[R] R won't connect to the internet on SUSE Linux 8.1

James MacDonald jmacdon at med.umich.edu
Fri Jul 25 17:58:13 CEST 2003


HTTP_PROXY issues aside, if all you want to do is install Bioconductor,
simply download the latest bioconductor_xx.tar.gz and use R CMD
INSTALL.

Jim



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623

>>> "michael watson (IAH-C)" <michael.watson at bbsrc.ac.uk> 07/25/03
07:18AM >>>
Hi Henrik

Thanks for your help, I really do appreciate it.

If I follow your instructions, R returns the value
http://wwwcache.bbsrc.ac.uk:8080.  That is good and it means that
indeed my http_proxy environment variable is set.

I have also added the lines

http_proxy=http://wwwcache.bbsrc.ac.uk:8080/
HTTP_PROXY=http://wwwcache.bbsrc.ac.uk:8080/

both to .Renviron in my home directory, and to /usr/lib/R/etc/Renviron
and /usr/lib/R/etc/Renviron.site.

All to no avail... R still doesn't try to connect through my proxy
server.  

Please, I genuinely think this is a bug in R 1.7.1 on Suse Linux 8.1.

NOW, here is a little detail I have just discovered that PROVES my
proxy is working.  

If I do:

update.packages(method="wget")

then everything works fine.... hmmmm, but I still have a problem as the
command I really want to run is :

source("http://wwwbioconductor.org/getBioC.R")

and source() does not accept an option 'method="wget"'....

SO... is there a way in R that I can set it up such that ALL internet
connections from within R use method="wget" ??

Thanks
Mick

-----Original Message-----
From: Henrik Bengtsson [mailto:hb at maths.lth.se] 
Sent: 25 July 2003 11:25
To: 'michael watson (IAH-C)'
Cc: R-help at stat.math.ethz.ch 
Subject: RE: [R] R won't connect to the internet on SUSE Linux 8.1


Could it be that you have redefined the command R in your shell such
that the http_proxy environment variable is set in one and R is
running
in another? (This is just a wild guess and I am myself only running
WinXP.) What do you get if you do

% env http_proxy=http://wwwcache.bbsrc.ac.uk:8080/
% R
> Sys.getenv("http_proxy")

Also, have you considered setting http_proxy in ~/.Renviron (see
?.Renviron).

Cheers

Henrik Bengtsson
Lund University


> -----Original Message-----
> From: r-help-bounces at stat.math.ethz.ch 
> [mailto:r-help-bounces at stat.math.ethz.ch] On Behalf Of 
> michael watson (IAH-C)
> Sent: den 25 juli 2003 10:24
> To: 'Prof Brian Ripley'
> Cc: 'R-help at stat.math.ethz.ch' 
> Subject: [R] R won't connect to the internet on SUSE Linux 8.1
> 
> 
> Hi
> 
> Thanks once again for your help, I do appreciate it..... however....
> 
> Here is what I get with your test.... (under tcsh - i 
> normally use bash, but I will keep everything the same)
> 
> users/mwatson> env http_proxy=http://wwwcache.bbsrc.ac.uk:8080/ R
> 
> >options(internet.info=0)
> >update.packages()
> trying URL `http://cran.r-project.org/src/contrib/PACKAGES' 
> unable to connect to 'cran.r-project.org' on port 80
> Error in download.file(url = paste(contriburl, "PACKAGES", 
> sep = "/"), :
> 	cannot open URL 'http://cran.r-project.org/src/contrib/PACKAGES'

> 
> 
> ... and THATS IT!  I don't get any "Using HTTP proxy ... " 
> message at all, which appears to suggest that R, under SUSE 
> Linux 8.1, is NOT PICKING up the http_proxy environment 
> variable - this isn't something thats wrong with my proxy, 
> that works with everything else - internet browsers, ftp 
> clients, wget, instant messenger clients etc etc.  The 
> problem is R, which isn't picking up that it needs to use the 
> http_proxy environment variable.  And I apologise for being 
> blunt, but that is an R problem, not a proxy problem!
> 
> Thanks for your help
> 
> Mick
> 
> 
> -----Original Message-----
> From: Prof Brian Ripley [mailto:ripley at stats.ox.ac.uk] 
> Sent: 24 July 2003 16:56
> To: michael watson (IAH-C)
> Subject: RE: [R] Your proxy seems not to work with R (was R 
> won't connect to the internet on Linux!)
> 
> 
> When I do (under tcsh)
> 
> env http_proxy=http://wwwcache.bbsrc.ac.uk:8080/ R
> > options(internet.info=0)
> > update.packages()
> trying URL `http://cran.r-project.org/src/contrib/PACKAGES' 
> Using HTTP proxy http://wwwcache.bbsrc.ac.uk:8080 
> 
> it tries to connect to your proxy (as it says) and gets no 
> response, which is not surprising from my site.  If you get 
> the same, your proxy is probably not behaving in the standard 
> way (since that has been tested by many users with standard
proxies).
> 
> I've changed the emphasis of the subject line to one I feel is more 
> equitable: many, many users have counter-evidence to your original 
> assertion, which was rather arrogant.
> 
> On Thu, 24 Jul 2003, michael watson (IAH-C) wrote:
> 
> > Hello Professor
> > 
> > If you are suggesting that I am simply missing the 
> "http://" part of 
> > my cache URL, or that I am missing a trailing "/", then I 
> pre-empted 
> > this response and it still doesn't work.
> 
> I was suggesting that `simply' you were not reading the documentation

> correctly. 
> 
> > I have tried setting both http_proxy and HTTP_PROXY to all of:
> 
> I hope you set to *each* of these.  The first and third are 
> documented to be incorrect, so using those was perverse.
> 
> > wwwcache.bbsrc.ac.uk:8080
> > http://wwwcache.bbsrc.ac.uk:8080 
> > wwwcache.bbsrc.ac.uk:8080/
> > http://wwwcache.bbsrc.ac.uk:8080/ 
> > 
> > and I still get the same response - R cannot open the URL.
> > 
> > And yes, that is thw right proxy address, I copied it straight from

> > Netscape on the same computer, and Netscape connects to the 
> internet 
> > fine.
> > 
> > Thanks
> > Mick
> >  
> > 
> > -----Original Message-----
> > From: Prof Brian Ripley [mailto:ripley at stats.ox.ac.uk] 
> > Sent: 24 July 2003 13:17
> > To: michael watson (IAH-C)
> > Cc: 'R-help at stat.math.ethz.ch '
> > Subject: Re: [R] R won't connect to the internet on Linux!
> > 
> > 
> > On Thu, 24 Jul 2003, michael watson (IAH-C) wrote:
> > 
> > > OK, I really am struggling with this one!  Forgive me if 
> I am being 
> > > stupid....
> > 
> > > I am running R 1.7.1 on Suse Linux 8.1.  I connect to the 
> internet 
> > > through a proxy so I have:
> > > 
> > > IAHC-LINUX03:~ # echo $http_proxy
> > > wwwcache.bbsrc.ac.uk:8080
> > > IAHC-LINUX03:~ # echo $HTTP_PROXY
> > > wwwcache.bbsrc.ac.uk:8080
> > > 
> > > just in case ;-)
> > > 
> > > SO, i go into R and I get:
> > > 
> > > > source("http://www.bioconductor.org/getBioC.R")
> > > unable to connect to 'www.bioconductor.org' on port 80. Error in

> > > file(file, "r") : cannot open URL 
> > > `http://www.bioconductor.org/getBioC.R' 
> > > 
> > > OK so is R just not picking up my proxy setting?
> > 
> > Your setting is wrong, so it is being ignored.  The help page says

> > quite explicitly
> > 
> >       The form of `"http_proxy"' should be 
> `"http://proxy.dom.com/"' or
> >      `"http://proxy.dom.com:8080/"' where the port defaults 
> to `80' and
> >      the trailing slash may be omitted.
> > 
> > > It seems to be trying
> > > port 80 on something, and I have specifically set it to 
> port 8080 in 
> > > my environment variables.  As far as I can see I have 
> followed the 
> > > reference manual suggestion, so does anyone else have one?
> > 
> > The problem is in your seeing, it seems.
> > 
> > 
> 
> -- 
> Brian D. Ripley,                  ripley at stats.ox.ac.uk 
> Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/

> University of Oxford,             Tel:  +44 1865 272861 (self)
> 1 South Parks Road,                     +44 1865 272866 (PA)
> Oxford OX1 3TG, UK                Fax:  +44 1865 272595
> 
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list 
> https://www.stat.math.ethz.ch/mailman/listinfo> /r-help
> 
> 
>

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