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

[Sean Davis]

On Mon, Jun 20, 2011 at 2:08 PM, Simon Urbanek
<simon.urbanek at r-project.org> wrote:
>
> 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 ;).

The grouping of terms above should have been clearer.  I meant that
the bug fix (in GEOquery) is nasty, not that R has a nasty bug.  I
have no idea whether there is a bug in the internal method, but the
behavior under linux has been reported by users to be different than
under windows and mac and leads to the file download failing.  This
does not appear to happen with ftp sites other than NCBI, so I did not
think of it a bug in R.

>
>> 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 ;).

Yeah for me!  I'm fixing the issue more appropriately now.

Sean


>
>>> 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]]
>>>>
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>>>>
>>>
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>>
>>
>
>