[BioC] R: GEOquery -> cannot open URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/ ....

[Manca Marco (PATH)]

Dear Sean,

thank you for your prompt reply.

It works like a charm once options('download.file.method'='curl') as you suggested.

All the best, Marco

--
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 at maastrichtuniversity.nl
Office telephone: +31(0)433874633
Personal mobile: +31(0)626441205
Twitter: @markomanka


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________________________________________
Da: seandavi at gmail.com [seandavi at gmail.com] per conto di Sean Davis [sdavis2 at mail.nih.gov]
Inviato: martedì 8 febbraio 2011 15.29
A: Manca Marco (PATH)
Cc: bioconductor mailing list
Oggetto: Re: [BioC] GEOquery -> cannot open URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/ ....

On Tue, Feb 8, 2011 at 9:18 AM, Manca Marco (PATH) <m.manca at maastrichtuniversity.nl<mailto:m.manca at 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 at maastrichtuniversity.nl<mailto:m.manca at maastrichtuniversity.nl>
Office telephone: +31(0)433874633
Personal mobile: +31(0)626441205
Twitter: @markomanka


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