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.
startup(debug = TRUE) did not report on global
variables starting with a period, e.g. .Last().startup::startup(debug = TRUE) now reports on
environment variable R_ENABLE_JIT and whether the R
just-in-time (JIT) compiler will be enabled or not, and at what
level.When startup() tried to rename .RData
file (e.g. when environment variable
R_STARTUP_RDATA=rename), it would produce
.Rprofile error: cannot xtfrm data frames.
startup() would give ‘.Rprofile error …: could not
find function “anyNA”’ in R (< 3.1.0).
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.
startup(debug = TRUE) would report file information on
R_PROFILE and R_PROFILE_USER files as if they
were Renviron files, not Rprofile files.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).
startup(unload = TRUE) failed when there was an .RData
file and environment variable R_STARTUP_RDATA or R option
startup.rdata specifies "prompt".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::restart(quiet = TRUE) would give an error in
radian saying --quiet is not supported, but it’s supported
in radian (>= 0.2.8) since 2018-08-27.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.install(backup = TRUE) guarantees that the
.Rprofile file is backed up, otherwise, an error is produced. Previously
it could silently fail if a backup file with the exact same name already
existed.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.A file extension *.R would incorrectly become part of the
<value> in a trailing
<key>=<value> specification.
Now R_STARTUP_DEBUG=TRUE also works for Rscript;
used to work only for the R executable.
Some macOS backup files would not be filtered out when running on Windows.
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.