Set http_proxy and ftp_proxy using Sys.putenv()
Also, unset no_proxy if using linux.
-----Original Message-----
From: bioconductor-bounces@stat.math.ethz.ch on behalf of Sean Davis
Sent: Wed 12/12/2007 12:58 PM
To: Bruce Tabor
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] GEOquery downloading problems
On Dec 12, 2007 2:03 AM, Bruce Tabor <btabor at="" ccia.unsw.edu.au="">
wrote:
> Dear BioC crew - especially Sean,
>
> I'm a newbie to R and Bioconductor. I've just started looking a
> microarray data.
>
> I've had a few problems downloading GEO data with GEOquery.
>
> My source data is here:
>
http://www.ncbi.nlm.nih.gov/projects/geo/gds/gds_browse.cgi?gds=1816
>
> Here's the code:
> > gse4271<-getGEO("GSE4271")
> trying URL
> '
ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SOFT/by_series/GSE4271/GSE4271_
fami
> ly.soft.gz'
> Error in download.file(myurl, destfile, mode = mode) :
> cannot open URL
> '
ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SOFT/by_series/GSE4271/GSE4271_
fami
> ly.soft.gz'
> In addition: Warning message:
> In download.file(myurl, destfile, mode = mode) :
> failed to create a data connection
>
> > gds1816<-getGEO("GSE1816")
> trying URL
> '
ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SOFT/by_series/GSE1816/GSE1816_
fami
> ly.soft.gz'
> Error in download.file(myurl, destfile, mode = mode) :
> cannot open URL
> '
ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SOFT/by_series/GSE1816/GSE1816_
fami
> ly.soft.gz'
> In addition: Warning message:
> In download.file(myurl, destfile, mode = mode) :
> failed to create a data connection
> >
>
> Other datasets are not working either:
> > gds <- getGEO("GDS1")
> trying URL
'
ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SOFT/GDS/GDS1.soft.gz'
> Error in download.file(myurl, destfile, mode = mode) :
> cannot open URL
> '
ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SOFT/GDS/GDS1.soft.gz'
> In addition: Warning message:
> In download.file(myurl, destfile, mode = mode) :
> failed to create a data connection
> >
>
> Although sample data appears to be working:
> > gsm97138 <- getGEO("GSM97138")
> trying URL
> '
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?targ=self&acc=GSM9713
8&fo
> rm=text&view=full'
> Content type 'geo/text' length unknown
> opened URL
> downloaded 377 Kb
>
> File stored at:
> C:\DOCUME~1\btabor\LOCALS~1\Temp\RtmpsW3lE1/GSM97138.soft
> >
>
> Unfortunately I don't want raw data at this stage.
>
This won't get you raw data, either--at least not in all cases. A GSE
record is a concatenation of the GSM records. A GSEMatrix record is
simply
the "VALUE" column from each GSE record in a single table.
>
> Session info is:
>
> > sessionInfo()
> R version 2.6.0 (2007-10-03)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia.1252;LC
_MON
> ETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Australia.
1252
>
> attached base packages:
> [1] tools stats graphics grDevices utils datasets
methods
> base
>
> other attached packages:
> [1] GEOquery_2.2.0 RCurl_0.8-1 Biobase_1.16.1
> >
>
> PS. I'm running R off an external drive as my network privileges
wont
> let me put it on my C-drive:
> E:\R-2.6.0\bin
> E:\R-2.6.0\library\GEOquery
>
Running off an external drive probably isn't the problem. This looks
like a
proxy problem, especially since the http:// download to get a sample
works
(note that I think it is the fact that http:// is used, not the fact
that
you are trying to retrieve a sample). So, you will need to see if you
can
set up a proxy for ftp connections. You might start with the help for
download.file() for how to do that, but you may also need to contact
your
computer support staff for some assistance.
Hope that helps.
Sean
[[alternative HTML version deleted]]
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