Question: Hm... segfault when using qvalue 1.39.1, has anyone else encountered this?
gravatar for Leonardo Collado Torres
3.1 years ago by
United States
Leonardo Collado Torres560 wrote:


I am tracing down a problem with qvalue 1.39.1 (current version from BioC 3.0). I have been running some batch jobs that take 3-5 days, get a set of p-values and then use qvalue::qvalue(). Some of them are working ok, but two recently (and a third from another user) segfaulted. It could be an issue with our cluster, or maybe there is a problem with the input p-values (I didn't save them so I have to re-generate them to confirm this). Anyhow, I am just curious if others have experienced problems like this.


Error output on on *.e* file

*** caught segfault ***
address (nil), cause 'unknown'

 1: smooth.spline(lambda, pi0, df = smooth.df)
 2: qvalue(regs$pvalues)


## note regs$pvalues is the object that is created prior to using qvalue::qvalue() and has the p-values

## There's also no other info, for example, if qvalue::qvalue() detected a problem with the input.


As proof that this doesn't always happen, I could use the example data without any problems.


> library(qvalue)
> data(hedenfalk)
> q <- qvalue(hedenfalk)
> head(q$qvalues)
[1] 0.0873481 0.2073648 0.6616095 0.1600905 0.6264245 0.3681680
> devtools::session_info()
Session info-------------------------------------------------------------------
 setting  value
 version  R version 3.1.1 Patched (2014-10-14 r66758)
 system   x86_64, linux-gnu
 ui       X11
 language (EN)
 collate  en_US.UTF-8
 tz       <NA>

 package    * version date       source
 colorout   * 1.0.2   2014-05-30 local
 devtools     1.6.1   2014-10-07 CRAN (R 3.1.1)
 qvalue     * 1.39.1  2014-05-30 Bioconductor
 rstudioapi   0.1     2014-03-27 CRAN (R 3.1.1)


Our other lead is that in our cluster, R 3.1.x gets re-compiled every morning and in some cases this could break things. It's the price payed for keeping everything updated (once BioC 3.0 is released, stability over up-datedness will be favored).






ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by Leonardo Collado Torres560

It'll be helpful to provide an example of the data that *does* segfault, e.g., a subset of the vector regs$pvalues; as you say the example provided does not, so hard to track down...

ADD REPLYlink written 3.1 years ago by Martin Morgan ♦♦ 20k

I am in the process of re-generating that vector. But for now we are leaning towards this being caused by our cluster setup.

ADD REPLYlink written 3.1 years ago by Leonardo Collado Torres560
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