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

[Tom Harrop]

Hi Arun,

Of course. Thanks for pointing that out.

Tom

> On 22 Aug 2015, at 11:11, Arunkumar Srinivasan <aragorn168b at gmail.com> wrote:
> 
> v1.9.5 https://github.com/Rdatatable/data.table <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 <mailto: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 
>> > 
>> 
>> 
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