[BioC] SNPRMA: Normalizing...Error in readChar(con, 5) : cannot open the connection

[Alex Lisovich]

Benilton,

The OS is Mac OSX Tiger on dual-core intel MacPro.

The pd.mapping250k.sty was built from Affymetris .cdf, .csv and
probe_tab files using pdInfoBuilder and installed through R
-arch=x86_64 CMD INSTALL.

The sessioInfo() and traceback():

> sessionInfo()
R version 2.5.0 Patched (2007-05-02 r41420)
x86_64-apple-darwin8.9.1

locale:
C

attached base packages:
[1] "splines"   "tools"     "stats"     "graphics"  "grDevices" "utils"
[7] "datasets"  "methods"   "base"

other attached packages:
   pd.mapping250k.sty                 oligo BufferedMatrixMethods
              "0.1.5"             "1.0.2-6"               "1.0.0"
       BufferedMatrix               RSQLite                   DBI
              "1.0.0"               "0.5-4"               "0.2-3"
               affyio               Biobase
              "1.4.0"              "1.14.0"
>

> traceback()
3: readChar(con, 5)
2: load(system.file("extdata", paste(annot, "Ref.rda", sep = ""),
       package = annot))
1: snprma(rawData)
>

Thank you,

Alex

On 6/23/07, Benilton Carvalho <bcarvalh at jhsph.edu> wrote:
> What are your sessionInfo() and traceback()?
>
> If you installed the pd.mapping pkgs from the source, make sure
> you're using the latest version.
>
> If your OS is windows, we're working on a solution for the pd.mapping
> pkgs.
>
> b
>
> On Jun 23, 2007, at 10:56 AM, Alex Lisovich wrote:
>
> > Dear All,
> >
> > I am getting the following error when using snprma() on oligo
> > v.1.0.2-6 with pd.mapping250k.sty which I believe was once discussed
> > on the list on June 4, 2007 (see below):
> >
> >> library(oligo)
> >> library(pd.mapping250k.sty)
> >> rawData<-read.celfiles(list.celfiles())
> >> rma<-snprma(rawData)
> >
> >> Normalizing...Error in readChar(con, 5) : cannot open the connection
> >> In addition: Warning message:
> >> cannot open compressed file
> >
> > I am wondering if this problem was solved and if yes what was a
> > solution.
> >
> > Thank you in advance for your help!
> >
> > Alex
> >
> >
> >
> >
> >> Hi An,
> >>
> >> that's problably R complaining a file that it didn't find. The
> >> strange thing is that I can't reproduce it here. Could you please
> >> forward me the results of traceback()?
> >>
> >> This would happen if, for example, oligo finds the old version of the
> >> pd.mapping250k.sty package.
> >>
> >> b
> >
> > On Jun 4, 2007, at 8:07 AM, De Bondt, An-7114 [PRDBE] wrote:
> >
> >>> Hi Ben,
> >>>
> >>> When using oligo version 1.0.2-3, the pmStrand function indeed
> >>> works :-)
> >>> but the snprma function results in an error:
> >>>
> >>>      fsetSty <- read.celfiles(dir()[grep("S.CEL", dir())])
> >>>      rmaSty <- snprma(fsetSty)
> >>>
> >>> Normalizing...Error in readChar(con, 5) : cannot open the connection
> >>> In addition: Warning message:
> >>> cannot open compressed file
> >>>
> >>> How can I check which connection needs to be established?
> >>>
> >>> Thanks in advance for your help!
> >>> An
> >>>
> >
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>