Dear list, As my own computer is currently out of action I have tried to install the latest version of R (2.2.1) and Bioconductor release (1.7) on another one (operating system is windows XP). The R installation worked fine, but the Bioconductor download didn't work. I get this error message: > source("http://www.bioconductor.org/getBioC.R") Error in file(file, "r", encoding = encoding) : unable to open connection In addition: Warning message: unable to connect to 'www.bioconductor.org' on port 80. I have not found the error in the mailing archives, but did find several references to the warning message. Trying both suggestions in the R FAQ "internet download fails", this is what happens: (a) if I add --internet2 to the target of the shortcut: [The name '"C:\Program Files\R\R-2.2.1\bin\Rgui.exe"--internet2' specified in the Target box is not valid. Make sure the path and file name are correct.] (b) I am connected to the internet via a LAN, which has a proxy so: > "path_to_R-2.2.1\bin\RGui.exe" http_proxy=http://www.abdn.ac.uk/local/autoproxy.pac Error: syntax error in ""path_to_R-2.2.1\bin\RGui.exe" http_proxy" that doesn't work either... What am I doing wrong, any ideas? I should add that on my other computer (same OS, same network connections) I installed Bioconductor packages from a CD rom but also had trouble getting extra packages from the internet. If I try downloading biocLite, I get the same error message and warning. Looking forward to any suggestions, Cheers, Amy. ------------------------------------------- Amy Mikhail Research student University of Aberdeen Zoology Building Tillydrone Avenue Aberdeen AB24 2TZ Scotland Email: a.mikhail at abdn.ac.uk Phone: 00-44-1224-272880 (lab)

Hi Amy, > > source("http://www.bioconductor.org/getBioC.R") > Error in file(file, "r", encoding = encoding) : > unable to open connection > In addition: Warning message: > unable to connect to 'www.bioconductor.org' on port 80. It seems that your LAN has some special settings (such as firewall?) so that you are unable to find the file getBioC.R. Could you try to put the address "http://www.bioconductor.org/getBioC.R" in your browser to see if you can browse this script in your browsers? I will guess that you are unable to see it in the browsers. In my XP machine, I can see the script in the browser (FireFox), and I can use getBioC without any errors in R (2.2.1). Could you check with the LAN administrator to see if there is any firewall or something? HTH, Ting-Yuan > > I have not found the error in the mailing archives, but did find several > references to the warning message. Trying both suggestions in the R FAQ > "internet download fails", this is what happens: > > (a) if I add --internet2 to the target of the shortcut: > > [The name '"C:\Program Files\R\R-2.2.1\bin\Rgui.exe"--internet2' specified > in the Target box is not valid. Make sure the path and file name are > correct.] > > (b) I am connected to the internet via a LAN, which has a proxy so: > > > "path_to_R-2.2.1\bin\RGui.exe" > http_proxy=http://www.abdn.ac.uk/local/autoproxy.pac > Error: syntax error in ""path_to_R-2.2.1\bin\RGui.exe" http_proxy" > > that doesn't work either... > > What am I doing wrong, any ideas? > > I should add that on my other computer (same OS, same network connections) > I installed Bioconductor packages from a CD rom but also had trouble > getting extra packages from the internet. > > If I try downloading biocLite, I get the same error message and warning. > > Looking forward to any suggestions, > > Cheers, > Amy. > > ------------------------------------------- > Amy Mikhail > Research student > University of Aberdeen > Zoology Building > Tillydrone Avenue > Aberdeen AB24 2TZ > Scotland > Email: a.mikhail at abdn.ac.uk > Phone: 00-44-1224-272880 (lab) > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >

On 3 Feb 2006, tliu at fhcrc.org wrote: > > Hi Amy, > >>> source("http://www.bioconductor.org/getBioC.R") >> Error in file(file, "r", encoding = encoding) : >> unable to open connection >> In addition: Warning message: >> unable to connect to 'www.bioconductor.org' on port 80. > > It seems that your LAN has some special settings (such as firewall?) > so that you are unable to find the file getBioC.R. Could you try to > put the address "http://www.bioconductor.org/getBioC.R" in your > browser to see if you can browse this script in your browsers? I > will guess that you are unable to see it in the browsers. A proxy that requires authentication is more likely the issue here and so it is entirely possible that the web browser is properly configured but that R is not. >> (a) if I add --internet2 to the target of the shortcut: >> >> [The name '"C:\Program Files\R\R-2.2.1\bin\Rgui.exe"--internet2' >> specified in the Target box is not valid. Make sure the path and >> file name are correct.] Did you add a space betfore --internet2 ? >> (b) I am connected to the internet via a LAN, which has a proxy so: >> >>> "path_to_R-2.2.1\bin\RGui.exe" >> http_proxy=http://www.abdn.ac.uk/local/autoproxy.pac >> Error: syntax error in ""path_to_R-2.2.1\bin\RGui.exe" http_proxy" >> >> that doesn't work either... >> >> What am I doing wrong, any ideas? The help page for download.file() has details about proxy configuration. Without knowing more about your proxy setup it may be hard for us to help further. Also, there may be more expertise with using R with web proxies on the R-help mail list. Hope that helps some. Best, + seth

On 6 Feb 2006, khansen at stat.berkeley.edu wrote: > This is not the same error as the original poster. > > I am currently unable to get the file in a browser (and so is > another user, see recent post). Perhaps the website is down? (You > might have a cached copy?) Yes, it seems we have been having server and/or network issues. I will send an update to the list as soon as things are resolved. + seth

Hi all, Currently having the same issue, although I don't use any proxy. I can see the file perfectly when I enter its http-adress in FireFox, so a Firewall block ought to be out of the question. Even disabling the firewall didn't solve it. The error I get is: -------------------------------------------------- >source("http://www.bioconductor.org/getBioC.R) Error in file(file, "r", encoding = encoding) : Unable to open connection In addition: Warning Message: Cannot open: HTTP status was '0 (null)' -------------------------------------------------- If I interpret this correctly, then it would appear that no connection could be made to the url, although it is possible with FireFox. Strange thing is that I installed the same R version on my notebook, and there it worked perfectly (same network, same firewall). Could this question be solved here, or do I need to send it towards the general R maling-list? Kind regards, - Stan -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Seth Falcon Sent: 03 February 2006 19:42 To: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] getBioC problem On 3 Feb 2006, tliu at fhcrc.org wrote: > > Hi Amy, > >>> source("http://www.bioconductor.org/getBioC.R") >> Error in file(file, "r", encoding = encoding) : >> unable to open connection >> In addition: Warning message: >> unable to connect to 'www.bioconductor.org' on port 80. > > It seems that your LAN has some special settings (such as firewall?) > so that you are unable to find the file getBioC.R. Could you try to > put the address "http://www.bioconductor.org/getBioC.R" in your > browser to see if you can browse this script in your browsers? I > will guess that you are unable to see it in the browsers. A proxy that requires authentication is more likely the issue here and so it is entirely possible that the web browser is properly configured but that R is not. >> (a) if I add --internet2 to the target of the shortcut: >> >> [The name '"C:\Program Files\R\R-2.2.1\bin\Rgui.exe"--internet2' >> specified in the Target box is not valid. Make sure the path and >> file name are correct.] Did you add a space betfore --internet2 ? >> (b) I am connected to the internet via a LAN, which has a proxy so: >> >>> "path_to_R-2.2.1\bin\RGui.exe" >> http_proxy=http://www.abdn.ac.uk/local/autoproxy.pac >> Error: syntax error in ""path_to_R-2.2.1\bin\RGui.exe" http_proxy" >> >> that doesn't work either... >> >> What am I doing wrong, any ideas? The help page for download.file() has details about proxy configuration. Without knowing more about your proxy setup it may be hard for us to help further. Also, there may be more expertise with using R with web proxies on the R-help mail list. Hope that helps some. Best, + seth _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor

Once again hi, Appears that the problem solved itself. Just tried it again and it's working like a charm now (-: After sending this mail towards the BioC-list I retried the same command on my notebook and it failed there as well (same error, although it worked one hour ago). And then suddenly, it worked again... Still don't know what the issue was, so I hope you can tell me! Kind regards, Stan -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Gaj Stan (BIGCAT) Sent: 06 February 2006 14:52 To: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] getBioC problem Hi all, Currently having the same issue, although I don't use any proxy. I can see the file perfectly when I enter its http-adress in FireFox, so a Firewall block ought to be out of the question. Even disabling the firewall didn't solve it. The error I get is: -------------------------------------------------- >source("http://www.bioconductor.org/getBioC.R) Error in file(file, "r", encoding = encoding) : Unable to open connection In addition: Warning Message: Cannot open: HTTP status was '0 (null)' -------------------------------------------------- If I interpret this correctly, then it would appear that no connection could be made to the url, although it is possible with FireFox. Strange thing is that I installed the same R version on my notebook, and there it worked perfectly (same network, same firewall). Could this question be solved here, or do I need to send it towards the general R maling-list? Kind regards, - Stan -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Seth Falcon Sent: 03 February 2006 19:42 To: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] getBioC problem On 3 Feb 2006, tliu at fhcrc.org wrote: > > Hi Amy, > >>> source("http://www.bioconductor.org/getBioC.R") >> Error in file(file, "r", encoding = encoding) : >> unable to open connection >> In addition: Warning message: >> unable to connect to 'www.bioconductor.org' on port 80. > > It seems that your LAN has some special settings (such as firewall?) > so that you are unable to find the file getBioC.R. Could you try to > put the address "http://www.bioconductor.org/getBioC.R" in your > browser to see if you can browse this script in your browsers? I > will guess that you are unable to see it in the browsers. A proxy that requires authentication is more likely the issue here and so it is entirely possible that the web browser is properly configured but that R is not. >> (a) if I add --internet2 to the target of the shortcut: >> >> [The name '"C:\Program Files\R\R-2.2.1\bin\Rgui.exe"--internet2' >> specified in the Target box is not valid. Make sure the path and >> file name are correct.] Did you add a space betfore --internet2 ? >> (b) I am connected to the internet via a LAN, which has a proxy so: >> >>> "path_to_R-2.2.1\bin\RGui.exe" >> http_proxy=http://www.abdn.ac.uk/local/autoproxy.pac >> Error: syntax error in ""path_to_R-2.2.1\bin\RGui.exe" http_proxy" >> >> that doesn't work either... >> >> What am I doing wrong, any ideas? The help page for download.file() has details about proxy configuration. Without knowing more about your proxy setup it may be hard for us to help further. Also, there may be more expertise with using R with web proxies on the R-help mail list. Hope that helps some. Best, + seth _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor

On 7 Feb 2006, a.mikhail at abdn.ac.uk wrote: > Just to let you know that when I added that space before > "--internet2" and tried to download BioC after your web/browser > problems were fixed, the downloads worked perfectly. Glad to hear it!

Dear list, Just to let you know that when I added that space before "--internet2" and tried to download BioC after your web/browser problems were fixed, the downloads worked perfectly. Thanks, Amy ------------------------------------------- Amy Mikhail Research student University of Aberdeen Zoology Building Tillydrone Avenue Aberdeen AB24 2TZ Scotland Email: a.mikhail at abdn.ac.uk Phone: 00-44-1224-272880 (lab)