[R] R won't connect to the internet on SUSE Linux 8.1
michael watson (IAH-C)
michael.watson at bbsrc.ac.uk
Sat Jul 26 11:55:16 CEST 2003
:-))
Installing Bioconductor was how it all began, so I ended up doing what you suggested (in fact I downloaded just the packages I needed as in the full tar ball, rhdf5 wouldn't compile, probably as I don't have the right hdf5 installed but thats not a problem).
BUT it just bugged me that I couldn't get R to work, and unfortunately in my frustration I appear to have upset a few people - for this I deeply apologise. IT still remains the case that, even with http_proxy set (and HTTP_PROXY set) i get the following results:
> update.packages()
doesn't work :-(
> update.packages(method = "wget")
works! :-D
> options(download.file.method = "wget")
> update.packages()
works! :-D
> options(download.file.method = "wget")
> source("http://www.bioconductor.org/getBioC.R")
doesn't work :-(
> download.file("http://www.bioconductor.org/getBioC.R", destfile = getBioC.R, method = "wget")
> source("getBioC.R")
> getBioC(method = "wget")
the first two commands work fine, the last doesn't and bombs out with the usual "can't connect to the internet"
OK I now have Bioconductor installed by the traditional method of downloading via Netscape and installing .tar.gz's, so I am happy, and for the record I think R is a miraculous piece of software and a testament to the wonders of free, open-source development, as is Bioconductor, both of which make my job, and life, a WHOLE lot easier. So I thank everyone on this list who has contributed to either or both :-D But I can't be the only one who wouldn't be curious if the above sequence of events occurred on their system.... ;-)
Have a good weekend one and all :-D
M
-----Original Message-----
From: James MacDonald
To: michael.watson at bbsrc.ac.uk; hb at maths.lth.se
Cc: R-help at stat.math.ethz.ch
Sent: 25/07/03 16:58
Subject: RE: [R] R won't connect to the internet on SUSE Linux 8.1
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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