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

[Simon Urbanek]

On Jun 20, 2011, at 1:34 PM, Sean Davis wrote:

> 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)

Did you post it? Unless the site has a buggy ftp server the preferred way to fix it would be in the internal R ftp code ;).


> 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.
> 

At least you do warn the users ;).


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

I have ported the changes to R-patched and also to Windows, so it should be working across the board.

Cheers,
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]]
>>> 
>>> _______________________________________________
>>> R-SIG-Mac mailing list
>>> R-SIG-Mac at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>> 
>>> 
>> 
>> _______________________________________________
>> R-SIG-Mac mailing list
>> R-SIG-Mac at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>> 
> 
>