Seth, I can update packages from the Windows menu of R 2.3.1, but not from R 2.4. I get the following error message: Warning: unable to access index for repository http://www.bioconductor.org/bin/windows/contrib/2.4 sessionInfo() R version 2.4.0 Under development (unstable) (2006-08-29 r39012) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] "methods" "stats" "graphics" "grDevices" "utils" "datasets" "base" Thanks, Mark Mark W. Kimpel MD (317) 490-5129 Work, & Mobile (317) 663-0513 Home (no voice mail please) 1-(317)-536-2730 FAX -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Seth Falcon Sent: Monday, September 04, 2006 2:32 PM To: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] Hostname bug? Seth Falcon <sfalcon at="" fhcrc.org=""> writes: > Hi Taejoon, > > Taejoon Kwon <tk320 at="" cam.ac.uk=""> writes: >> Hi all, >> >> When I tried to re-install bioconductor package in my new linux laptop, I >> found that http://bioconductor.org and http://www.bioconductor.org were >> used inconsistently. I guess that two sites are slightly differently >> configured, so some scripts (such as biocLite.R) are not working properly. >> >> Could you check this? > > Thanks for the report. We are tracking this issue and trying to find > a fix. For now, please use http://www.bioconductor.org. Things should be fixed now. http://bioconductor.org should be serving all content (along with it's www-prefixed cousin). Please let us know of any problems (posting to this list is good). Best, + seth _______________________________________________ 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

Seth, can't you set the web server so that also the old URL maps to the new one during the migration period? /Henrik On 9/5/06, Seth Falcon <sfalcon at="" fhcrc.org=""> wrote: > Hi Mark, > > "Kimpel, Mark William" <mkimpel at="" iupui.edu=""> writes: > > I can update packages from the Windows menu of R 2.3.1, but not from R > > 2.4. I get the following error message: > > > > Warning: unable to access index for repository > > http://www.bioconductor.org/bin/windows/contrib/2.4 > > > > sessionInfo() > > > > R version 2.4.0 Under development (unstable) (2006-08-29 r39012) > > i386-pc-mingw32 > > > > locale: > > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > > States.1252;LC_MONETARY=English_United > > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > > > attached base packages: > > [1] "methods" "stats" "graphics" "grDevices" "utils" > > "datasets" "base" > > Thanks for the report. We have not added the BioC 1.9 repository to > the location that the Windows R GUI searches and hence the warning > message (and failure to update). > > At present, I suspect that even in R 2.3.z, this doesn't work as > desired because the operation only searches one of Bioconductor's > repositories. As a result, various dependencies will not be updated. > > We will look into addressing both of these issues for R 2.4 and the > upcoming BioC release. > > For now, I would recommend the following to update your packages > (should work for R 2.4 series): > > library("Biobase") > update.packages(repos=biocReposList(), dependencies=TRUE) > > Bw, > > + seth > > _______________________________________________ > 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 >