Dear list members, I have used Bioconductor fairly extensively over the past 6 months but have encountered a problem that i have been unable to overcome. I am using R 1.6.2, BioC 1.1 on Windows 2000. I have also installed and configured wget ...options(download.file.option="wget")... to input a proxy authentication password. I am able to install and update packages through CRAN, and also through bioconductor.org if I use download.file(), but getBioC() and many other functions for downloading files from the bioconductor web site fail. Can anyone tell me why and how to rectify the situation. Three examples are shown below. Regards Chris Bye > getBioC() Running getBioC version 1.2.18.... If you encounter problems, first make sure that you are running the latest version of getBioC() which can be found at: www.bioconductor.org/getBioC.R Please direct any concerns or questions to bioconductor@stat.math.ethz.ch. Error in getBioC() : Your R is not currently configured to allow HTTP connections, which is required for getBioC to work properly. ---------------------------------------------------------------------- ------------------------------------------------ > tmpLib <- tempfile() > dir.create(tmpLib) > syncLocalLibList(tmpLib) > getOption("repositories") CRAN "http://cran.r-project.org/src/contrib" > z <- getReposEntry("http://www.bioconductor.org/repository/sample/package") unable to connect to 'www.bioconductor.org'. Note: http://www.bioconductor.org/repository/sample/package does not seem to have a valid repository, skipping ---------------------------------------------------------------------- ----------------------------------------------- > ll <- "http://www.bioconductor.org/datafiles/wwwsources/Tll_tmpl.gz" > llSource <- fileFetcher(ll) unable to connect to 'www.bioconductor.org'. Error in urlOK() : The given URL is incorrect or the target site is not responding! ---------------------------------------------------------------------- -----------------------------------------------

On Mon, Feb 17, 2003 at 04:45:03PM +1100, Chris Bye wrote: > Dear list members, > I have used Bioconductor fairly extensively over the past 6 months but have encountered a problem that i have been unable to overcome. I am using R 1.6.2, BioC 1.1 on Windows 2000. I have also installed and configured wget ...options(download.file.option="wget")... to input a proxy authentication password. > I am able to install and update packages through CRAN, and also through bioconductor.org if I use download.file(), but getBioC() and many other functions for downloading files from the bioconductor web site fail. Can anyone tell me why and how to rectify the situation. Three examples are shown below. > Regards > Chris Bye Hi, the messages are quite explanatory, we are using http for the connection and you do not have http connectivity. So it won't work. We probably should not be so reliant on http connectivity (as you have noted there are other options such as wget). We will be looking in to that as soon as we can; but it will take some time. Thanks for bringing this to our attention, Robert ps you may be able to overcome the problem by 1) remove the line in getBioc that checks for capabilities 2) set the option download.file.method to wget > > > > getBioC() > Running getBioC version 1.2.18.... > If you encounter problems, first make sure that > you are running the latest version of getBioC() > which can be found at: www.bioconductor.org/getBioC.R > > Please direct any concerns or questions to bioconductor@stat.math.ethz.ch. > > Error in getBioC() : Your R is not currently configured to allow HTTP > connections, which is required for getBioC to work properly. > -------------------------------------------------------------------- -------------------------------------------------- > > tmpLib <- tempfile() > > dir.create(tmpLib) > > syncLocalLibList(tmpLib) > > getOption("repositories") > CRAN > "http://cran.r-project.org/src/contrib" > > z <- > getReposEntry("http://www.bioconductor.org/repository/sample/package") > unable to connect to 'www.bioconductor.org'. > Note: http://www.bioconductor.org/repository/sample/package does not > seem to have a valid repository, skipping > -------------------------------------------------------------------- ------------------------------------------------- > > ll <- "http://www.bioconductor.org/datafiles/wwwsources/Tll_tmpl.gz" > > llSource <- fileFetcher(ll) > unable to connect to 'www.bioconductor.org'. > Error in urlOK() : The given URL is incorrect or the target site is not > responding! > -------------------------------------------------------------------- ------------------------------------------------- > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- +--------------------------------------------------------------------- ------+ | Robert Gentleman phone : (617) 632-5250 | | Associate Professor fax: (617) 632-2444 | | Department of Biostatistics office: M1B20 | | Harvard School of Public Health email: rgentlem@jimmy.dfci.harvard.edu | +--------------------------------------------------------------------- ------+