[Rcpp-devel] Debug RInside crash

[Jose]

Unfortunately, I have not been able to find any common pattern.
I run it 10 times with the same dataset and It would crash only sometimes.

There's gotta be a race condition most likely related to threading as you
said.

I explicitly tell DESeq to not use multi-threading though but I believe that
doesn't necessarily affect locfit.

Anyways, by digging into DESeq's R code I am able to avoid the potentially
race conditioned part by using a simpler fitting parameter.

So, the behaviour of RInside may be undefined if the R library does
threading?

Thanks for help!

Best,
Jose



2017-12-13 15:31 GMT+01:00 Dirk Eddelbuettel <edd at debian.org>:

>
> On 13 December 2017 at 14:51, Jose wrote:
> | Hello,
> |
> | I am invoking some R code using RInside from a
> | C++ tool. Every time I invoke the code it crashes
> | randomly. Sometimes even with the same data. It never
> | crashes when I use R directly.
> |
> | I am invoking this function DESeq2::DESeq(data) which runs
> | a set of statistical operaions. It always crashes (when it does)
> | at this point "mean-dispersion relationship" and the system's log
> | shows that it always crashes at the same point:
> |
> | Thread 3 Crashed:: Thread (pooled)
> | 0   locfit.so                      0x00000001229b4b34 atree_grow + 20
> | (ev_atree.c:92)
> | 1   locfit.so                      0x00000001229b4d06 atree_grow + 486
> | (ev_atree.c:124)
> | 2   locfit.so                      0x00000001229b4d06 atree_grow + 486
> | (ev_atree.c:124)
> | 3   locfit.so                      0x00000001229b4d06 atree_grow + 486
> | (ev_atree.c:124)
> | 4   locfit.so                      0x00000001229b5259 atree_start + 1033
> | (ev_atree.c:167)
> | 5   locfit.so                      0x00000001229e384d startlf + 1053
> | (startlf.c:160)
> | 6   locfit.so                      0x00000001229a7147 slocfit + 1335
> | (S_enter.c:301)
> | 7   libR.dylib                    0x000000010d0ebcd5 do_dotCode + 5973
> | 8   libR.dylib                    0x000000010d1183d9 Rf_eval + 1657
> | (eval.c:728)
> |
> | locfit seems to be the R library for local regression fit.
> |
> | Is there something that I can do to overcome this issue?
>
> Create smaller and smaller example that this exhibit the issue?
>
> | Why would this happen if it never happens when I invoke DESeq from R
> | directly?.
>
> Maybe locfit does something it is not supposed to do like threading?
>
> Dirk
>
> | Thanks for the help.
> |
> | Best,
> | Jose
> | _______________________________________________
> | Rcpp-devel mailing list
> | Rcpp-devel at lists.r-forge.r-project.org
> | https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
>
> --
> http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
>
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