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 <[email protected]> wrote: > On Mon, Jun 20, 2011 at 2:08 PM, Simon Urbanek > <[email protected]> wrote: > > > > On Jun 20, 2011, at 1:34 PM, Sean Davis wrote: > > > >> On Mon, Jun 20, 2011 at 1:27 PM, Simon Urbanek > >> <[email protected]> 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 > >>>> [email protected] > >>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac > >>>> > >>>> > >>> > >>> _______________________________________________ > >>> R-SIG-Mac mailing list > >>> [email protected] > >>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac > >>> > >> > >> > > > > > [[alternative HTML version deleted]] _______________________________________________ R-SIG-Mac mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-mac
