On Tue, Feb 8, 2011 at 9:18 AM, Manca Marco (PATH) <
m.manca@maastrichtuniversity.nl> wrote:

>
> Dear Sean, dear BioConductors
>
> I am having some troubles using GEOquery. In fact, it won't connect to the
> GEO to download any data... I have tried even with datasets from the
> vignette and the result is the same. The website is working though (I can
> access the data if I use a browser i.e.: Firefox3.6.13) and my R can
> currently connect, as I have no problem using KEGGSOAP as instance.
>
> Any suggestion? I am attaching my "code" and sessionInfo().
>
>
Hi, Marco.

Try:

options('download.file.method'='curl')

This is related to an issue between the internal download.file method under
linux and the NCBI ftp servers.

Sean


> Thank you in advance and best regards,
> Marco
>
>
> #####@Workstation1:~$ R
>
> R version 2.12.1 (2010-12-16)
> Copyright (C) 2010 The R Foundation for Statistical Computing
> ISBN 3-900051-07-0
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
>
>  Natural language support but running in an English locale
>
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
>
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
>
> > 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)'.
>
> > gds <- getGEO("GDS1")
> Error in download.file(myurl, destfile, mode = mode, quiet = TRUE) :
>  cannot open URL '
> ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SOFT/GDS/GDS1.soft.gz'
> > gse <- getGEO("GSE462")
> Found 1 file(s)
> GSE462_series_matrix.txt.gz
> trying URL '
> ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE462/GSE462_series_matrix.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/GSE462/GSE462_series_matrix.txt.gz
> '
>
> > sessionInfo()
> R version 2.12.1 (2010-12-16)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8
>  [5] LC_MONETARY=C             LC_MESSAGES=en_US.utf8
>  [7] LC_PAPER=en_US.utf8       LC_NAME=C
>  [9] LC_ADDRESS=C              LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] GEOquery_2.16.3 Biobase_2.10.0
>
> loaded via a namespace (and not attached):
> [1] RCurl_1.5-0 XML_3.2-0
> >
>
>
>
> --
> Marco Manca, MD
> University of Maastricht
> Faculty of Health, Medicine and Life Sciences (FHML)
> Cardiovascular Research Institute (CARIM)
>
> Mailing address: PO Box 616, 6200 MD Maastricht (The Netherlands)
> Visiting address: Experimental Vascular Pathology group, Dept of Pathology
> - Room5.08,  Maastricht University Medical Center, P. Debyelaan 25, 6229  HX
> Maastricht
>
> E-mail: m.manca@maastrichtuniversity.nl
> Office telephone: +31(0)433874633
> Personal mobile: +31(0)626441205
> Twitter: @markomanka
>
>
>
> *********************************************************************************************************************
>
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