Thanks in advance for the support, we all know how valuable it is. Many thanks.
I am a Linux engineer that supports a RStudio host. No knowledge in RStudio and no access to the Graphical interface.
The user is not able to plot if uses a large amount of Data. Starting with 10 numbers is OK, 10K numbers is OK, 10G numbers is OK, but when taking the entire 20G file size RStudio chokes, does not return, and needs to be restarted.
I did not find any log on /var/log refering to RStudio.
Questions: Were RStudio logs are located? Can we access them through the GUI? If so do you have detailed steps, as I do not have access to the GUI and will have to instruct user?
If anyone have any path for solution please advise.
Sorry, I took RStudio host to mean a server, rather than a desktop client.
So, the answer to log location depends on the OS under which the desktop program is running:
However, on my PopOS! 20.10 Ubuntu work-alike, the files are in ~/local/share/rstudio/log.
Log file: /home/roc/.local/share/rstudio/log/rsession-roc.log
--------------------------------------------------
2022-01-25T21:15:10.201400Z [rsession-roc] ERROR r error 4 (R code execution error) [errormsg: subscript out of bounds]; OCCURRED AT rstudio::core::Error rstudio::r::exec::executeSafely(rstudio_boost::function<void()>) src/cpp/r/RExec.cpp:252; LOGGED FROM: void rstudio::session::{anonymous}::processEvents() src/cpp/session/SessionHttpMethods.cpp:114
2022-01-25T21:15:10.201400Z [rsession-roc] ERROR r error 4 (R code execution error) [errormsg: subscript out of bounds]; OCCURRED AT rstudio::core::Error rstudio::r::exec::executeSafely(rstudio_boost::function<void()>) src/cpp/r/RExec.cpp:252; LOGGED FROM: void rstudio::session::{anonymous}::processEvents() src/cpp/session/SessionHttpMethods.cpp:114
Where in your overall system is the users RStudio application mounted, generally, and can you get the user to send you the output shown from the RStudio menu bar with Help | Diagnostics | Write Diagnostics Report ?
Does it really make sense to load 20GB worth of data into memory ?
I wonder if an approach as discussed in Bigger data would be better ? There an example is shown how to work with 37 GB of data on a laptop with 16 GB of RAM.
Yes, most plots typically make use of much less data than that, since our visual perception, let alone ability to distinguish and interpret information, has much lower bandwidth.
Typically, a multi-GB data set would be summarized before a plotting step, since we can't visually process even 1 million things, let alone 20 billion.
Below are the log lines I found the last try to replicate the error.
Can we make any sense out out it?
Is there anything the log points we can adjust?
It mentions: **is_closing_session(): no DBUS_SESSION_BUS_ADDRESS in environment**
Please advise
Many thanks
Marcelo_
root@atrssflinvm01:/var/log/BAK# grep 2035345 *
apport.log.1:ERROR: apport (pid 2035345) Tue Feb 1 12:51:02 2022: called for pid 2024533, signal 11, core limit 0, dump mode 1
apport.log.1:ERROR: apport (pid 2035345) Tue Feb 1 12:51:02 2022: executable: /usr/lib/rstudio-server/bin/rsession (command line "/usr/lib/rstudio-server/bin/rsession -u xxxxxxxx --session-use-secure-cookies 0 --session-root-path / --session-same-site 0 --launcher-token XXXXXXXX --r-restore-workspace 2 --r-run-rprofile 2")
apport.log.1:ERROR: apport (pid 2035345) Tue Feb 1 12:51:02 2022: is_closing_session(): no DBUS_SESSION_BUS_ADDRESS in environment
apport.log.1:ERROR: apport (pid 2035345) Tue Feb 1 14:06:49 2022: wrote report /var/crash/_usr_lib_rstudio-server_bin_rsession.1002.crash
echo $DBUS_SESSION_BUS_ADDRESS <<<<< Returned empty
Question: **Would the following be a solution?** (I only have access to the OS, I cannot try, have to bring the user which is very busy. I a trying to have some solution before bringing user back to the table.)
See this S/O thread. dbus provides interprocess communications on desktop environments. I can speculate that RStudio Server doesn't need to call it except in unusual circumstances, such as chewing very large data, so that is why small plots work.
I can't get a link to the appropriate RStudio Server github page (github is having issues this morning), but I'll flag this to see if anyone else has ideas.