Luke, you are an absolute genius. For anyone who is still interested (and I doubt anyone is ;-) for some reason in SUSE an environment variable "no_proxy" is set to localhost, as described below, and that prevents R from connecting to the internet.
Thank you everyone for your responses Regards Mick -----Original Message----- From: Luke Tierney [mailto:[EMAIL PROTECTED] Sent: 26 July 2003 16:40 To: michael watson (IAH-C) Cc: 'James MacDonald '; '[EMAIL PROTECTED] ' Subject: RE: [R] R won't connect to the internet on SUSE Linux 8.1 On the SuSE setup I have access to it seems that for whatever reason the environment variable no_proxy is defined as 'localhost' in the shell initialization files /etc/SuSEconfig/csh.cshrc and /etc/SuSEconfig/profile. This turns use of proxy's off in the R internals. See if you have it defined, and if so see if something like (unset no_proxy; R) in bash or (unsetenv no_proxy; R) in tcsh handles proxies properly; it seems to for me. When no_proxy is not defined I get > Sys.putenv("http_proxy"="http://foo.bar.com";) > download.file("http://blah.blah.net/foo.R";, "bar.R") trying URL `http://blah.blah.net/foo.R' unable to resolve 'foo.bar.com'. Error in download.file("http://blah.blah.net/foo.R";, "bar.R") : cannot open URL `http://blah.blah.net/foo.R' when proxy's are disabled by no_proxy being defined the "unable to resolve..." line is missing. Best, luke On Sat, 26 Jul 2003, michael watson (IAH-C) wrote: > :-)) > > 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: [EMAIL PROTECTED]; [EMAIL PROTECTED] > Cc: [EMAIL PROTECTED] > 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)" <[EMAIL PROTECTED]> 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:[EMAIL PROTECTED] > Sent: 25 July 2003 11:25 > To: 'michael watson (IAH-C)' > Cc: [EMAIL PROTECTED] > 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: [EMAIL PROTECTED] > > [mailto:[EMAIL PROTECTED] On Behalf Of > > michael watson (IAH-C) > > Sent: den 25 juli 2003 10:24 > > To: 'Prof Brian Ripley' > > Cc: '[EMAIL PROTECTED]' > > 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:[EMAIL PROTECTED] > > 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:[EMAIL PROTECTED] > > > Sent: 24 July 2003 13:17 > > > To: michael watson (IAH-C) > > > Cc: '[EMAIL PROTECTED] ' > > > 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, [EMAIL PROTECTED] > > 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 > > > > ______________________________________________ > > [EMAIL PROTECTED] mailing list > > https://www.stat.math.ethz.ch/mailman/listinfo> /r-help > > > > > > > > ______________________________________________ > [EMAIL PROTECTED] mailing list > https://www.stat.math.ethz.ch/mailman/listinfo/r-help > > ______________________________________________ > [EMAIL PROTECTED] mailing list > https://www.stat.math.ethz.ch/mailman/listinfo/r-help > -- Luke Tierney University of Iowa Phone: 319-335-3386 Department of Statistics and Fax: 319-335-3017 Actuarial Science 241 Schaeffer Hall email: [EMAIL PROTECTED] Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu ______________________________________________ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
