[BioC] Error using GEOquery

[Sean Davis]

On Mon, Jun 2, 2008 at 10:39 AM, Markus Schmidberger
<schmidb at ibe.med.uni-muenchen.de> wrote:
> Hi Sean,
>
> here is the translation:
>
> Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,
> :
>
> Line 1 has no 5 elements
>
> Additional Warnings:
> 1: In if (nchar(val) == nchar(x)) return(NA) :
> Condition hat length > 1 and only first element will be used
> 2 : ... - same -
> 3 : ... - same -
>
> 4: In read.table(con, sep = "\t", header = FALSE, nrows = i) :
> incomplete last line in readTableHeader

Thanks, Markus, for the translation.  I'll have to find a windows
machine on which to try this, but there could also be a character
encoding issue--I have seen that before.  NCBI has (I think) switched
everything to UTF-8, so I haven't seen it be a problem recently.

Sean

> Sean Davis schrieb:
>>
>> 2008/6/2 Markus Schmidberger <schmidb at ibe.med.uni-muenchen.de>:
>>
>>>
>>> Hi,
>>>
>>> I am using the package GEOquery.
>>> But there is an error getting the GEO Series information:
>>>
>>>
>>>>
>>>> gds <- getGEO("GSE2")
>>>>
>>>
>>> Found 1 file(s)
>>> GSE2_series_matrix.txt.gz
>>> versuche URL
>>>
>>> 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE2/GSE2_series_matrix.txt.gz'
>>> ftp data connection made, file length 14773 bytes
>>> URL geöffnet
>>> downloaded 14 Kb
>>>
>>> Fehler in scan(file, what, nmax, sep, dec, quote, skip, nlines,
>>> na.strings,
>>>  :
>>>  Zeile 1 hatte keine 5 Elemente
>>> Zusätzlich: Warning messages:
>>> 1: In if (nchar(val) == nchar(x)) return(NA) :
>>>  Bedingung hat Länge > 1 und nur das erste Element wird benutzt
>>> 2: In if (nchar(val) == nchar(x)) return(NA) :
>>>  Bedingung hat Länge > 1 und nur das erste Element wird benutzt
>>> 3: In if (nchar(val) == nchar(x)) return(NA) :
>>>  Bedingung hat Länge > 1 und nur das erste Element wird benutzt
>>> 4: In read.table(con, sep = "\t", header = FALSE, nrows = i) :
>>>  unvollständige letzte Zeile von readTableHeader gefunden in
>>> 'C:\TEMP\Rtmp4xCqxE\file6df11649'
>>>
>>>
>>>
>>>>
>>>> sessionInfo()
>>>>
>>>
>>> R version 2.7.0 (2008-04-22)
>>> i386-pc-mingw32
>>>
>>> locale:
>>>
>>> LC_COLLATE=German_Germany.1252;LC_CTYPE=German_Germany.1252;LC_MONETARY=German_Germany.1252;LC_NUMERIC=C;LC_TIME=German_Germany.1252
>>>
>>> attached base packages:
>>> [1] tools     stats     graphics  grDevices utils     datasets  methods
>>> base
>>> other attached packages:
>>> [1] GEOquery_2.4.0 RCurl_0.9-3    Biobase_2.0.0
>>>
>>>
>>> What is wrong?
>>>
>>
>> Hi, Markus.  Unfortunately, I read no German, so I can't be sure what
>> the exact error is.  However, I cannot reproduce the error on R 2.7.0
>> on my Mac.  Perhaps it is a windows-specific problem.  Could you do me
>> a favor and translate the error as best you can?
>>
>> Thanks,
>> Sean
>>
>
>
> --
> Dipl.-Tech. Math. Markus Schmidberger
>
> Ludwig-Maximilians-Universität München
> IBE - Institut für medizinische Informationsverarbeitung,
> Biometrie und Epidemiologie
> Marchioninistr. 15, D-81377 Muenchen
> URL: http://ibe.web.med.uni-muenchen.de Mail: Markus.Schmidberger [at]
> ibe.med.uni-muenchen.de
> Tel: +49 (089) 7095 - 4599
>
>