michael watson (IAH-C)
2003-Jul-25 08:23 UTC
[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
Henrik Bengtsson
2003-Jul-25 10:24 UTC
[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 > > >
michael watson (IAH-C)
2003-Jul-25 11:18 UTC
[R] R won't connect to the internet on SUSE Linux 8.1
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
>
>
>
James MacDonald
2003-Jul-25 15:58 UTC
[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> 07/25/0307:18AM >>> 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 standardproxies).> > 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 > > >______________________________________________ R-help at stat.math.ethz.ch mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
michael watson (IAH-C)
2003-Jul-26 09:55 UTC
[R] R won't connect to the internet on SUSE Linux 8.1
:-)) 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> 07/25/0307:18AM >>> 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 standardproxies).> > 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 > > >______________________________________________ R-help at stat.math.ethz.ch mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
michael watson (IAH-C)
2003-Jul-29 15:12 UTC
[R] R won't connect to the internet on SUSE Linux 8.1
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:luke at stat.uiowa.edu]
Sent: 26 July 2003 16:40
To: michael watson (IAH-C)
Cc: 'James MacDonald '; 'R-help at stat.math.ethz.ch '
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: 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
> >
> >
> >
>
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://www.stat.math.ethz.ch/mailman/listinfo/r-help
>
> ______________________________________________
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--
Luke Tierney
University of Iowa Phone: 319-335-3386
Department of Statistics and Fax: 319-335-3017
Actuarial Science
241 Schaeffer Hall email: luke at stat.uiowa.edu
Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu