Dear Andrie,
Following your suggestion, we installed R from source for version 3.5.1 and then for 3.4.4 however it did not work and had the same issue.
We went back to the previous working version R 3.4.1 and got the same issue. I wonder if we need to go back to the same GCC compiler version?
The problem is our shiny app works fine for few hours and then randomly crashes with error in the log file like this:
Loading required package: rcdk
Loading required package: rcdklibs
Loading required package: rJava
Loading required package: fingerprint
Loading required package: rcellminerData
Error: C stack usage 82761618932 is too close to the limit
Execution halted
**** caught segfault ****
address 0x7fe99265f070, cause 'invalid permissions'
An irrecoverable exception occurred. R is aborting now ...
/opt/shiny-server/scripts/shiny-run: line 3: 63094 Segmentation fault /bin/bash --login -c "$SHINY_EXEC_COMMAND SHINY_R_PATH "*
As you can read above in, this happened randomly (in the majority of the cases) after loading the library rcellminer. We are looking at the dependencies if there are some issues with some packages like rcdk and fingerprint.
Lately, we disabled the JIT (just in time compilation). It worked for few hours with some warnings in the messages log file: “server kernel: R[56104] general protection ip:7fa358ce2f73 sp:7fff6f20fd00 error:0 in libR.so[7fa358bc8000+2c2000]” and then it crashed. We re-started the shiny-server to have the app running.
I have to note that the shiny-server.log reported some warnings like:
[2018-09-26T18:28:11.343] [WARN] shiny-server - Expected 1 processes, got 0
(node:63173) MaxListenersExceededWarning: Possible EventEmitter memory leak detected. 101 release-socket listeners added. Use emitter.setMaxListeners() to increase limit
[2018-09-26T19:21:43.171] [WARN] shiny-server - Expected 2 processes, got 1
[2018-09-26T23:21:07.068] [WARN] shiny-server - Expected 1 processes, got 0
[2018-09-27T01:03:11.030] [WARN] shiny-server - Expected 1 processes, got 0
We reached the shiny support team for help however they reported that is an R issue.
Any hint or help will be appreciated.
Thanks.