Description of The Problem:
As of today, RStudio Desktop fails to startup properly on my Linux machine. It was working yesterday. RStudio Desktop runs properly if started as the root user or when started with the command rstudio-bin --no-sandbox as a normal user. When started normally then it simply produces displays a grey window. See the image below:
Clicking on the menu items does not do anything.
Basic System Information
RStudio 2021.09.2 Build 382
R version 4.1.2 (2021-11-01) -- "Bird Hippie"
EndeavourOS (an Arch-based Linux distribution)
See the output from rstudio-bin --run-diagnostics at the end of this message.
What I have tried to resolve the issue.
- Uninstalled and reinstalled RStudio.
- I tried different "versions" of RStudio Desktop available for installation on EndeavourOS via the AUR, e.g., rstudio-desktop-bin, rstudio-desktop, rstudio-desktop-git, etc. I basically tried all of them, same issue.
- I reset RStudio Desktop's state, as per https://support.rstudio.com/hc/en-us/articles/200534577-Resetting-RStudio-Desktop-s-State.
RStudio Diagnostics Report
RStudio Diagnostics Report
WARNING: This report may contain sensitive security information and / or
personally identifiable information. Please audit the below and redact any
sensitive information before submitting your diagnostics report.
Generated: Tue Feb 15 12:40:52 2022
RStudio Version
2021.09.2+382
Session Information
R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: EndeavourOS
Matrix products: default
BLAS: /usr/lib/libopenblasp-r0.3.19.so
LAPACK: /usr/lib/liblapack.so.3.10.0
locale:
[1] LC_CTYPE=en_ZA.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_ZA.UTF-8 LC_COLLATE=en_ZA.UTF-8
[5] LC_MONETARY=en_ZA.UTF-8 LC_MESSAGES=en_ZA.UTF-8
[7] LC_PAPER=en_ZA.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_ZA.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.1.2 tools_4.1.2
System Information
sysname : Linux
release : 5.16.9-arch1-1
version : #1 SMP PREEMPT Fri, 11 Feb 2022 22:42:06 +0000
nodename : my_pc_name
machine : x86_64
login : my_username
user : my_username
effective_user : my_username
Platform Information
OS.type : unix
file.sep : /
dynlib.ext : .so
GUI : X11
endian : little
pkgType : source
path.sep : :
r_arch :
Environment Variables
_CE_CONDA :
_CE_M :
CLICOLOR_FORCE : 1
COLORFGBG : 15;0
COLORTERM : truecolor
CONDA_EXE : /home/my_username/miniconda3/bin/conda
CONDA_PYTHON_EXE : /home/my_username/miniconda3/bin/python
CONDA_SHLVL : 0
CUDA_PATH : /opt/cuda
DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/1000/bus
DESKTOP_SESSION : lxqt
DISPLAY : :0
DOTNET_BUNDLE_EXTRACT_BASE_DIR : /home/my_username/.cache/dotnet_bundle_extract
DOTNET_ROOT : /usr/share/dotnet
EDITOR : vi
FUNCNEST : 100
GIT_ASKPASS : rpostback-askpass
GTK_CSD : 0
GTK_MODULES : canberra-gtk-module:appmenu-gtk-module
GTK_OVERLAY_SCROLLING : 0
HOME : /home/my_username
KDEDIRS : /usr
LANG : en_ZA.UTF-8
LANGUAGE :
LC_ADDRESS : en_ZA.UTF-8
LC_IDENTIFICATION : en_ZA.UTF-8
LC_MEASUREMENT : en_ZA.UTF-8
LC_MONETARY : en_ZA.UTF-8
LC_NAME : en_ZA.UTF-8
LC_NUMERIC : en_ZA.UTF-8
LC_PAPER : en_ZA.UTF-8
LC_TELEPHONE : en_ZA.UTF-8
LC_TIME : en_ZA.UTF-8
LD_LIBRARY_PATH : /usr/lib64/R/lib:/lib:/usr/lib/jvm/java-17-openjdk/lib/server
LN_S : ln -s
LOGNAME : *** redacted ***
LV2_PATH : /home/my_username/.vst
LXQT_SESSION_CONFIG : session
MAIL : /var/spool/mail/my_username
MAKE : make
MATHEMATICA_HOME : /usr/local/Wolfram/WolframEngine/13.0
MOTD_SHOWN : pam
MOZ_PLUGIN_PATH : /usr/lib/mozilla/plugins
PAGER : /usr/bin/less
PATH : /home/my_username/miniconda3/condabin:/home/my_username/.cargo/bin:/usr/local/sbin:/usr/local/bin:/usr/bin:/opt/cuda/bin:/opt/cuda/nsight_compute:/opt/cuda/nsight_systems/bin:/home/my_username/.dotnet/tools:/var/lib/flatpak/exports/bin:/usr/lib/jvm/default/bin:/usr/bin/site_perl:/usr/bin/vendor_perl:/usr/bin/core_perl:/home/my_username/scripts:/home/my_username/.local/bin:/home/my_username/go/bin:/home/my_username/Android/Sdk/platform-tools:/home/my_username/Android/Sdk/emulator:/usr/lib/rstudio/bin/postback
PWD : *** redacted ***
PYTHONIOENCODING : utf-8
QT_DIR : /usr/lib/rstudio
QT_PLATFORM_PLUGIN : lxqt
QT_PLUGIN_PATH : /usr/lib/rstudio/plugins
QT_QPA_PLATFORM_PLUGIN_PATH : /usr/lib/rstudio/plugins/platforms
QT_QPA_PLATFORMTHEME : lxqt
R_BROWSER :
R_BZIPCMD : /usr/bin/bzip2
R_DOC_DIR : /usr/share/doc/R/
R_GZIPCMD : /usr/bin/gzip
R_HOME : /usr/lib64/R
R_INCLUDE_DIR : /usr/include/R/
R_LIBS_SITE :
R_LIBS_USER : ~/R/x86_64-pc-linux-gnu-library/4.1
R_PAPERSIZE : letter
R_PDFVIEWER :
R_PLATFORM : x86_64-pc-linux-gnu
R_PRINTCMD :
R_RD4PDF : times,hyper
R_SESSION_TMPDIR : /tmp/RtmpRwRZoL
R_SHARE_DIR : /usr/share/R/
R_STRIP_SHARED_LIB : strip --strip-unneeded
R_STRIP_STATIC_LIB : strip --strip-debug
R_SYSTEM_ABI : linux,gcc,gxx,gfortran,gfortran
R_TEXI2DVICMD : /usr/bin/texi2dvi
R_UNZIPCMD : /usr/bin/unzip
R_ZIPCMD : /usr/bin/zip
RMARKDOWN_MATHJAX_PATH : /usr/lib/rstudio/resources/mathjax-27
RS_PPM_FD_READ : 25
RS_PPM_FD_WRITE : 26
RS_RPOSTBACK_PATH : /usr/lib/rstudio/bin/rpostback
RS_SHARED_SECRET : *** redacted ***
RSTUDIO : 1
RSTUDIO_CONSOLE_COLOR : 256
RSTUDIO_CONSOLE_WIDTH : 80
RSTUDIO_PANDOC : /usr/lib/rstudio/bin/pandoc
RSTUDIO_PROGRAM_MODE : desktop
RSTUDIO_SESSION_PORT : 20428
RSTUDIO_USER_IDENTITY : my_username
RSTUDIO_WINUTILS : bin/winutils
SED : /usr/bin/sed
SHELL : /bin/bash
SHLVL : 1
TAR : /usr/bin/tar
TERM : xterm-256color
UBUNTU_MENUPROXY : 1
USER : my_username
WINDOWID : 0
XAUTHORITY : /home/my_username/.Xauthority
XDG_CACHE_HOME : /home/my_username/.cache
XDG_CONFIG_DIRS : /etc:/etc/xdg:/usr/share
XDG_CONFIG_HOME : /home/my_username/.config
XDG_CURRENT_DESKTOP : LXQt
XDG_DATA_DIRS : /home/my_username/.local/share/flatpak/exports/share:/var/lib/flatpak/exports/share:/usr/local/share:/usr/share
XDG_DATA_HOME : /home/my_username/.local/share
XDG_MENU_PREFIX : lxqt-
XDG_RUNTIME_DIR : /run/user/1000
XDG_SEAT : seat0
XDG_SEAT_PATH : /org/freedesktop/DisplayManager/Seat0
XDG_SESSION_CLASS : user
XDG_SESSION_DESKTOP : LXQt
XDG_SESSION_ID : 1
XDG_SESSION_PATH : /org/freedesktop/DisplayManager/Session0
XDG_SESSION_TYPE : x11
XDG_VTNR : 1
R Version
platform : x86_64-pc-linux-gnu
arch : x86_64
os : linux-gnu
system : x86_64, linux-gnu
status :
major : 4
minor : 1.2
year : 2021
month : 11
day : 01
svn rev : 81115
language : R
version.string : R version 4.1.2 (2021-11-01)
nickname : Bird Hippie
R Home
/usr/lib64/R
R Search Path
.GlobalEnv
tools:rstudio
package:stats
package:graphics
package:grDevices
package:utils
package:datasets
package:methods
Autoloads
package:base
R Library Paths
/home/my_username/R/x86_64-pc-linux-gnu-library/4.1
/usr/lib/R/library
Loaded Packages
compiler : /usr/lib/R/library/compiler
datasets : /usr/lib/R/library/datasets
graphics : /usr/lib/R/library/graphics
grDevices : /usr/lib/R/library/grDevices
methods : /usr/lib/R/library/methods
stats : /usr/lib/R/library/stats
tools : /usr/lib/R/library/tools
utils : /usr/lib/R/library/utils
base : /usr/lib64/R/library/base
Installed Packages
Package LibPath Version
1 abind /home/my_username/R/x86_64-pc-linux-gnu-library/4.1 1.4-5
...
610 utils /usr/lib/R/library 4.1.2
R System Profile: /usr/lib64/R/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(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)
})
.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")))
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(strsplit(.Library.site, ":"))
.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,
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)
})
R Site Profile: /usr/lib64/R/etc/Rprofile.site
(File does not exist)
R User Profile: /home/my_username/.Rprofile
(File does not exist)
R Site Environ: /usr/lib64/R/etc/Renviron.site
(File does not exist)
R User Environ: /home/my_username/.Renviron
(File does not exist)
R Temporary Directory
/tmp/RtmpRwRZoL
Files in R Temporary Directory
rs-graphics-5d5b92ea-3115-4218-91b8-f8cc483555ae
Log file: /home/my_username/.local/share/rstudio/log/rdesktop.log
(Not Found)
Log file: /home/my_username/.local/share/rstudio/log/rsession-my_username.log
2022-02-15T10:40:29.010314Z [rsession-my_username] ERROR Parent terminated; LOGGED FROM: void {anonymous}::detectParentTermination() src/cpp/session/SessionMain.cpp:1431 # NOTE THAT THE ERROR MESSAGE IS FROM WHEN I KILL THE RSTUDIO PROCESS.
User prefs: /home/my_username/.config/rstudio/rstudio-prefs.json
{}
System prefs: /etc:/etc/xdg:/usr/share/rstudio/rstudio-prefs.json
(Not Found)
User state: /home/my_username/.local/share/rstudio/rstudio-desktop.json
{
"context_id": "A8CA201B",
"error_handler_type": "traceback"
}