[BioC] Fwd: *** caught segfault *** ....cause 'invalid permissions' with PUMA pachage

[Richard Pearson]

Hi Alberto

I have just run this same command, also on 64 bit ubuntu, with no problems. I think you didn't paste the full output of sessionInfo() - e.g. there are 
no attached packages shown. You do have version 2.2.0 of puma, right?

Here's my full sessionInfo:

 > sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
  [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C               LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8     LC_MONETARY=C 
LC_MESSAGES=en_GB.UTF-8    LC_PAPER=en_GB.UTF-8       LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices datasets  grid      utils     methods   base

other attached packages:
  [1] pumadata_1.0.3 puma_2.2.0     mclust_3.4.6   affy_1.28.0    Biobase_2.10.0 xtable_1.5-6   ggplot2_0.8.8  proto_0.3-8    reshape_0.8.3 
plyr_1.2.1     t2d_0.0.1      GWAS_0.0.1     abind_1.1-0

loaded via a namespace (and not attached):
[1] affyio_1.18.0         preprocessCore_1.12.0 tools_2.12.0

Best wishes

Richard

On 21/10/2010 09:02, Alberto Goldoni wrote:
> sorry i forget
>
> my sessionInfo
>
>> sessionInfo()
> R version 2.12.0 (2010-10-15)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
>   [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C
>   [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8
>   [5] LC_MONETARY=C             LC_MESSAGES=en_US.utf8
>   [7] LC_PAPER=en_US.utf8       LC_NAME=C
>   [9] LC_ADDRESS=C              LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> ---------- Forwarded message ----------
> From: Alberto Goldoni<alberto.goldoni1975 at gmail.com>
> Date: 2010/10/21
> Subject: *** caught segfault *** ....cause 'invalid permissions' with
> PUMA pachage
> To: BioC<bioconductor at stat.math.ethz.ch>
>
>
> Dear all,
> today i have installed "puma" package in my second computer with
> ubuntu 64 bit and when i try to run this command:
>
> eset_estrogen_mmgmos<- mmgmos(affybatch.estrogen, gsnorm="none")
>
> it return this error:
>
> Model optimising
>   *** caught segfault ***
> address 0x7f307c7102ec, cause 'invalid permissions'
>
> Traceback:
>   1: .Call("mmgmos_c", pm(object), mm(object), genes,
> probeNames(object),     phis, prctiles, length(prctiles), savepar,
> eps, PACKAGE = "puma")
>   2: mmgmos(data, gsnorm = "none")
>
> Possible actions:
> 1: abort (with core dump, if enabled)
> 2: normal R exit
> 3: exit R without saving workspace
> 4: exit R saving workspace
>
> IT'S VERY STRANGE!!!!! because yesterday with the other computer with
> ubuntu 32 bit puma was able to perform this type of calculation...
>
> it seems an error due to the R 64 bit version....
>
> someone can help me because in internet i was not able to find a trick!
>
> best regards
>
> --
> -----------------------------------------------------
> Dr. Alberto Goldoni
> Parma, Italy
> -----------------------------------------------------
>
>
>

-- 
Dr Richard D Pearson                       richard.pearson at well.ox.ac.uk
Wellcome Trust Centre for Human Genetics   http://www.well.ox.ac.uk/~rpearson
University of Oxford                       Tel: +44 (0)1865 617890
Roosevelt Drive                            Mob: +44 (0)7971 221181
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