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 <e...@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@lists.r-forge.r-project.org > | https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel > > -- > http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org >
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