[BioC] cannot open file './', reason 'Permission denied' in: file(file, "r")

[mete at seas.upenn.edu]

Hi Wolfgang,

Thanks for your quick reply. To answer your questions. TargetInfo is

> TargetInfo
An object of class "marrayInfo"
@maLabels
[1] "AbA1NEW.txt" "AbA2NEW.txt" "AbA3NEW.txt" "AbA4NEW.txt" "AbA5NEW.txt"
111 more elements ...

@maInfo
      FileName SampleID HybridizationSeq    Cy3  Cy5   HybDate
1 AbA1NEW.txt      113               61 RefRNA AbA1 9/28/2006
2 AbA2NEW.txt      114               77 RefRNA AbA2 10/6/2006
3 AbA3NEW.txt      115               59 RefRNA AbA3 9/29/2006
4 AbA4NEW.txt      116               57 RefRNA AbA4 9/28/2006
5 AbA5NEW.txt      117               55 RefRNA AbA5 9/23/2006
111 more rows ...

@maNotes
[1] "TargetMSS.txt"

and sessionInfo is:

> sessionInfo()
R version 2.5.1 (2007-06-27)
i386-pc-mingw32

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United  
States.1252;LC_MONETARY=English_United  
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

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

other attached packages:
arrayQuality RColorBrewer     gridBase       hexbin      lattice      convert
     "1.12.0"      "1.0-1"      "0.4-3"     "1.10.0"     "0.16-2"     "1.10.0"
       marray    tkWidgets       DynDoc      Biobase  widgetTools        limma
     "1.14.0"     "1.14.0"     "1.14.0"     "1.14.1"     "1.12.0"     "2.9.17"



Quoting Wolfgang Huber <huber at ebi.ac.uk>:

> Dear Mete,
>
> what is the value of your Variable "TargetInfo"? Does it contain empty
> strings? Also, what is the output of sessionInfo()?
>
>  Best wishes
> 	Wolfgang
>
> @seas.upenn.edu ha scritto:
>> Dear All,
>>
>> I get an error message after executing the following commands on RGUI
>>
>>> library(arrayQuality)
>>> library(marray)
>>> TargetInfo<-read.marrayInfo("TargetMSS.txt")
>>> mraw<-read.Agilent(targets=TargetInfo)
>>
>>
>> I get the following:
>>
>> Reading ...  ./RCP6NEW.txt
>> Reading ...  ./RCP7NEW.txt
>> Reading ...  ./RCP8NEW.txt
>> Reading ...  ./
>> Error in file(file, "r") : unable to open connection
>> In addition: Warning message:
>> cannot open file './', reason 'Permission denied' in: file(file, "r")
>>
>> The working directory is correct and I do have an active internet    
>> connection. I am not sure why I am getting this warning message.   
>> Any  comments will be appreciated.
>>
>> Best,
>>
>> Mete Civelek
>>