Is there any way to run an applescript within R?
I found this reference in an R FAQ on CRAN
From release 1.3.1 R has partial support for AppleScripts. This means two things: you can run applescripts from inside R using the command applescript() (see the corresponding help)
But in my current version of R
R version 3.4.1 (2017-06-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6
neither applescript() nor ?applescript() returns anything.
Thanks, Simon
Those features aren't in modern R versions (IIRC they harken back to pre-macOS/Mac OS X days).
However, the applescript() function performed no magic:
applescript <- function(script_source, extra_args = c()) {
script_source <- paste0(script_source, collapse = "\n")
tf <- tempfile(fileext = ".applescript")
on.exit(unlink(tf), add=TRUE)
cat(script_source, file = tf)
osascript <- Sys.which("osascript")
args <- c(extra_args, tf)
system2(
command = osascript,
args = args,
stdout = TRUE
) -> res
invisible(res)
}
So you can do anything with it, like open a folder:
applescript(
sprintf(
'tell app "Finder" to open POSIX file "%s"',
Sys.getenv("R_DOC_DIR")
)
)
or, query an app and return data:
res <- applescript('
tell application "iTunes"
set r_name to name of current track
set r_artist to artist of current track
end
return "artist=" & r_artist & "\ntrack=" & r_name
')
print(res)
## [1] "artist=NICO Touches the Walls" "track=Hologram"
For (mebbe) easier usage (I say "mebbe" as the pkg relies on reticulate for some things) I added this to the macthekinfe macOS-centric R package.
Related
Everytime I open a new session in RStudio, I'm greeted with the error message:
Error: C stack usage 7953936 is too close to the limit
Based on suggestions for similar issues posted here and here, I tried using the ulimit command in terminal, but get the following error.
Isabels-MacBook-Pro ~ % ulimit -s
8176
Isabels-MacBook-Pro ~ % R --slave -e 'Cstack_info()["size"]'
Error: C stack usage 7954496 is too close to the limit
Execution halted
Yet, when I run ulimit on it's own, I get:
Isabels-MacBook-Pro ~ % ulimit
unlimited
Just to double-check, I try setting it to unlimited again:
Isabels-MacBook-Pro ~ % ulimit -s unlimited
but then get a new error:
Isabels-MacBook-Pro ~ % R --slave -e 'Cstack_info()["size"]'
Error: evaluation nested too deeply: infinite recursion / options(expressions=)?
Execution halted
I have no clue what this means in this context. Is the Cstack_info() the bit getting stuck on infinite recursion?? I'd love to get this figured out, as it's getting in the way of installing some necessary packages!
In case it's helpful, here's my session info
R version 4.1.3 (2022-03-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.2.1
And contents of .Rprofile
# REMEMBER to restart R after you modify and save this file!
# First, execute the global .Rprofile if it exists. You may configure blogdown
# options there, too, so they apply to any blogdown projects. Feel free to
# ignore this part if it sounds too complicated to you.
if (file.exists("~/.Rprofile")) {
base::sys.source("~/.Rprofile", envir = environment())
}
# Now set options to customize the behavior of blogdown for this project. Below
# are a few sample options; for more options, see
# https://bookdown.org/yihui/blogdown/global-options.html
options(
# to automatically serve the site on RStudio startup, set this option to TRUE
blogdown.serve_site.startup = FALSE,
# to disable knitting Rmd files on save, set this option to FALSE
blogdown.knit.on_save = TRUE,
# build .Rmd to .html (via Pandoc); to build to Markdown, set this option to 'm$
blogdown.method = 'html'
)
# fix Hugo version
options(blogdown.hugo.version = "0.82.0")
Here are the contents from /Library/Frameworks/R.framework/Resources/library/base/R/Rprofile
### This is the system Rprofile file. It is always run on startup.
### Additional commands can be placed in site or user Rprofile files
### (see ?Rprofile).
### Copyright (C) 1995-2020 The R Core Team
### Notice that it is a bad idea to use this file as a template for
### personal startup files, since things will be executed twice and in
### the wrong environment (user profiles are run in .GlobalEnv).
.GlobalEnv <- globalenv()
attach(NULL, name = "Autoloads")
.AutoloadEnv <- as.environment(2)
assign(".Autoloaded", NULL, envir = .AutoloadEnv)
T <- TRUE
F <- FALSE
R.version <- structure(R.Version(), class = "simple.list")
version <- R.version # for S compatibility
## for backwards compatibility only
R.version.string <- R.version$version.string
## NOTA BENE: options() for non-base package functionality are in places like
## --------- ../utils/R/zzz.R
options(keep.source = interactive())
options(warn = 0)
# options(repos = c(CRAN="#CRAN#"))
# options(BIOC = "http://www.bioconductor.org")
## setting from an env variable added in 4.0.2
local({to <- as.integer(Sys.getenv("R_DEFAULT_INTERNET_TIMEOUT", 60))
if (is.na(to) || to <= 0) to <- 60L
options(timeout = to)
})
options(encoding = "native.enc")
options(show.error.messages = TRUE)
## keep in sync with PrintDefaults() in ../../main/print.c :
options(show.error.messages = TRUE)
## keep in sync with PrintDefaults() in ../../main/print.c :
options(scipen = 0)
options(max.print = 99999)# max. #{entries} in internal printMatrix()
options(add.smooth = TRUE)# currently only used in 'plot.lm'
if(isFALSE(as.logical(Sys.getenv("_R_OPTIONS_STRINGS_AS_FACTORS_",
"FALSE")))) {
options(stringsAsFactors = FALSE)
} else {
options(stringsAsFactors = TRUE)
}
if(!interactive() && is.null(getOption("showErrorCalls")))
options(showErrorCalls = TRUE)
local({dp <- Sys.getenv("R_DEFAULT_PACKAGES")
if(identical(dp, "")) ## it fact methods is done first
dp <- c("datasets", "utils", "grDevices", "graphics",
"stats", "methods")
else if(identical(dp, "NULL")) dp <- character(0)
else dp <- strsplit(dp, ",")[[1]]
dp <- sub("[[:blank:]]*([[:alnum:]]+)", "\\1", dp) # strip whitespace
options(defaultPackages = dp)
})
## Expand R_LIBS_* environment variables.
Sys.setenv(R_LIBS_SITE =
.expand_R_libs_env_var(Sys.getenv("R_LIBS_SITE")))
Sys.setenv(R_LIBS_USER =
.expand_R_libs_env_var(Sys.getenv("R_LIBS_USER")))
local({
if(nzchar(tl <- Sys.getenv("R_SESSION_TIME_LIMIT_CPU")))
setSessionTimeLimit(cpu = tl)
if(nzchar(tl <- Sys.getenv("R_SESSION_TIME_LIMIT_ELAPSED")))
setSessionTimeLimit(elapsed = tl)
})
setSessionTimeLimit(elapsed = tl)
})
.First.sys <- function()
{
for(pkg in getOption("defaultPackages")) {
res <- require(pkg, quietly = TRUE, warn.conflicts = FALSE,
character.only = TRUE)
if(!res)
warning(gettextf('package %s in options("defaultPackages") was not found', sQuote(pkg)$
call. = FALSE, domain = NA)
}
}
## called at C level in the startup process prior to .First.sys
.OptRequireMethods <- function()
{
pkg <- "methods" # done this way to avoid R CMD check warning
if(pkg %in% getOption("defaultPackages"))
if(!require(pkg, quietly = TRUE, warn.conflicts = FALSE,
character.only = TRUE))
warning('package "methods" in options("defaultPackages") was not found',
call. = FALSE)
}
if(nzchar(Sys.getenv("R_BATCH"))) {
.Last.sys <- function()
{
cat("> proc.time()\n")
print(proc.time())
}
## avoid passing on to spawned R processes
## A system has been reported without Sys.unsetenv, so try this
try(Sys.setenv(R_BATCH=""))
}
local({
if(nzchar(rv <- Sys.getenv("_R_RNG_VERSION_")))
local({
if(nzchar(rv <- Sys.getenv("_R_RNG_VERSION_")))
suppressWarnings(RNGversion(rv))
})
.sys.timezone <- NA_character_
.First <- NULL
.Last <- NULL
###-*- R -*- Unix Specific ----
.Library <- file.path(R.home(), "library")
.Library.site <- Sys.getenv("R_LIBS_SITE")
.Library.site <- if(!nzchar(.Library.site)) file.path(R.home(), "site-library") else unlist(strspl$
.Library.site <- .Library.site[file.exists(.Library.site)]
invisible(.libPaths(c(unlist(strsplit(Sys.getenv("R_LIBS"), ":")),
unlist(strsplit(Sys.getenv("R_LIBS_USER"), ":")
))))
local({
popath <- Sys.getenv("R_TRANSLATIONS", "")
if(!nzchar(popath)) {
paths <- file.path(.libPaths(), "translations", "DESCRIPTION")
popath <- dirname(paths[file.exists(paths)][1])
}
bindtextdomain("R", popath)
bindtextdomain("R-base", popath)
assign(".popath", popath, .BaseNamespaceEnv)
})
local({
## we distinguish between R_PAPERSIZE as set by the user and by configure
papersize <- Sys.getenv("R_PAPERSIZE_USER")
if(!nchar(papersize)) {
lcpaper <- Sys.getlocale("LC_PAPER") # might be null: OK as nchar is 0
papersize <- if(nchar(lcpaper))
if(length(grep("(_US|_CA)", lcpaper))) "letter" else "a4"
else Sys.getenv("R_PAPERSIZE")
}
options(papersize = papersize,
}
options(papersize = papersize,
printcmd = Sys.getenv("R_PRINTCMD"),
dvipscmd = Sys.getenv("DVIPS", "dvips"),
texi2dvi = Sys.getenv("R_TEXI2DVICMD"),
browser = Sys.getenv("R_BROWSER"),
pager = file.path(R.home(), "bin", "pager"),
pdfviewer = Sys.getenv("R_PDFVIEWER"),
useFancyQuotes = TRUE)
})
## non standard settings for the R.app GUI of the macOS port
if(.Platform$GUI == "AQUA") {
## this is set to let RAqua use both X11 device and X11/TclTk
if (Sys.getenv("DISPLAY") == "")
Sys.setenv("DISPLAY" = ":0")
## this is to allow gfortran compiler to work
Sys.setenv("PATH" = paste(Sys.getenv("PATH"),":/usr/local/bin",sep = ""))
}## end "Aqua"
## de-dupe the environment on macOS (bug in Yosemite which affects things like PATH)
if (grepl("^darwin", R.version$os)) local({
## we have to de-dupe one at a time and re-check since the bug affects how
## environment modifications propagate
while(length(dupes <- names(Sys.getenv())[table(names(Sys.getenv())) > 1])) {
env <- dupes[1]
value <- Sys.getenv(env)
Sys.unsetenv(env) ## removes the dupes, good
.Internal(Sys.setenv(env, value)) ## wrapper requries named vector, a pain, hence internal
}
})
local({
tests_startup <- Sys.getenv("R_TESTS")
if(nzchar(tests_startup)) source(tests_startup)
})
Is there anything glaring here that could be causing the issue?
Your user .Rprofile file is loading itself recursively for some reason:
if (file.exists("~/.Rprofile")) {
base::sys.source("~/.Rprofile", envir = environment())
}
From your comments it seems that these lines are inside ~/.Rprofile (~ expands to the user home directory, i.e. /Users/mycomputer in your case, assuming mycomputer is your user name).
Delete these lines (or comment them out), they don’t belong here. In fact, the file looks like it’s a template for a project-specific .Rprofile configuration. It would make sense inside a project directory, but not as the profile-wide user .Rprofile.
The logic for these files is as follows:
If there is an .Rprofile file in the current directory, R attempts to load that.
Otherwise, if the environment variable R_PROFILE_USER is set to the path of a file, R attempts to load this file.
Otherwise, if the file ~/.Rprofile exists, R attempts to load that.
Now, this implies that ~/.Rprofile is not loaded automatically if a projects-specific (= in the current working directory) .Rprofile exists. This is unfortunate, therefore many projects add lines similar to the above to their project-specific .Rprofile files to cause the user-wide ~/.Rprofile to be loaded as well. However, the above implementation ignores the R_PROFILE_USER environment variable. A better implementation would therefore look as follows:
rprofile = Sys.getenv('R_PROFILE_USER', '~/.Rprofile')
if (file.exists(rprofile)) {
base::sys.source(rprofile, envir = environment())
}
rm(rprofile)
Success! Thank you to everyone in the comment. The issue was resolved by deleting /Library/Frameworks/R.framework/Resources/library/base/R/Rprofile and re-installing R and Rstudio.
I am trying to get H2O working with Sparklyr on my spark cluster (yarn)
spark_version(sc) = 2.4.4
My spark cluster is running V2.4.4
According to this page the compatible version with my spark is 2.4.5 for Sparkling Water and the H2O release is rel-xu patch version 3. However when I install this version I am prompted to update my H2O install to the next release (REL-ZORN). Between the H2O guides and the sparklyr guides it's very confusing and contradictory at times.
Since this is a yarn deployment and not local, unfortunately I can't provide a repex to help with trobleshooting.
url <- "http://h2o-release.s3.amazonaws.com/sparkling-water/rel-2.4/5/sparkling-water-2.4.5.zip"
download.file(url = url,"sparkling-water-2.4.5.zip")
unzip("sparkling-water-2.4.5.zip")
# RUN THESE CMDs FROM THE TERMINAL
cd sparkling-water-2.4.5
bin/sparkling-shell --conf "spark.executor.memory=1g"
# RUN THESE FROM WITHIN RSTUDIO
install.packages("sparklyr")
library(sparklyr)
# REMOVE PRIOR INSTALLS OF H2O
detach("package:rsparkling", unload = TRUE)
if ("package:h2o" %in% search()) { detach("package:h2o", unload = TRUE) }
if (isNamespaceLoaded("h2o")){ unloadNamespace("h2o") }
remove.packages("h2o")
# INSTALLING REL-ZORN (3.36.0.3) WHICH IS REQUIRED FOR SPARKLING WATER 3.36.0.3
install.packages("h2o", type = "source", repos = "https://h2o-release.s3.amazonaws.com/h2o/rel-zorn/3/R")
# INSTALLING FROM S3 SINCE CRAN NO LONGER SUPPORTED
install.packages("rsparkling", type = "source", repos = "http://h2o-release.s3.amazonaws.com/sparkling-water/spark-2.4/3.36.0.3-1-2.4/R")
# AS PER THE GUIDE
options(rsparkling.sparklingwater.version = "2.4.5")
library(rsparkling)
# SPECIFY THE CONFIGURATION
config <- sparklyr::spark_config()
config[["spark.yarn.queue"]] <- "my_data_science_queue"
config[["sparklyr.backend.timeout"]] <- 36000
config[["spark.executor.cores"]] <- 32
config[["spark.driver.cores"]] <- 32
config[["spark.executor.memory"]] <- "40g"
config[["spark.executor.instances"]] <- 8
config[["sparklyr.shell.driver-memory"]] <- "16g"
config[["spark.default.parallelism"]] <- "8"
config[["spark.rpc.message.maxSize"]] <- "256"
# MAKE A SPARK CONNECTION
sc <- sparklyr::spark_connect(
master = "yarn",
spark_home = "/opt/mapr/spark/spark",
config = config,
log = "console",
version = "2.4.4"
)
When I try to establish a H2O context using the next chunk I get the following error
h2o_context(sc)
Error in h2o_context(sc) : could not find function "h2o_context"
Any pointers as to where I'm going wrong would be greatly appreciated.
See this tutorial please. The newer versions of Rsparkling use {H2OContext.getOrCreate(h2oConf)} instead of {h2o_context(sc)}.
I am attempting to run an NLRX simulation in Manjaro Linux (RNetLogo wouldn't work for some reason either), and am running into the following error when attempting to set up an dummy experiment:
cp: cannot stat '~/.netlogo/NetLogo 6.1.1/netlogo-headless.sh': No such file or directory
sed: can't read /tmp/Rtmpj15Yf7/netlogo-headless365385fb4bdc0.sh: No such file or directory
sed: can't read /tmp/Rtmpj15Yf7/netlogo-headless365385fb4bdc0.sh: No such file or directory
sh: /tmp/Rtmpj15Yf7/netlogo-headless365385fb4bdc0.sh: No such file or directory
Error in util_gather_results(nl, outfile, seed, siminputrow) :
Temporary output file /tmp/Rtmpj15Yf7/nlrx5493_1365385ab03157.csvnot found. On unix systems this can happen if the default system temp folder is used.
Try reassigning the default temp folder for this R session (unixtools package).
In addition: Warning message:
In system(NLcall, wait = TRUE) : error in running command
Given that I am running R 4.0.0, the Unixtools package doesn't work, so that's out of the question. How would I go about fixing this?
Code for those curious:
library(nlrx)
netlogopath <- file.path("~/.netlogo/NetLogo 6.1.1")
modelpath <- file.path(netlogopath, "app/models/Sample Models/Biology/Wolf Sheep Predation.nlogo")
outpath <- file.path("/home/out")
nl <- nl(nlversion = "6.0.3",
nlpath = netlogopath,
modelpath = modelpath,
jvmmem = 1024)
nl#experiment <- experiment(expname="wolf-sheep",
outpath=outpath,
repetition=1,
tickmetrics="true",
idsetup="setup",
idgo="go",
runtime=50,
evalticks=seq(40,50),
metrics=c("count sheep", "count wolves", "count patches with [pcolor = green]"),
variables = list('initial-number-sheep' = list(min=50, max=150, qfun="qunif"),
'initial-number-wolves' = list(min=50, max=150, qfun="qunif")),
constants = list("model-version" = "\"sheep-wolves-grass\"",
"grass-regrowth-time" = 30,
"sheep-gain-from-food" = 4,
"wolf-gain-from-food" = 20,
"sheep-reproduce" = 4,
"wolf-reproduce" = 5,
"show-energy?" = "false"))
nl#simdesign <- simdesign_lhs(nl=nl,
samples=100,
nseeds=3,
precision=3)
results <- run_nl_all(nl = nl)
R Version for those who may want it:
platform x86_64-pc-linux-gnu
arch x86_64
os linux-gnu
system x86_64, linux-gnu
status
major 4
minor 0.0
year 2020
month 04
day 24
svn rev 78286
language R
version.string R version 4.0.0 (2020-04-24)
nickname Arbor Day
In case others find this helpful: I have encountered similar errors as the result of file path misspecification. For instance, double check model path. You may need to drop app/.
I've been using txtProgressBar() for a while now. Since today, it stopped working if using style=3.
It just shows an empty progress bar, and is not updated.
Yesterday I updated some packages, but not the utils package, AFAIK. Maybe the sysadmins updated R without me knowing.
To reproduce:
for (i in 1:10) {
pb <- txtProgressBar(max = 11, style = 3)
Sys.sleep(1)
setTxtProgressBar(pb, pb$getVal()+1)
}
close(pb)
In my case, this just shows:
| | 0%
All the time. Other styles (1 and 2) work fine.
My R details:
> R.version
_
platform x86_64-pc-linux-gnu
arch x86_64
os linux-gnu
system x86_64, linux-gnu
status
major 3
minor 2.2
year 2015
month 08
day 14
svn rev 69053
language R
version.string R version 3.2.2 (2015-08-14)
nickname Fire Safety
Is there something I'm missing, maybe something that could be wrongly set in my session, or is this a bug?
You put pb <- txtProgressBar(max = 11, style = 3) inside the loop. It should be outside the loop, before it.
Also, your max is not correct. It should be 10, as your for loop goes from 1 to 10.
pb <- txtProgressBar(max = 10, style = 3)
for (i in 1:10) {
Sys.sleep(0.5)
setTxtProgressBar(pb, pb$getVal()+1)
}
close(pb)
the following part of the code: pb <- txtProgressBar(max = 11, style = 3)
should be outside the for loop. In my interpretation, if you put it inside you re-initialize the progress bar at each cycle of the loop.
The following code does what you are expecting:
pb <- txtProgressBar(max = 11, style = 3)
for (i in 1:10) {
Sys.sleep(1)
setTxtProgressBar(pb, pb$getVal()+1)
}
close(pb)
I have a number of files that I would like to run using a batch file that will be executed from R using a for loop. As an example, let's assume that I have 2 runs that I would like to execute:
runs <- c(102, 103)
The syntax for the system command requires that the batch file be specified first, followed by the input data file for the run (102.txt and 103.txt) and the name of the output results file after the batch file has been executed (102.res and 103.res). I am attempting to run this using a for loop:
for (r in runs) {
cmd <- sprintf('C:/example1/test.bat %d.txt %d.res', runs, runs)[1]
print(eval(cmd))
command: system(cmd)
}
[1] "C:/example1/test.bat 102.txt 102.res"
Unfortunately, this only executes the first run (102) and does not advance to the next run (103). The R console displays the following warning:
Error in command:system(cmd) : NA/NaN argument
Thinking that this error is what is preventing R from advancing to the next run, I have attempted to use options(warn = -1) in the for loop:
for (r in runs) {
options(warn = -1)
cmd <- sprintf('C:/example1/test.bat %d.ctl %d.res', runs, runs)[1]
print(eval(cmd))
command: system(cmd)
options(warn = 0)
}
Unfortunately, this continues to throw the same error. For what it's worth, the output from my batch file (102.res) is exactly how I want it to be, I simply want to be able to bypass this error and continue on with the rest of my runs. Any thoughts on how best to do that?
Thanks in advance.
Here's what you had
runs <- c(102, 103)
for (r in runs) {
cmd <- sprintf('C:/example1/test.bat %d.txt %d.res', runs, runs)[1]
print(eval(cmd))
# command: system(cmd)
}
which outputs
[1] "C:/example1/test.bat 102.txt 102.res"
[1] "C:/example1/test.bat 102.txt 102.res"
try using the loop variable, r, instead of the array, runs, in the cmd <-... line
for (r in runs) {
cmd <- sprintf('C:/example1/test.bat %d.txt %d.res', r, r)[1] # <- change runs to r
print(eval(cmd))
# command: system(cmd)
}
output is
[1] "C:/example1/test.bat 102.txt 102.res"
[1] "C:/example1/test.bat 103.txt 103.res"