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

[Alberto Goldoni]

Yes i use the version 2.2.0 but with revolution R...

So when i type "R" the system doesn't load "R base", but the
"revolution-r" version 3.0.0 that is the last release on ubuntu 10.04
64 bit.

Please try to re-run you analysis with revolution-r and tell me if in
your computer all works fine.

Best regards.

2010/10/25 Richard Pearson <richard.pearson at well.ox.ac.uk>:
> 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
> Oxford OX3 7BN, UK                         Fax: +44 (0)1865 287664
>



-- 
-----------------------------------------------------
Dr. Alberto Goldoni
Parma, Italy