[Bioc-devel] Rprintf in a multi-threaded environment

[Yang Liao]

Hi,

I'm not sure if some C developers have gone through this problem: it seems that Rprintf cannot work safely in a multi-threaded environment. In particular, if I call Rprintf() from a then-created thread while the stack size checking is enabled (ie the "R_CStackLimit" pointer isn't set to -1), it is very likely to end up with some fatal error messages like:

Error: C stack usage  847645293284 is too close to the limit
> Error: C stack usage  847336061668 is too close to the limit
> Error: C stack usage  847666277092 is too close to the limit
> Error: C stack usage  847346551524 is too close to the limit
> Error: C stack usage  847367531236 is too close to the limit
> Error: C stack usage  847357041380 is too close to the limit
> Error: C stack usage  847378021092 is too close to the limit
> Error: C stack usage  847655787236 is too close to the limit

, and the R session terminates in a segfault.
After I used all means to confirm that there was no memory leakage and the real stack use was minimum, I thought it can only be the Rprintf issue. I then disabled all screen outputs from the then-created threads and the error was gone. It was also reported on stackoverflow:
https://stackoverflow.com/questions/50092949/why-does-rcout-and-rprintf-cause-stack-limit-error-when-multithreading
I tried using a semaphore to protect all Rprintf calls but it didn't prevent the error.

Since my program needs to report some messages from the worker threads (created by the main thread), I wonder if there is a solution to safely do so, or I have to pipe the messages to the main thread, which in turn calls Rprintf? I hope not to change "R_CStackLimit" to disable the stack size checks because it generates a "NOTE" in R check.

Cheers,
Yang

_______________________________________________

The information in this email is confidential and intend...{{dropped:15}}