Sean,

Thanks for your email, short term and longer term fixes.

Simon,

Sorry for posting to the wrong list.

Julin

On Mon, Jun 20, 2011 at 11:18 AM, Sean Davis <sdavis2@mail.nih.gov> wrote:

> On Mon, Jun 20, 2011 at 2:08 PM, Simon Urbanek
> <simon.urbanek@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@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]]
> >>>>
> >>>> _______________________________________________
> >>>> R-SIG-Mac mailing list
> >>>> R-SIG-Mac@r-project.org
> >>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> >>>>
> >>>>
> >>>
> >>> _______________________________________________
> >>> R-SIG-Mac mailing list
> >>> R-SIG-Mac@r-project.org
> >>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> >>>
> >>
> >>
> >
> >
>

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