<html><head><style>body{font-family:Helvetica,Arial;font-size:13px}</style></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;">v1.9.5 <a href="https://github.com/Rdatatable/data.table">https://github.com/Rdatatable/data.table</a> doesn’t sefgault, but returns an error (and it’s right).</div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;">The object returned from `multtest` is a list with 4 elements out of which 3rd and 4th are NULL.</div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;">Since the list elements are not of equal length, it errors when trying to convert the result to a </div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;">data.table.</div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;"><br></div> <br> <div id="bloop_sign_1440234554897161984" class="bloop_sign"><div style="font-family:helvetica,arial;font-size:13px">-- <br>Arun</div></div> <br><p class="airmail_on" style="color:#000;">On 20 Aug 2015 at 15:25:21, Tom Harrop (<a href="mailto:thomas.harrop@ird.fr">thomas.harrop@ird.fr</a>) wrote:</p> <blockquote type="cite" class="clean_bq"><span><div><div></div><div>Hello all,
<br>
<br>I'm running into a segfault using data.table with the multtest package:
<br>
<br>> > library(data.table)
<br>> data.table 1.9.4 For help type: ?data.table
<br>> *** NB: by=.EACHI is now explicit. See README to restore previous
<br>> behaviour.
<br>> > p <- data.table(pval = rnorm(100, 0.5, 0.1))
<br>> > p[, multtest::mt.rawp2adjp(pval, proc = "BH", alpha = 0.1)]
<br>>
<br>> *** caught segfault ***
<br>> address 0x500000005, cause 'memory not mapped'
<br>>
<br>> Traceback:
<br>> 1: `[.data.table`(x, i)
<br>> 2: x[i]
<br>> 3: head.data.table(x, topn)
<br>> 4: head(x, topn)
<br>> 5: rbind(head(x, topn), tail(x, topn))
<br>> 6: print.data.table(x)
<br>> 7: function (x, ...) UseMethod("print")(x)
<br>>
<br>> Possible actions:
<br>> 1: abort (with core dump, if enabled)
<br>> 2: normal R exit
<br>> 3: exit R without saving workspace
<br>> 4: exit R saving workspace
<br>
<br>Am I doing something wrong? The following executes without problems
<br>(otherwise I would be contacting the multtest authors!):
<br>
<br>> > library(data.table)
<br>> data.table 1.9.4 For help type: ?data.table
<br>> *** NB: by=.EACHI is now explicit. See README to restore previous
<br>> behaviour.
<br>> > p <- data.table(pval = rnorm(100, 0.5, 0.1))
<br>> > multtest::mt.rawp2adjp(p$pval, proc = "BH", alpha = 0.1)
<br>
<br>My sessionInfo is at the end. Please let me know if any more information
<br>is required.
<br>
<br>Thanks for reading,
<br>
<br>Tom
<br>
<br>> > sessionInfo()
<br>> R version 3.2.2 (2015-08-14)
<br>> Platform: x86_64-pc-linux-gnu (64-bit)
<br>> Running under: Ubuntu 14.04.3 LTS
<br>>
<br>> locale:
<br>> [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C
<br>> [3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8
<br>> [5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8
<br>> [7] LC_PAPER=en_AU.UTF-8 LC_NAME=C
<br>> [9] LC_ADDRESS=C LC_TELEPHONE=C
<br>> [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
<br>>
<br>> attached base packages:
<br>> [1] stats graphics grDevices utils datasets methods base
<br>>
<br>> other attached packages:
<br>> [1] data.table_1.9.4
<br>>
<br>> loaded via a namespace (and not attached):
<br>> [1] MASS_7.3-43 magrittr_1.5 plyr_1.8.3
<br>> [4] parallel_3.2.2 tools_3.2.2 survival_2.38-3
<br>> [7] reshape2_1.4.1 Rcpp_0.12.0 Biobase_2.28.0
<br>> [10] splines_3.2.2 multtest_2.24.0 stringi_0.5-5
<br>> [13] BiocGenerics_0.14.0 stringr_1.0.0 chron_2.3-47
<br>> [16] stats4_3.2.2
<br>>
<br>
<br>
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