On Jun 20, 2011, at 1:34 PM, Sean Davis wrote: > On Mon, Jun 20, 2011 at 1:27 PM, Simon Urbanek > <simon.urba...@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@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 >> > > _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac