[BioC] memory invalid permission with qc()

[Simon Noël]

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.



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