[BioC] memory invalid permission with qc()
Simon Noël
simon.noel.2 at ulaval.ca
Tue May 19 17:11:00 CEST 2009
Hello. I think that every thing is updated now. I still get the error.
My new sessionInfo() is
R version 2.9.0 (2009-04-17)
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] stats graphics grDevices utils datasets methods base
other attached packages:
[1] simpleaffy_2.20.0 gcrma_2.16.0 Biostrings_2.12.1 IRanges_1.2.2
[5] genefilter_1.24.0 affyio_1.12.0 affy_1.22.0 Biobase_2.4.1
loaded via a namespace (and not attached):
[1] annotate_1.22.0 AnnotationDbi_1.6.0 DBI_0.2-4
[4] preprocessCore_1.6.0 RSQLite_0.7-1 splines_2.9.0
[7] survival_2.35-4 tools_2.9.0 xtable_1.5-5
Selon "James W. MacDonald" <jmacdon at med.umich.edu>, 19.05.2009:
> 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
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
> --
> 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
>
>
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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