[BioC] GEOquery Error

Fri Feb 3 05:46:59 CET 2012

On Thu, Feb 2, 2012 at 11:37 PM, ying chen <ying_chen at live.com> wrote:
> 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)

It is hard to tell for sure, but I think you might be out of disk
space locally.  When you get the error, check to see if you have space
left on the device to which you are saving.  GEOquery should work fine
in a loop like this.

Sean

> 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 at mail.nih.gov
>> To: ying_chen at live.com
>> CC: bioconductor at r-project.org
>
>>
>> On Thu, Feb 2, 2012 at 12:38 PM, ying chen <ying_chen at 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]]
>> >
>> > _______________________________________________
>> > Bioconductor mailing list
>> > Bioconductor at r-project.org
>> > https://stat.ethz.ch/mailman/listinfo/bioconductor
>> > Search the archives:
>> > http://news.gmane.org/gmane.science.biology.informatics.conductor