[BioC] matchprobe

[Wolfgang Huber]

Dear Qing,

This could be a problem with your system (Windows), maybe you do not
have gzip? So please try unzipping the "HG-U95Av2_probe_tab.gz" file
manually and give the function makeProbePackage the full name (incl.
path) of the gunzipped file.

I cannot reproduce your problem. The matchprobes vignette works fine for
me (on Linux), and also for the (Windows) build system in Seattle:
http://bioconductor.org/checkResults/2.0

 Best wishes
 Wolfgang

> 
> Dear Dr. Huber,
> 
> 
>  
> 
> Thank you for your quick
> reponse.
> 
> 
>  
> 
> I am
> sorry that I got confusing about: The "datafile" arguments needs
> to be a character string with a filename, not a connection.
> 
>  
> 
> I read the getProbeDataAffy {matchprobes} and makeProbePackage
> {matchprobes},following the example,but
> still comes out the same result.
> 
>  
> 
> 
> 
>  
> 
>> filename <-
> file.path(.path.package("matchprobes"), "extdata",
> "HG-U95Av2_probe_tab.gz")
>> outdir牋 <- tempdir()
>> me牋牋牋 <- "Wolfgang
> Huber <huber at ebi.ac.uk>"
> 
>  
> 
>> makeProbePackage("HG-U95Av2",
> 
>  
> 
> +牋牋牋牋牋牋牋牋牋
> datafile牋 =
> gzfile(filename, open="r"),
> +牋牋牋牋牋牋牋牋牋
> outdir牋牋
> = outdir,
> 
>  
> 
> +牋牋牋牋牋牋牋牋牋
> maintainer = me,
> 
>  
> 
> +牋牋牋牋牋牋牋牋牋
> version牋  =
> "0.0.1",
> 
>  
> 
> +牋牋牋牋牋牋牋牋牋
> species="Homo_sapiens",
> +牋牋牋牋牋牋牋牋牋
> check牋牋 
> = FALSE,
> +牋牋牋牋牋牋牋牋牋
> force牋牋 
> = TRUE)
> Importing the data.
> Error in file(datafile, "r") :
> invalid 'description' argument
> 
> 
>  
> 
> What&rsquo;s wrong with me?
> 
>  
> 
> 
> 
>  
> 
> 
> 
>  
> 
>> sessionInfo()
> 
>  
> 
> R version 2.4.1 (2006-12-18)
> 牋i386-pc-mingw32
> 
>  
> 
> 
> 
>  
> 
> locale:
> LC_COLLATE=English_United
> Kingdom.1252;LC_CTYPE=English_United
> Kingdom.1252;LC_MONETARY=English_United
> Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United
> Kingdom.1252
> 
> 
>  
> 
> attached base packages:
> [1] "tools"牋牋
> "stats"牋牋 "graphics"  "grDevices"
> "utils"牋牋
> "datasets" 
> [7] "methods"牋 "base"牋牋
> 
> 
> 
>  
> 
> other attached packages:
>   hu6800probe牋牋 hu6800cdf hgu95av2probe牋 hgu95av2cdf牋 matchprobes
> 
> 牋牋 "1.14.0"牋牋  "1.14.0"牋牋 
> "1.14.0"牋牋  "1.14.0"牋牋牋
> "1.6.0" 
> 牋牋牋牋 affy牋牋牋 
> affyio牋牋牋 Biobase
> 
> 牋牋 "1.12.2"牋牋牋 "1.2.0"  牋牋"1.12.2"
> 
> 
>  
> 
> Thank you very much for your
> help.
> 
> 
>  
> 
> Best Wishes,
> 
> 
>  
> 
> Qing
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
>> Dear Qing, 
>>
>>> Error in file(datafile,
> "r") : 
>>> invalid 'description' argument 
> 
>> The "datafile" arguments needs to be a character
> string with a filename, 
>> not a connection. 
>>
>>
> Do read the man page of the function makeProbePackage and its helper 
>> function getProbeDataAffy, where this and many other useful pieces
> of 
>> information can be found. 
>>
>> Best wishes
> 
>> Wolfgang 
>>
>>
>>
>>
>>
> 
>> Qing Jing wrote: 
>>> Dear
> Bioconductor Users, 
>>>
>>>
>>>
>>>
>>> I am trying to use matchprobe
> under R2.4.1 
>>> windows XP professional. Here is a transcript
> of my session: 
>>>
>>>
>>>
> 
>>>
>>> filename <-
> system.file("extdata", 
> "HG-U95Av2_probe_tab.gz",+ package = 
> "matchprobes") 
>>>> outdir <- 
> tempdir() 
>>>> me <- "Wolfgang Huber 
> <w.huber at dkfz.de>" 
>>>> species <- 
>>> "Homo_sapiens" 
>>>
> makeProbePackage("HG-U95Av2", datafile = gzfile(filename, open =
> 
>>> "r"), 
>>> + outdir = outdir,
> maintainer = me, 
>>> species = species, version =
> "0.0.1",force = TRUE) 
>>> Importing the data. 
>>> Error in file(datafile, "r") : 
>>> invalid
> 'description' argument 
>>>
>>>
>>>
>>> It would be great, if someone could help 
>>> me! Thanks in Advance. 
>>>
>>>
>>>
>>>
>>> Best Wishes, 
>>> Qing
> 
>>> [[alternative HTML version deleted]] 
>>>
>>>
>>>
>>>
> ------------------------------------------------------------------------
> 
>>>
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>>
>> -- 
>>
> ------------------------------------------------------------------ 
>> Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber 
>>
>>
> 
> 


-- 
------------------------------------------------------------------
Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber