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

[Sean Davis]

On Mon, Jun 20, 2011 at 1:27 PM, Simon Urbanek
<simon.urbanek at r-project.org> wrote:
>
> 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:

This is a nasty bug fix (internal method on linux does not work with
the NCBI ftp site--no real idea why) introduced a while back that I
should not have allowed into the wild.  Clearly, I need to refactor a
bit to keep the user clean of such hacks on my part.

> download.file("http://www.r-project.org","/tmp/0 1","auto")
>
> Cheers,
> Simon
>
> * - it does now on unix in R-devel

Thanks, Simon.

>
>> 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"
>>
>>       [[alternative HTML version deleted]]
>>
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>>
>>
>
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