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Question: Hm... segfault when using qvalue 1.39.1, has anyone else encountered this?
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gravatar for Leonardo Collado Torres
3.7 years ago by
United States
Leonardo Collado Torres600 wrote:

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

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 4 months ago • written 3.7 years ago by Leonardo Collado Torres600

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 3.7 years ago by Martin Morgan ♦♦ 21k

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 3.7 years ago by Leonardo Collado Torres600

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

ADD REPLYlink written 4 months ago by ilikescience10

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

ADD REPLYlink written 4 months ago by Leonardo Collado Torres600
1
gravatar for Leonardo Collado Torres
4 months ago by
United States
Leonardo Collado Torres600 wrote:

Since I don't know any other way of "closing" a question, I'll just say that I failed in this case to provide a reproducible example 3.3 years ago. See C: Hm... segfault when using qvalue 1.39.1, has anyone else encountered this?.

ADD COMMENTlink written 4 months ago by Leonardo Collado Torres600
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