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? <- tempdir()
>> me??? <- "Wolfgang
> Huber <huber at="" ebi.ac.uk="">"
>
>
>
>> makeProbePackage("HG-U95Av2",
>
>
>
> +?????????
> datafile? =
> gzfile(filename, open="r"),
> +?????????
> outdir??
> = outdir,
>
>
>
> +?????????
> maintainer = me,
>
>
>
> +?????????
> version? =
> "0.0.1",
>
>
>
> +?????????
> species="Homo_sapiens",
> +?????????
> check??
> = FALSE,
> +?????????
> force??
> = TRUE)
> Importing the data.
> Error in file(datafile, "r") :
> invalid 'description' argument
>
>
>
>
> What’s wrong with me?
>
>
>
>
>
>
>
>
>
>
>
>> sessionInfo()
>
>
>
> R version 2.4.1 (2006-12-18)
> ?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"??
> "stats"?? "graphics" "grDevices"
> "utils"??
> "datasets"
> [7] "methods"? "base"??
>
>
>
>
>
> other attached packages:
> hu6800probe?? hu6800cdf hgu95av2probe? hgu95av2cdf? matchprobes
>
> ?? "1.14.0"?? "1.14.0"??
> "1.14.0"?? "1.14.0"???
> "1.6.0"
> ???? affy???
> affyio??? Biobase
>
> ?? "1.12.2"??? "1.2.0" ??"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]]
>>>
>>>
>>>
>>>
> --------------------------------------------------------------------
----
>
>>>
> _______________________________________________
> Bioconductor mailing list
>>> Bioconductor at stat.math.ethz.ch
>
>>>
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>>> Search the archives:
>>>
>
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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
