
Hi Sean,

Thanks a lot for the suggestion. I just tried simple test (> files <- getGEOSuppFiles("GSE23720")) and the problem is gone.

But when I tried to get a lot files at once, I got the following error message:

> gseids
  [1] GSE17907 GSE30010 GSE12790 GSE20711 GSE28821 GSE18864 GSE9195  GSE29431
  [9] GSE14020 GSE7904  GSE18728 GSE15181 GSE16391 GSE12777 GSE23593 GSE22035
 [17] GSE19383 GSE10281 GSE21217 GSE29672 GSE14986 GSE15026 GSE12763 GSE11001
 [25] GSE14017 GSE22513 GSE7515  GSE28796 GSE26910 GSE23994 GSE19639 GSE19697
 [33] GSE15477 GSE10270 GSE3893  GSE13787 GSE11078 GSE8977  GSE21834 GSE6885 
 [41] GSE24468 GSE20266 GSE21422 GSE3156  GSE22250 GSE18571 GSE11352 GSE7382 
 [49] GSE13806 GSE8565  GSE15619 GSE8597  GSE29832 GSE11791 GSE5102  GSE28645
 [57] GSE32160 GSE28789 GSE18331 GSE23640 GSE23399 GSE9086  GSE22865 GSE26298
 [65] GSE15893 GSE20086 GSE11324 GSE5116  GSE10879 GSE25407 GSE7700  GSE18912
 [73] GSE15043 GSE27515 GSE19777 GSE21832 GSE18070 GSE11506 GSE23921 GSE23905
 [81] GSE32158 GSE28305 GSE25162 GSE28415 GSE9015  GSE6800  GSE6548  GSE32161
 [89] GSE24249 GSE30775 GSE26884 GSE24473 GSE20719 GSE17636 GSE18773 GSE18931
 [97] GSE18146 GSE16070 GSE16080 GSE11683 GSE10046 GSE9747  GSE15749 GSE22664
[105] GSE21066 GSE9586  GSE17832 GSE11330 GSE17889 GSE12199 GSE28089 GSE31448
[113] GSE10810 GSE9196  GSE22840 GSE33658 GSE25487 GSE22544 GSE27220 GSE11581
120 Levels: GSE10046 GSE10270 GSE10281 GSE10810 GSE10879 GSE11001 ... GSE9747
> files <- sapply(gseids,getGEOSuppFiles,makeDirectory = TRUE, baseDir = getwd()
+ )
Error in dir.create(GEO) : invalid 'path' argument
[1] "ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/series/GSE17907/"
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0Warning: Failed to create the file 
Warning: /media/Passport01/My_DataSets/BreastCancerDataSet/GSE17907/GSE17907_RA
Warning: W.tar: No such file or directory
  0  328M    0  2896    0     0   3027      0 31:34:35 --:--:-- 31:34:35  3415
curl: (23) Failed writing body (0 != 2896)
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0Warning: Failed to create the file 
Warning: /media/Passport01/My_DataSets/BreastCancerDataSet/GSE17907/filelist.tx
Warning: t: No such file or directory
 24  5979   24  1448    0     0   2495      0  0:00:02 --:--:--  0:00:02  3061
curl: (23) Failed writing body (0 != 1448)
Error in dir.create(GEO) : invalid 'path' argument
In addition: 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
[1] "ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/series/GSE30010/"
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0Warning: Failed to create the file 
Warning: /media/Passport01/My_DataSets/BreastCancerDataSet/GSE30010/GSE30010_RA
Warning: W.tar: No such file or directory
  0  576M    0  2896    0     0   5191      0 32:22:29 --:--:-- 32:22:29  6464
curl: (23) Failed writing body (0 != 2896)
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0Warning: Failed to create the file 
Warning: /media/Passport01/My_DataSets/BreastCancerDataSet/GSE30010/GSE30010_di
Warning: scovery_clinical_info.txt.gz: No such file or directory
 81  1785   81  1448    0     0   3009      0 --:--:-- --:--:-- --:--:--  3506
 81  1785   81  1448    0     0   1978      0 --:--:-- --:--:-- --:--:--  1978curl: (23) Failed writing body (0 != 1448)


After I killed this job and tried:

> file <- getGEOSuppFiles("GSE17907")

I had no problem at all.

I really do not know what's wrong with the sapply() setting.

Any suggestion?

Thanks a lot for the help!

Ying

> Date: Thu, 2 Feb 2012 12:48:56 -0500
> Subject: Re: [BioC] GEOquery Error
> From: sdavis2@mail.nih.gov
> To: ying_chen@live.com
> CC: bioconductor@r-project.org
> 
> On Thu, Feb 2, 2012 at 12:38 PM, ying chen <ying_chen@live.com> wrote:
> >
> >
> >
> > Hi,
> >
> > I want to use GEOquery package to get the raw files of a lot GEO datasets at once ( > files <- sapply(mydata$GSE_ID, getGEOSuppFiles) ), but I got the following error message when I did a simple test run. Any suggestion?
> >
> 
> Hi, Ying.
> 
> This is not a GEOquery issue.  The directory housing the data is not
> on the FTP site.  NCBI GEO periodically rebuilds stuff on the site.
> That might be occurring now.  I'd suggest emailing NCBI GEO directly
> if you are in a hurry.  Alternatively, wait an hour or two to see if
> the problem is resolved.
> 
> Sean
> 
> 
> >> library(GEOquery)
> > Loading required package: Biobase
> > Welcome to Bioconductor
> >  Vignettes contain introductory material. To view, type
> >  'browseVignettes()'. To cite Bioconductor, see
> >  'citation("Biobase")' and for packages 'citation("pkgname")'.
> > Setting options('download.file.method.GEOquery'='curl')
> >> files <- getGEOSuppFiles("GSE23720")
> > [1] "ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/series/GSE23720/"
> > Error in function (type, msg, asError = TRUE)  :
> >  Server denied you to change to the given directory
> >> sessionInfo()
> > R version 2.14.1 (2011-12-22)
> > Platform: x86_64-pc-linux-gnu (64-bit)
> > locale:
> >  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
> >  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
> >  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
> >  [7] LC_PAPER=C                 LC_NAME=C
> >  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> > attached base packages:
> > [1] stats     graphics  grDevices utils     datasets  methods   base
> > other attached packages:
> > [1] GEOquery_2.20.8 Biobase_2.14.0
> > loaded via a namespace (and not attached):
> > [1] RCurl_1.9-5 XML_3.9-4
> >>
> >
> >
> >        [[alternative HTML version deleted]]
> >
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