Hello Stefano and others, I can download and install R with no difficulties. When I try to get Bioconductor by typing: source("http://www.bioconductor.org/getBioC.R") I get the error: Error in file(file, "r") : unable to open connection In addition: Warning message: unable to connect to 'www.bioconductor.org' on port 80. On windows, I solved this by: 1. Right click on the R icon on the desktop 2. Select properties 3. Change the target from "C:\Program Files\R\rw2001\bin\Rgui.exe" (or whatever your Rgui path is) to "C:\Program Files\R\rw2001\bin\Rgui.exe" --internet2 (i.e. add the flag --internet2 after the quoted path name) 4. Select OK As this involves the use of the internet2.dll, I assume this will not work on Mac OSX. My question is, what is the equivalent procedure on a Mac to solve this connection problem? Regards, Jonathan stefano iacus wrote: > Jonathan, > could you please be more specific? > R on OS X has such functionalities. > stefano > p.s. eventually R-sig-Mac for such OS X specific issues > > Il giorno 30/mar/06, alle ore 06:28, Jonathan Arthur ha scritto: > >> Hello all, >> >> I am trying to install Bioconductor on a Mac and having difficulty >> getting the internet download functions to work. On Windows, I solved >> this by using the internet2.dll >> >> I have not been able to find, in the R or Bioconductor documentation, >> details on the equivalent process required on a Mac to get the internet >> download functions to work. Could anybody help me out with the required >> commands? >> >> Thanks, >> >> Jonathan >> >> -- >> Dr Jonathan Arthur >> Sesqui Lecturer in Bioinformatics >> Central Clinical School, Faculty of Medicine and SUBIT >> Medical Foundation Building, K25 >> University of Sydney >> Ph: +61 2 9036 3132 >> Email: jarthur at med.usyd.edu.au >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/ >> gmane.science.biology.informatics.conductor > > -- Dr Jonathan Arthur Sesqui Lecturer in Bioinformatics Central Clinical School, Faculty of Medicine and SUBIT Medical Foundation Building, K25 University of Sydney Ph: +61 2 9036 3132 Email: jarthur at med.usyd.edu.au

It sounds like you have firewall issues. My guess is that your site uses some sort of proxy server rather than allowing direct connections. Your IT department probably correctly configures IE on the Win32 boxen so the internet2 flag works. On Apr 2, 2006, at 4:30 PM, Jonathan Arthur wrote: > Hello Stefano and others, > > I can download and install R with no difficulties. When I try to get > Bioconductor by typing: > > source("http://www.bioconductor.org/getBioC.R") > > I get the error: > > Error in file(file, "r") : unable to open connection > In addition: Warning message: > unable to connect to 'www.bioconductor.org' on port 80. > > On windows, I solved this by: > > 1. Right click on the R icon on the desktop > 2. Select properties > 3. Change the target from "C:\Program Files\R\rw2001\bin\Rgui.exe" (or > whatever your Rgui path is) to "C:\Program Files\R\rw2001\bin > \Rgui.exe" > --internet2 (i.e. add the flag --internet2 after the quoted path name) > 4. Select OK > > As this involves the use of the internet2.dll, I assume this will not > work on Mac OSX. My question is, what is the equivalent procedure on a > Mac to solve this connection problem? > > Regards, > > Jonathan > > > stefano iacus wrote: > >> Jonathan, >> could you please be more specific? >> R on OS X has such functionalities. >> stefano >> p.s. eventually R-sig-Mac for such OS X specific issues >> >> Il giorno 30/mar/06, alle ore 06:28, Jonathan Arthur ha scritto: >> >>> Hello all, >>> >>> I am trying to install Bioconductor on a Mac and having difficulty >>> getting the internet download functions to work. On Windows, I >>> solved >>> this by using the internet2.dll >>> >>> I have not been able to find, in the R or Bioconductor >>> documentation, >>> details on the equivalent process required on a Mac to get the >>> internet >>> download functions to work. Could anybody help me out with the >>> required >>> commands? >>> >>> Thanks, >>> >>> Jonathan >>> >>> -- >>> Dr Jonathan Arthur >>> Sesqui Lecturer in Bioinformatics >>> Central Clinical School, Faculty of Medicine and SUBIT >>> Medical Foundation Building, K25 >>> University of Sydney >>> Ph: +61 2 9036 3132 >>> Email: jarthur at med.usyd.edu.au >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/ >>> gmane.science.biology.informatics.conductor >> >> > > > -- > Dr Jonathan Arthur > Sesqui Lecturer in Bioinformatics > Central Clinical School, Faculty of Medicine and SUBIT > Medical Foundation Building, K25 > University of Sydney > Ph: +61 2 9036 3132 > Email: jarthur at med.usyd.edu.au > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/ > gmane.science.biology.informatics.conductor --- Byron Ellis (ellis at stat.harvard.edu) "Oook" -- The Librarian

Byron Ellis <ellis at="" stat.harvard.edu=""> writes: > It sounds like you have firewall issues. My guess is that your site > uses some sort of proxy server rather than allowing direct > connections. Your IT department probably correctly configures IE on > the Win32 boxen so the internet2 flag works. It does sound like a http proxy issue. The there are some ways of working with that and they are described in the R help page for the download.file function. + seth

It seems a proxy problem. Please try this http://docs.info.apple.com/article.html?path=Mac/10.4/en/mh609.html for a system-level approach or http://spider.stat.umn.edu/R/library/utils/html/download.file.html for a R-specific solution. You can ask for help to your IT for the proxy details, or look into your web browser proxy settings. Let us know. stefano Il giorno 03/apr/06, alle ore 01:30, Jonathan Arthur ha scritto: > Hello Stefano and others, > > I can download and install R with no difficulties. When I try to > get Bioconductor by typing: > > source("http://www.bioconductor.org/getBioC.R") > > I get the error: > > Error in file(file, "r") : unable to open connection > In addition: Warning message: > unable to connect to 'www.bioconductor.org' on port 80. > > On windows, I solved this by: > > 1. Right click on the R icon on the desktop > 2. Select properties > 3. Change the target from "C:\Program Files\R\rw2001\bin > \Rgui.exe" (or whatever your Rgui path is) to "C:\Program Files\R > \rw2001\bin\Rgui.exe" --internet2 (i.e. add the flag --internet2 > after the quoted path name) > 4. Select OK > > As this involves the use of the internet2.dll, I assume this will > not work on Mac OSX. My question is, what is the equivalent > procedure on a Mac to solve this connection problem? > > Regards, > > Jonathan > > > stefano iacus wrote: > >> Jonathan, >> could you please be more specific? >> R on OS X has such functionalities. >> stefano >> p.s. eventually R-sig-Mac for such OS X specific issues >> >> Il giorno 30/mar/06, alle ore 06:28, Jonathan Arthur ha scritto: >> >>> Hello all, >>> >>> I am trying to install Bioconductor on a Mac and having difficulty >>> getting the internet download functions to work. On Windows, I >>> solved >>> this by using the internet2.dll >>> >>> I have not been able to find, in the R or Bioconductor >>> documentation, >>> details on the equivalent process required on a Mac to get the >>> internet >>> download functions to work. Could anybody help me out with the >>> required >>> commands? >>> >>> Thanks, >>> >>> Jonathan >>> >>> -- >>> Dr Jonathan Arthur >>> Sesqui Lecturer in Bioinformatics >>> Central Clinical School, Faculty of Medicine and SUBIT >>> Medical Foundation Building, K25 >>> University of Sydney >>> Ph: +61 2 9036 3132 >>> Email: jarthur at med.usyd.edu.au >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/ >>> gmane.science.biology.informatics.conductor >> >> > > > -- > Dr Jonathan Arthur > Sesqui Lecturer in Bioinformatics > Central Clinical School, Faculty of Medicine and SUBIT > Medical Foundation Building, K25 > University of Sydney > Ph: +61 2 9036 3132 > Email: jarthur at med.usyd.edu.au > >