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Question: Hm... segfault when using qvalue 1.39.1, has anyone else encountered this?
0
4.1 years ago by
United States

Hi,

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 ***

Traceback:
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$qvalues) [1] 0.0873481 0.2073648 0.6616095 0.1600905 0.6264245 0.3681680 > devtools::session_info() Session info------------------------------------------------------------------- setting value version R version 3.1.1 Patched (2014-10-14 r66758) system x86_64, linux-gnu ui X11 language (EN) collate en_US.UTF-8 tz <NA> Packages----------------------------------------------------------------------- package * version date source colorout * 1.0.2 2014-05-30 local devtools 1.6.1 2014-10-07 CRAN (R 3.1.1) qvalue * 1.39.1 2014-05-30 Bioconductor rstudioapi 0.1 2014-03-27 CRAN (R 3.1.1) Our other lead is that in our cluster, R 3.1.x gets re-compiled every morning and in some cases this could break things. It's the price payed for keeping everything updated (once BioC 3.0 is released, stability over up-datedness will be favored). Thanks, Leo ADD COMMENTlink modified 9 months ago • written 4.1 years ago by Leonardo Collado Torres610 It'll be helpful to provide an example of the data that *does* segfault, e.g., a subset of the vector regs$pvalues; as you say the example provided does not, so hard to track down...

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

I too am having this problem. Did you figure out a solution?

Sorry, this was so long ago that I don't remember. I even forgot about this thread and as you can see, I never got around to providing a reproducible example. Guess I can use this thread as an example of what not to do in the Bioc support website.

My guess from using qvalue in other projects is that it sometimes fails if nearly all the p-values are very low to begin with (like no data from 0.5 to 1). Anyhow, if you are having this same problem I recommend that you post a new question with a reproducible example so that you'll get an answer.

Best,

Leonardo

1
9 months ago by
United States