[R-SIG-Mac] GEO querry, Rcurl, and paths

[Simon Urbanek]

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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