[BioC] memory invalid permission with qc()

[James W. MacDonald]

Hi Simon,

Simon Noël wrote:
> My sessionInfo() is
> 
> R version 2.8.1 (2008-12-22)
> i486-pc-linux-gnu
> 
> locale:
> LC_CTYPE=fr_CA.UTF-8;LC_NUMERIC=C;LC_TIME=fr_CA.UTF-8;LC_COLLATE=fr_CA.UTF-8;LC_MONETARY=C;LC_MESSAGES=fr_CA.UTF-8;LC_PAPER=fr_CA.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=fr_CA.UTF-8;LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] splines   tools     stats     graphics  grDevices utils     datasets
> [8] methods   base
> 
> other attached packages:
> [1] simpleaffy_2.18.0  gcrma_2.14.1       matchprobes_1.14.1 genefilter_1.22.0
> [5] survival_2.35-4    affyio_1.10.1      affy_1.20.2        Biobase_2.2.2
> 
> loaded via a namespace (and not attached):
> [1] annotate_1.20.1      AnnotationDbi_1.4.3  DBI_0.2-4
> [4] preprocessCore_1.4.0 RSQLite_0.7-1
> 
> For the relase, I am new to R and Bioconductor.  I have started the 12 May... 
> SO I think that I use the lastest.  Is's the same thing with my computer OS. 
> My first job was to install everything.  I am newly out of school for the
> summer.

Actually, you have an old version of R and BioC. You want to upgrade to 
R-2.9.0 and BioC 2.4 and then see if you still have the same problem

Best,

Jim


> 
> 
> 
> Selon Wolfgang Huber <huber at ebi.ac.uk>, 17.05.2009:
> 
>> Simon Noël ha scritto:
>>> Hello.  I have some problem using qc().  I have an old data set that work
>>> perfectly with qc() but a nuw one just arrive from affymetrix and I am not
>> able
>>> to run qc() on it.  I use the code :
>>>
>>> library(affy)
>>>
>>>
>>>
>>> library(affyio)
>>>
>>>
>>> library(simpleaffy)
>>>
>>> Data <-ReadAffy()
>>>
>>> qc <- qc(Data)
>>>
>>> and I recive this error message :
>>>
>>> *** caught segfault ***
>>> address 0xb6cf9000, cause 'invalid permissions'
>>>
>>> Traceback:
>>>  1: .C("GetExpressionLevels", as.double(pms[, x]), as.double(mms[,     x]),
>>> as.character(pns), as.integer(length(mms[, x])), as.double(ct),
>>> as.double(st), exprs = double(length(unique.pns)), length(unique.pns),
>>> PACKAGE = "simpleaffy")
>>>  2: FUN(1:2[[1L]], ...)
>>>  3: lapply(X, FUN, ...)
>>>  4: sapply(1:length(pms[1, ]), function(x) {    .C("GetExpressionLevels",
>>> as.double(pms[, x]), as.double(mms[,         x]), as.character(pns),
>>> as.integer(length(mms[, x])),         as.double(ct), as.double(st), exprs =
>>> double(length(unique.pns)),         length(unique.pns), PACKAGE =
>>> "simpleaffy")$exprs})
>>>  5: justMAS(x, tgt = sc)
>>>  6: call.exprs(unnormalised, "mas5")
>>>  7: qc.affy(unnormalised, ...)
>>>  8: qc(Data)
>>>  9: qc(Data)
>>> 10: eval.with.vis(expr, envir, enclos)
>>> 11: eval.with.vis(ei, envir)
>>> 12: source("tmp.R")
>>>
>>> Possible actions:
>>> 1: abort (with core dump, if enabled)
>>> 2: normal R exit
>>> 3: exit R without saving workspace
>>> 4: exit R saving workspace
>>> Selection:
>>>
>>> What should I do to correct the problem?
>>>
>>> Simon Noël
>>> VP Externe CADEUL
>>> Association des étudiants et étudiantes en Biochimie, Bio-
>>> informatique et Microbiologie de l'Université Laval
>>> CdeC
>>
>>
>> Dear Simon
>>
>> what is your "sessionInfo()"?
>>
>> Are you using the latest release of R (2.9) and Bioconductor?
>>
>> Best wishes
>>       Wolfgang
>>
>> ------------------------------------------------
>> Wolfgang Huber, EMBL, http://www.ebi.ac.uk/huber
>>
>>
> 
> 
> Simon Noël
> VP Externe CADEUL
> Association des étudiants et étudiantes en Biochimie, Bio-
> informatique et Microbiologie de l'Université Laval
> CdeC
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826