug = TRUE) reports on .Last() and .Last.sys().
Now startup(debug = TRUE) gives a note if it detects that an Rprofile script updated the state of R’s random number generator (RNG).
Harmonized cache folder options toward tools::R_user_dir() of R (>= 4.0.0).
Now startup(debug = TRUE) reports on R_SCRIPT_DEFAULT_PACKAGES.
Now startup(debug = TRUE) reports on tempdir() and environment variables TMPDIR, TMP, and TEMP that controls the root of the temporary folder.
Now it is sufficient to call startup(dryrun = TRUE) to see what the R startup would have been. Previously one would also have to specify debug = TRUE.
Now startup(debug = TRUE) reports on packages loaded, attached, unloaded, and detached per Rprofile file processed. It also reports on other environments attached and detached.
Now startup(debug = TRUE) reports also on the Rprofile file in the base package, i.e. system.file("R", "Rprofile", package = "base").
startup::startup(check = TRUE) no longer warns if environment variables R_LIBS_SITE or R_LIBS_USER have value NULL, which in R (>= 4.2.0) corresponds to setting them to be empty.
startup(debug = TRUE) now reports on number of lines and file size also for the R_TESTS file.
startup(debug = TRUE) [sic!] now checks that the environment variables that the different Renviron files set are actually set and produce an informative warning message if not. This confirms that, at least for R 4.0.2 for Windows, Rgui does not process ~/.Renviron unless Rgui is launched from that folder.
Using regular, non-fancy single quotes in any output produced.
startup.disable (R_STARTUP_DISABLE), startup.init (R_STARTUP_INIT), and startup.rdata (R_STARTUP_RDATA).help("startup.options", package = "startup"), which lists environment variables and R options that the startup package use.The new default of option stringsAsFactors in R (>= 4.0.0) would trigger a startup warning.
It was not possible to disable the validation of R option error and environment variables such as R_LIBS_USER, R_PROFILE_SITE, and R_CHECK_ENVIRON. These validations can now be disabled by specifying argument check = FALSE, or the corresponding R option, or environment variable. Validation of error specifically can be disable by adding "error" to environment variable R_STARTUP_CHECK_OPTIONS_IGNORE or to option startup.check.options.ignore. The default is to ignore error.
startup(all = TRUE) now processes any startup folders in the home directory before those in the current working directory. Previously it was vice verse. With the new way, it is possible to override settings made in ~/.Renviron.d/ or ~/.Rprofile.d/ with custom ones in local ./.Renviron.d/ and ./.Rprofile.d/ folders.Setting environment variable R_STARTUP_RDATA to "remove" will cause an existing ‘./.RData’ file to be skipped by automatically removing it. If "rename", it will be renamed to ‘./.RData.YYYYMMDD_hhmmss’ where the timestamp is the last time the file was modified. If "prompt", then the user is prompted whether they want to load the file or rename it. In non-interactive session, "prompt" will fallback to loading by default. To fallback to renaming the file, use "prompt,rename". Thus, setting R_STARTUP_RDATA=rename in an .Renviron file will make sure no .RData file is ever loaded while still preserving them.
RStudio Console: The only way to prompt a user during the R startup process in the RStudio Console is via a graphical popup window. Because of this, R_STARTUP_RDATA=prompt will trigger a popup window in RStudio if there is a .RData file.
startup(debug = TRUE) would not only report on the name of an environment variable, but also parts of its value, if the value contained equal signs.
The source information, that is, the filename and line locations, were dropped from functions defined via startup(). To get the filename where a function was defined use getSrcFilename(my_fcn, full.names = TRUE).
RStudio: Using renv together with startup() while in the RStudio Console would produce a false warning on the error option being set.
startup::startup() will return immediately without processing R startup files if environment variable R_STARTUP_DISABLE is set to TRUE.
Added flag radian to sysinfo() indicating whether R runs in radian (previously known as rtichoke and rice) or not. Please stop using the rice and rtichoke flags.
The startup::startup() code snipped injected in the .Rprofile file by startup::install() now prefix error messages with ‘.Rprofile error:’ to help troubleshooting errors.
The validation of R_LIBS, R_LIBS_SITE, R_LIBS_USER by startup::check() had a _R_CHECK_LENGTH_1_LOGIC2_ bug.
The startup checks asserting that update.packages() is not called would pick up not only those with the period (‘.’) but any character in that position.
startup::startup() no longer warn about startup files with non-declared key names being skipped. This warning was introduced in startup 0.10.0 due to how such files were filtered out.Renviron and Rprofile startup files that use <key>!=<value> filters with non-defined keys are now included. Previously they were skipped. Note that <key>=<value> files are indeed skipped when <key> is not defined.
startup() now produces an informative warning if it detects that an R option that is considered unsafe to change from its default, e.g. changing encoding other than in interactive mode may break package installations and changing stringsAsFactors will summon the dead.
Added support for when=<periodicity> file declarations, where <periodicity> can be ‘once’, ‘hourly’, ‘daily’, ‘weekly’, ‘fortnightly’, and ‘monthly’. A startup file with such a declaration will be processed at most once per <periodicity>, e.g. a file with ‘when=daily’ somewhere in the pathname will be processed once per day. The periodicity is based on the walltime in the local time zone, e.g. if a file with ‘when=daily’ was processed one minute before midnight, it will be processed again if an R session is started one minute past midnight. Updating the file timestamp of a ‘when’ file will reset its timer.
Code in environment variable R_STARTUP_INIT will now be evaluated by startup::startup() after Renviron and Rprofile files have been processed. For example, R_STARTUP_INIT="x <- 1" R will launch R with x == 1.
startup(debug = TRUE) now also reports on .First().
The messages of warnings and errors produced by the startup package itself now mention which startup function they originate from. This helps to identify the origin of these when produced during the R startup process.
Added warn(), which produces a warning with information on which R source file it was produced in, if any.
R CMD check --as-cran NOTEs.startup() did not ignore files with names such as #foo.R#.renviron() and rprofile(). Use renviron_d() and rprofile_d().startup(debug = TRUE) now also displays the expanded path to any file or folder listed. It also gives information on files that known environment variables (e.g. R_ENVIRON_USER) point to. For Renviron files, it also reports on names of the environment variables set in each of those files.
startup(debug = TRUE) reports on the search path and loaded namespaces, and what packages will be attached after R’s startup finishes.
Added character dirname to sysinfo() specifying the basename of the current working directory.
startup(check = TRUE), warns if R_ENVIRON, R_ENVIRON_USER, R_PROFILE, R_PROFILE_USER, R_BUILD_ENVIRON, or R_CHECK_ENVIRON specifies non-existing files.
startup::check(fix = TRUE) now returns the pathnames of any files that needed to be fixed and was successfully updated.
RStudio: startup() now gives an informative warning if option error is set during the R startup and it will be overridden by RStudio’s debug settings.
Windows: Calling startup::restart() in the Windows RGui now produces an error clarifying that the RGui cannot be restarted this way.
startup::install() would append the startup::startup() statement to the last line in .Rprofile if that line (incorrectly) did not have a newline.
startup::startup(check = TRUE) would give “Error in if (!eof_ok(file)) { argument is of length zero” on Windows if the Rprofile file checked is a symbolic link.
<key>=<value> filters with non-declared keys are skipped. Previously they were always processed. This update makes it easier to include “secrets”, e.g. files in folder ~/.Renviron.d/private/SECRET=banana/ will only be included if the environment variable SECRET is set to exactly ‘banana’. An informative warning, which can be disabled, will be produced by startup 0.10.* until startup 0.11.0 is released.Added is_debug_on() which returns TRUE if the startup debug mode is on. To control the debug mode, see ?startup::startup.
startup(debug = TRUE) reports on several R_* environment variables.
restart() gained argument quiet for controlling whether the restart should be quiet or not.
Added flag microsoftr to sysinfo() indicating whether R runs in Microsoft R Open or not.
Added flag pqr to sysinfo() indicating whether running pqR (“A Pretty Quick # Version of R”), or not.
Added flag rstudioterm to sysinfo() indicating whether R runs in an RStudio Terminal or not. To test whether R runs via the RStudio Console, use the rstudio flag.
Added flag rtichoke to sysinfo() indicating whether R runs in rtichoke (previously known as Rice) or not. Please stop using the rice flag and start using the rtichoke instead (both have identical values).
The ess flag of sysinfo() is now based on whether “ESSR” is in search() or not - used to check for environment variable EMACS equaling “t” or not.
Now startup::restart() also work when running R via rtichoke.
startup::restart() would not work in the RStudio Terminal. Note that it does not work in the RStudio Console due to limitations in RStudio.
On Windows, startup::startup() would produce a false warning on non-existing R_LIBS_USER folders.
restart() for restarting the current R session. It can also be used to adjust various R command-line arguments and environment variables, e.g. restart(as = "R CMD build") mimics the R CMD build setup as far as possible.Added startup::current_script() which returns the .Rprofile.d/ pathname that is currently processed by startup::startup().
Added flag rice to sysinfo() indicating whether R runs via Rice or not, meaning it can be used as a file and directory name tag, e.g. rice=TRUE.
startup(debug = TRUE) outputs much more information on what has taken place and what will take place through R’s startup process.
startup() gained argument check for controlling whether the content of startup files should be validated or not.
check(), and therefore also startup(check = TRUE), warns if R_LIBS, R_LIBS_SITE, or R_LIBS_USER specifies non-existing directory.
renviron() and rprofile() are now defunct. Removed api()$renviron() and api()$rprofile(). Use renviron_d() and rprofile_d() instead.Convenient session details are now gathered and recorded as R options immediately after processing ‘.Renviron.d’ files. These options, prefixed startup.session., are available while processing ‘.Rprofile.d’ files and, by default, also after startup::startup() has completed. For information on session details recorded, see help("startup_session_options").
Added a package vignette (available only in R >= 3.0.2).
startup() ignores more of the hidden files and folders that macOS may create and which should not be sourced during startup. For instance, when copying a file ‘foo.R’ to a non-macOS file system, an auxiliary file ‘._foo.R’ may be created as well.New conditional <key>=<value> specification: an unknown <key> (i.e. one that is not one of the known sysinfo() fields or ‘package’) will be interpreted as the name of an environment variable. For instance, files path/LANGUAGE=en/*.R will be included only if system environment variable LANGUAGE equals ‘en’ (or is not set).
startup::install() now injects try(startup::startup()) such that install.packages("startup") will work even when startup is not installed, e.g. after a major-version R update.
startup::install() and startup::uninstall() now output messages on what is done and why, and they now return the R startup file modified. They also produce a warning if startup is already installed or uninstalled, respectively.
startup::install() gained argument overwrite to control whether to append (default) to a pre-existing R startup file or to overwrite it.
ROBUSTNESS: Backups now assert that not only the backup files are created, but also that they have the same file size as the original file.
Startup directory or file names that start with two or more periods are now excluded, e.g. ~/.Rprofile.d/..hide/test.R.
startup() protects against attempts to update R packages also via pacman::p_up() in addition to utils::update.packages().
Added flag ess to sysinfo() indicating whether R runs under Emacs Speaks Statistics (ESS) or not.
startup(debug = TRUE) detects if R_TESTS is set and reports which the file is and that the base package has already processed it.
startup() ignores macOS files named .DS_Store and directories named __MACOSX (and their content). Previously, such files could result in startup errors.Now it is possible to do negated filename specifications, e.g. hpc,package=future/os!=windows.
Filename flags can now be specified a TRUE, FALSE, T, F, 1, and 0 (non-case sensitive), e.g. interactive=false and interactive=0.
Added element gui to sysinfo().
Added flags rstudio and wine to sysinfo() indicating whether R runs via RStudio and via Linux Wine, respectively.
New conditional <key>=<value> specification: Directory and file names containing a package=<name> specification will be processed if and only if package <name> is installed.
Errors occurring while sourcing an Rprofile file now also contain information about in file the error occurred. Lines with invalid syntax in Renviron files are ignored with a message outputted saying so. Due to limitations in how base::readRenviron() works, it is not possible to detect these errors nor capture the outputted message.
Now objects are auto printed to match the behavior of the R startup process.
startup(debug = TRUE) now outputs time stamps since start per entry.
renviron() and rprofile() were renamed to renviron_d() and rprofile_d(), respectively.sibling = FALSE to startup(). If sibling = TRUE, the corresponding startup file needs to exist in the same location as the directory in order for the directory to be processed.