[BioC] getGEO invalid multibyte string

[Tobias Straub]

ok, I figured it out myself! modified GEOquery

*** GEOquery    Fri Aug 10 08:24:53 2007
--- GEOquery_new     Fri Aug 31 14:43:15 2007
***************
*** 495,500 ****
--- 495,501 ----
     nextEntity <- ""
     while(!finished) {
       line <- readLines(con,1)
+     line <- iconv(line, "LATIN2", "UTF-8")
       if(length(line)==0) finished <- TRUE
       a[lines] <- line
       lines <- lines+1
***************
*** 510,515 ****
--- 511,517 ----
     finished <- FALSE
     while(!finished) {
       line <- readLines(con,1)
+     line <- iconv(line, "LATIN2", "UTF-8")
       if(length(line)==0) {
         finished <- TRUE
       } else {


On Aug 31, 2007, at 2:17 PM, Tobias Straub wrote:

> I tried to fetch and parse the GSE94 series from GEO using GEOquery
> library (gse<-getGEO('GSE94')). Operation is aborted with the message:
>
> Error in make.names(as.character(names), allow_) :
> 	invalid multibyte string 29
> In addition: There were 12 warnings (use warnings() to see them)
>
> is that an error of getGEO or a problem of the data set?
>
> Tobias
>
>> sessionInfo()
> R version 2.5.1 (2007-06-27)
> i386-apple-darwin8.9.1
>
> locale:
> en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] "stats"     "graphics"  "grDevices" "utils"     "datasets"
> "methods"   "base"
>
> other attached packages:
> GEOquery
> "2.0.6"
>
>
> ======================================================================
> Dr. Tobias Straub         Adolf-Butenandt-Institute, Molecular Biology
> tel: +49-89-2180 75 439         Schillerstr. 44, 80336 Munich, Germany
>
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======================================================================
Dr. Tobias Straub         Adolf-Butenandt-Institute, Molecular Biology
tel: +49-89-2180 75 439         Schillerstr. 44, 80336 Munich, Germany