[BioC] GEOquery not working, NCBI changes?

[Sean Davis]

On Wed, Mar 3, 2010 at 6:32 AM, Gad Abraham
<gabraham at csse.unimelb.edu.au> wrote:
> Hi,
>
> I'm having trouble getting GEOquery to work recently.
>
> On Ubuntu 9.10/R-2.10.1/BioC 2.6.1, GEOquery 2.11.3, download.file
> stops with "cannot open URL",
> On Ubuntu 8.04.1/R-2.9.2/BioC 2.4.1, GEOquery 2.8.0, curlPerform stops
> with "Server denied you to change to the given directory"
>
> wget downloads the file fine, but requires PASV which download.file()
> doesn't support
> (http://tolstoy.newcastle.edu.au/R/e6/help/09/01/0969.html)
>
> I suspect that NCBI has changes some server settings, is this a known issue?

Hi, Gad.  I'll follow up with the GEO folks, but it appears that the
issue was temporary.  I was able to reproduce your findings for until
7am EST and then the problem was gone.  Currently, GEOquery appears to
work fine for me.  Let me know if you are still having problems.

Sean


>> library(GEOquery)
> Loading required package: Biobase
>
> Welcome to Bioconductor
>
>  Vignettes contain introductory material. To view, type
>  'openVignette()'. To cite Bioconductor, see
>  'citation("Biobase")' and for packages 'citation(pkgname)'.
>
> Loading required package: RCurl
> Loading required package: bitops
>> g <- getGEO("GSE2034")
> Found 2 file(s)
> GSE2034_series_matrix-1.txt.gz
> trying URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE2034/GSE2034_series_matrix-1.txt.gz'
> Error in download.file(sprintf("ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/%s/%s",
>  :
>  cannot open URL
> 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE2034/GSE2034_series_matrix-1.txt.gz'
>> sessionInfo()
> R version 2.10.1 (2009-12-14)
> x86_64-pc-linux-gnu
>
> locale:
>  [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8
>  [5] LC_MONETARY=C              LC_MESSAGES=en_AU.UTF-8
>  [7] LC_PAPER=en_AU.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] GEOquery_2.11.3 RCurl_1.3-1     bitops_1.0-4.1  Biobase_2.6.1
>
>
> $ wget ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE2034/GSE2034_series_matrix-1.txt.gz
> --2010-03-03 22:08:59--
> ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE2034/GSE2034_series_matrix-1.txt.gz
>           => `GSE2034_series_matrix-1.txt.gz'
> Resolving ftp.ncbi.nih.gov... 130.14.29.30
> Connecting to ftp.ncbi.nih.gov|130.14.29.30|:21... connected.
> Logging in as anonymous ... Logged in!
> ==> SYST ... done.    ==> PWD ... done.
> ==> TYPE I ... done.  ==> CWD /pub/geo/DATA/SeriesMatrix/GSE2034 ... done.
> ==> SIZE GSE2034_series_matrix-1.txt.gz ... 12800217
> ==> PASV ... done.    ==> RETR GSE2034_series_matrix-1.txt.gz ... done.
> Length: 12800217 (12M)
> etc.
>
> --
> Gad Abraham
> PhD Student, Dept. CSSE and NICTA
> The University of Melbourne
> Parkville 3010, Victoria, Australia
> email: gabraham at csse.unimelb.edu.au
> web: http://www.csse.unimelb.edu.au/~gabraham
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>