[datatable-help] Segfault using data.table 1.9.4 with multtest 2.24.0 on R 3.2.2

[Arunkumar Srinivasan]

v1.9.5 https://github.com/Rdatatable/data.table doesn’t sefgault, but returns an error (and it’s right).
The object returned from `multtest` is a list with 4 elements out of which 3rd and 4th are NULL.
Since the list elements are not of equal length, it errors when trying to convert the result to a 
data.table.


-- 
Arun

On 20 Aug 2015 at 15:25:21, Tom Harrop (thomas.harrop at ird.fr) wrote:

Hello all,  

I'm running into a segfault using data.table with the multtest package:  

> > library(data.table)  
> data.table 1.9.4 For help type: ?data.table  
> *** NB: by=.EACHI is now explicit. See README to restore previous  
> behaviour.  
> > p <- data.table(pval = rnorm(100, 0.5, 0.1))  
> > p[, multtest::mt.rawp2adjp(pval, proc = "BH", alpha = 0.1)]  
>  
> *** caught segfault ***  
> address 0x500000005, cause 'memory not mapped'  
>  
> Traceback:  
> 1: `[.data.table`(x, i)  
> 2: x[i]  
> 3: head.data.table(x, topn)  
> 4: head(x, topn)  
> 5: rbind(head(x, topn), tail(x, topn))  
> 6: print.data.table(x)  
> 7: function (x, ...) UseMethod("print")(x)  
>  
> Possible actions:  
> 1: abort (with core dump, if enabled)  
> 2: normal R exit  
> 3: exit R without saving workspace  
> 4: exit R saving workspace  

Am I doing something wrong? The following executes without problems  
(otherwise I would be contacting the multtest authors!):  

> > library(data.table)  
> data.table 1.9.4 For help type: ?data.table  
> *** NB: by=.EACHI is now explicit. See README to restore previous  
> behaviour.  
> > p <- data.table(pval = rnorm(100, 0.5, 0.1))  
> > multtest::mt.rawp2adjp(p$pval, proc = "BH", alpha = 0.1)  

My sessionInfo is at the end. Please let me know if any more information  
is required.  

Thanks for reading,  

Tom  

> > sessionInfo()  
> R version 3.2.2 (2015-08-14)  
> Platform: x86_64-pc-linux-gnu (64-bit)  
> Running under: Ubuntu 14.04.3 LTS  
>  
> locale:  
> [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C  
> [3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8  
> [5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8  
> [7] LC_PAPER=en_AU.UTF-8 LC_NAME=C  
> [9] LC_ADDRESS=C LC_TELEPHONE=C  
> [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C  
>  
> attached base packages:  
> [1] stats graphics grDevices utils datasets methods base  
>  
> other attached packages:  
> [1] data.table_1.9.4  
>  
> loaded via a namespace (and not attached):  
> [1] MASS_7.3-43 magrittr_1.5 plyr_1.8.3  
> [4] parallel_3.2.2 tools_3.2.2 survival_2.38-3  
> [7] reshape2_1.4.1 Rcpp_0.12.0 Biobase_2.28.0  
> [10] splines_3.2.2 multtest_2.24.0 stringi_0.5-5  
> [13] BiocGenerics_0.14.0 stringr_1.0.0 chron_2.3-47  
> [16] stats4_3.2.2  
>  


_______________________________________________  
datatable-help mailing list  
datatable-help at lists.r-forge.r-project.org  
https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/datatable-help  
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.r-forge.r-project.org/pipermail/datatable-help/attachments/20150822/e8a1a8e8/attachment.html>