RStudio crashes when opening and produces the failure report below. Did not understand what to do really. How do I solve it?
R Session Startup Failure Report
RStudio Version
RStudio 2022.12.0+353 "Elsbeth Geranium " (7d165dcf, 2022-12-03) for macOS
Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_4) AppleWebKit/537.36 (KHTML, like Gecko) RStudio/2022.12.0+353 Chrome/102.0.5005.167 Electron/19.1.3 Safari/537.36
Error message
[No error available]
Process Output
The R session exited with code 1.
Error output:
dyld: Library not loaded: #executable_path/../Frameworks/libssl.1.1.dylib
Referenced from: /Applications/RStudio.app/Contents/Resources/app/bin/rsession
Reason: no suitable image found. Did find:
/Applications/RStudio.app/Contents/Resources/app/bin/../Frameworks/libssl.1.1.dylib: cannot load 'libssl.1.1.dylib' (load command 0x80000034 is unknown)
/Applications/RStudio.app/Contents/Resources/app/bin/../Frameworks/libssl.1.1.dylib: stat() failed with errno=1
/Applications/RStudio.app/Contents/Resources/app/bin/../Frameworks/libssl.1.1.dylib: cannot load 'libssl.1.1.dylib' (load command 0x80000034 is unknown)
/Applications/RStudio.app/Contents/Resources/app/bin/../Frameworks/libssl.1.1.dylib: stat() failed with errno=1
Standard output:
[No output emitted]
Logs
/Users/Oz/.local/share/rstudio/log/rsession-Oz.log
27 Jan 2023 00:51:29 [rsession-Oz] ERROR Handle httpd request error: Error : mutate.Rd:134: object 'methods_rd' not found
; LOGGED FROM: void rstudio::session::modules::help::(anonymous namespace)::handleHttpdRequest(const std::string &, const rstudio::session::modules::help::(anonymous namespace)::HandlerSource &, const http::Request &, const Filter &, http::Response *) [Filter = rstudio::session::modules::help::(anonymous namespace)::HelpContentsFilter] src/cpp/session/modules/SessionHelp.cpp:855
01 Feb 2023 00:22:34 [rsession-Oz] ERROR system error 2 (No such file or directory) [path: /Users/Oz/.local/share/rstudio/notebooks/C80BEAAD-bias-in-turnout/1/63BE219BEDFCCF2/chunks.json, target-path: /Users/Oz/.local/share/rstudio/notebooks/C80BEAAD-bias-in-turnout/1/s/chunks.json]; OCCURRED AT rstudio::core::Error rstudio::core::FilePath::copy(const rstudio::core::FilePath &, bool) const src/cpp/shared_core/FilePath.cpp:779; LOGGED FROM: void rstudio::session::modules::rmarkdown::notebook::(anonymous namespace)::onDocPendingRemove(boost::shared_ptr<source_database::SourceDocument>) src/cpp/session/modules/rmarkdown/NotebookCache.cpp:249
I was having some problems with my existing RStudio. I deleted and reinstalled it. It did not work and produced the report I post here.
Related
I used different rocker images without (almost) any problems formerly, but now I cannot connect to my container derived from rocker/rstudio:4.2.1 (9cb48eb2f045) which is latest at the moment. The browser says unable to connect and the docker logs show the following messages:
TTY detected. Printing informational message about logging configuration. Logging configuration loaded from '/etc/rstudio/logging.conf'. Logging to ''.
rserver[283]: ERROR system error 1 (Operation not permitted) [path: /var/lib/rstudio-server/offline]; OCCURRED AT bool rstudio::core::FilePath::exists() const src/cpp/shared_core/FilePath.cpp:886; LOGGED FROM: bool rstudio::core::FilePath::exists() const src/cpp/shared_core/FilePath.cpp:886
2022-08-02T16:21:32.097617Z [rserver] ERROR system error 1 (Operation not permitted) [path: /var/lib/rstudio-server/offline]; OCCURRED AT bool rstudio::core::FilePath::exists() const src/cpp/shared_core/FilePath.cpp:886; LOGGED FROM: bool rstudio::core::FilePath::exists() const src/cpp/shared_core/FilePath.cpp:886
The host system is a Oracle Linux Server release 7.7.
sestatus says SELinux status: disabled btw.
On Debian (testing) everything is running fine.
Earlier versions (e.g. rocker/rstudio:4.2.0 8325ff274512) are also working fine.
Any ideas about it?
I am working with a remote server running Ubuntu 19.10. I'd like to initiate a non-headless chrome server and have developed the following script:
require(RSelenium)
eCaps <- list(chromeOptions = list(
args = c('--window-size=1280,800',
"--disable-extensions",
"--use-gl=swiftshader",
"--user-data-dir=/home/user/.config/google-chrome/Profile1",
"--remote-debugging-port=9222")
))
# Google Chrome version is 81.0.4044.138
rD <- rsDriver(browser = "chrome",
chromever = "81.0.4044.138",
extraCapabilities = eCaps,
port =
as.integer(base::sample(seq(32768,65535, by=1),1)))
remDr <- rD[["client"]]
remDr$navigate("https://stackoverflow.com/")
If I log into the box via SSH and start a new R session I can paste the above commands and Chrome server launches with the correct profile and saved passwords required for my purposes.
If, however, I run the exact same commands from RStudio Server this results in an error:
Selenium message:unknown error: Chrome failed to start: exited abnormally.
(chrome not reachable)
(The process started from chrome location /usr/bin/google-chrome is no longer running, so ChromeDriver is assuming that Chrome has crashed.)
Build info: version: '4.0.0-alpha-2', revision: 'f148142cf8', time: '2019-07-01T21:30:10'
System info: host: 'xxx', ip: '127.0.1.1', os.name: 'Linux', os.arch: 'amd64', os.version: '5.3.0-59-generic', java.version: '1.8.0_252'
Driver info: driver.version: unknown
remote stacktrace: #0 0x55918478e189 <unknown>
Could not open chrome browser.
Client error message:
Summary: UnknownError
Detail: An unknown server-side error occurred while processing the command.
Further Details: run errorDetails method
Check server log for further details.
Some thoughts:
I'm only running the selenium server in non-headless mode as I cannot seem to launch Chrome with a saved profile (and saved passwords) when using the --headless argument.
If I use the --headless argument as above then the sever can be sucessfully launched both from within RStudio Server and an R terminal session
It feels like a permissions issue, and I have experimented with changing the RStudio Server user to my same username that I SSH into the box with, as per these instructions. This does not resolve the problem.
version.string R version 3.6.1 (2019-07-05)
[Package RSelenium version 1.7.7 Index]
Any help appreciated!
I try to connect with Selenium in R using the Chrome browser on Win10.
I installed Chrome 74.0.3729.61 and added the chrome.exe path to the Environment Variables.
devtools::install_github("johndharrison/seleniumPipes")
devtools::install_github("ropensci/Rselenium")
#start selenium
selServ <- selenium()
# check ports
selServ$log()$stderr
# conect using port
sel <- remoteDr(browserName = "chrome", port = 4567)
gives me the following error message:
Called newSession - Try no: 1 of 3
Called newSession - Try no: 2 of 3
Called newSession - Try no: 3 of 3
Error detected:
Response status code : 500
Selenium Status code: 13
Selenium Status summary: UnknownError
Selenium Status detail: An unknown server-side error occurred while processing the command.
Selenium message: unknown error: cannot find Chrome binary
(Driver info: chromedriver=74.0.3729.6 (255758eccf3d244491b8a1317aa76e1ce10d57e9-refs/branch-heads/3729#{#29}),platform=Windows NT 10.0.17134 x86_64) (WARNING: The server did not provide any stacktrace information)
Command duration or timeout: 40 milliseconds
Build info: version: '3.141.59', revision: 'e82be7d358', time: '2018-11-14T08:25:53'
System info: host: ... , os.name: 'Windows 10', os.arch: 'amd64', os.version: '10.0', java.version: '1.8.0_201'
Driver info: driver.version: unknown
Please check the response with errorResponse()
Please check the content returned with errorContent()
I found some guidance for Python (Cannot find Chrome binary with Selenium in Python for older versions of Google Chrome) and c# (Selenium WebDriver - Could not find Chrome binary), however, I do not know how to implement it in R.
IMHO you need to download and run chomedriver.exe(if you are using Windows 10, as you mentioned) before to use selenium.
Could you try below solution?
Solution 1. on command window
java -Dwebdriver.chrome.driver="C:/{yourPath}/selenium/chromedriver.exe" -jar "C:/{yourPath}/selenium/selenium-server-standalone-3.141.59.jar" -port 4567
or
Solution 2. direct use R script
rstudioapi::terminalExecute('java -Dwebdriver.chrome.driver="C:/{yourPath}/selenium/chromedriver.exe" -jar "C:/{yourPath}/selenium/selenium-server-standalone-3.141.59.jar" -port 4567')
Yes, both are same command exactly. You are able to use anyone you want.
I have an error, where I cant find anything related to it on the www:
The error pops up everythime I start/login into Rstudio-Server(installed on an Linux-Server). It worked for month.
05 Jan 2016 07:13:38 [rsession-me] ERROR system error 24 (Too many open files); OCCURRED AT: core::system::file_monitor::Handle core::system::file_monitor::detail::registerMonitor(const core::FilePath&, bool, const boost::function<bool(const core::FileInfo&)>&, const core::system::file_monitor::Callbacks&) /home/ubuntu/rstudio/src/cpp/core/system /file_monitor/LinuxFileMonitor.cpp:455; LOGGED FROM: void session::module_context::<unnamed>::onMonitoringError(const core::Error&) /home/ubuntu/rstudio/src/cpp/session/SessionModuleContext.cpp:360
I tried:
sudo rstudio-server suspend-all
sudo rstudio-server stop
sudo rstudio-server restart
But the error still pops up.
I am having issues connecting to a rstudio server I just installed. Can you please let me know if you know how to solve this? Thanks!
I just installed Rstudio server 0.99.485 64-bit on Ubuntu 13.10 (saucy) and am getting this error below:
The error in /var/log/syslog says:
ERROR Unexpected exception: locale::facet::Screateclocale name not valid;
LOGGED FROM: int main(int, char* const*) /home/ubuntu/rstudio/src/cpp/session/SessionMain.cpp:3166
The symptom is that the web UI says it's "unable to connect to service"
I have followed everything mentioned on this post, but it doesn't seem to work.
When I trace the rstudio-server process using sudo strace -f -e 'trace=!clockgettime,gettimeofday,futex,timerfdsettime,epollwait,epollctl' -p 10208 -o trace.txt, I am seeing this in the trace.txt ( below is what I used to log in:
10226 connect(10, {safamily=AFLOCAL, sunpath="/tmp/rstudio-rsession/"}, 28) = -1 ECONNREFUSED (Connection refused)
I've tried logged in using an invalid id to confirm that pam authentication is working fine
Also looked at this question and made sure there exists /home/<USERID> but still the problem is there.