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

[Martin Morgan]

On 10/25/2010 01:40 AM, Alberto Goldoni wrote:
> 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.

Hi Alberto -- I believe that Revolution R lags release R at least by
months, perhaps longer; please correct me if I am wrong.

Use a current R with current Bioconductor packages, or seek technical
support from Revolution.

Martin

> 
> 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
>>
> 
> 
> 


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