[BioC] getBioC problem

Ting-Yuan Liu tliu at fhcrc.org
Fri Feb 3 19:14:18 CET 2006

Hi Amy,

> > source("http://www.bioconductor.org/getBioC.R")
> Error in file(file, "r", encoding = encoding) :
>         unable to open connection
> In addition: Warning message:
> unable to connect to 'www.bioconductor.org' on port 80.

It seems that your LAN has some special settings (such as firewall?) so 
that you are unable to find the file getBioC.R.  Could you try to put the 
address "http://www.bioconductor.org/getBioC.R" in your browser to see if 
you can browse this script in your browsers?  I will guess that you are 
unable to see it in the browsers.  

In my XP machine, I can see the script in the browser (FireFox), and I can 
use getBioC without any errors in R (2.2.1).  Could you check with the LAN 
administrator to see if there is any firewall or something?  


> I have not found the error in the mailing archives, but did find several
> references to the warning message. Trying both suggestions in the R FAQ
> "internet download fails", this is what happens:
> (a) if I add --internet2 to the target of the shortcut:
> [The name '"C:\Program Files\R\R-2.2.1\bin\Rgui.exe"--internet2' specified
> in the Target box is not valid.  Make sure the path and file name are
> correct.]
> (b) I am connected to the internet via a LAN, which has a proxy so:
> > "path_to_R-2.2.1\bin\RGui.exe"
> http_proxy=http://www.abdn.ac.uk/local/autoproxy.pac
> Error: syntax error in ""path_to_R-2.2.1\bin\RGui.exe" http_proxy"
> that doesn't work either...
> What am I doing wrong, any ideas?
> I should add that on my other computer (same OS, same network connections)
> I installed Bioconductor packages from a CD rom but also had trouble
> getting extra packages from the internet.
> If I try downloading biocLite, I get the same error message and warning.
> Looking forward to any suggestions,
> Cheers,
> Amy.
> -------------------------------------------
> Amy Mikhail
> Research student
> University of Aberdeen
> Zoology Building
> Tillydrone Avenue
> Aberdeen AB24 2TZ
> Scotland
> Email: a.mikhail at abdn.ac.uk
> Phone: 00-44-1224-272880 (lab)
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