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 ([email protected]) 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 [email protected] https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/datatable-help
_______________________________________________ datatable-help mailing list [email protected] https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/datatable-help
