On Jun 20, 2011, at 12:32 PM, Julin Maloof wrote:
> Hello,
>
> Not sure if this is a mac problem or not, so feel free to suggest a
> redirect.
>
It's not, and it has nothing to do with your subject line, either.
GEOquery forces download type to curl (no idea why) and none of the external
methods supports spaces in filenames*. To replicate you can simply use
download.file("http://www.r-project.org","/tmp/0 1","curl")
But the default (which is rather rudely changed by GEOquery) is "auto" which in
turn is internal on the Mac and works just fine:
download.file("http://www.r-project.org","/tmp/0 1","auto")
Cheers,
Simon
* - it does now on unix in R-devel
> I am using GEOquerry to download raw microarray files. If there is a space
> in the path then curl gives an error. If I remove the space from the path,
> no error. I am pretty sure that this error did not exist on R 2.12.2
>
>> library(GEOquery)
>> library(limma)
>> library(affy)
>>
>> vte.supp <- getGEOSuppFiles(GEO="GSE4847")
> [1] "ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/series/GSE4847/";
> 100 53.8M 100 53.8M 0 0 468k 0 0:01:57 0:01:57 --:--:--
> 493k 0:00:01 --:--:-- 0
>
> curl: (6) Couldn't resolve host 'Club'
> 106 1063 106 1063 0 0 47 0 0:00:22 0:00:22 --:--:--
> 7433 0:00:22 --:--:-- 0
>
> curl: (6) Couldn't resolve host 'Club'
> Warning messages:
> 1: In download.file(file.path(url, i), destfile = file.path(storedir, :
> download had nonzero exit status
> 2: In download.file(file.path(url, i), destfile = file.path(storedir, :
> download had nonzero exit status
>> sessionInfo()
> R version 2.13.0 (2011-04-13)
> Platform: i386-apple-darwin9.8.0/i386 (32-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] affy_1.30.0 limma_3.8.2 GEOquery_2.18.0 Biobase_2.12.1
>
> loaded via a namespace (and not attached):
> [1] affyio_1.20.0 preprocessCore_1.14.0 RCurl_1.6-5
> tools_2.13.0 XML_3.4-0
>> pwd()
> Error: could not find function "pwd"
>> getwd()
> [1] "/Users/jmaloof/Documents/Teaching/R Club"
>
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>
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>
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