Hi guys, Is there a BSgenome.Dmelanogaster.UCSC.dm3 package for R 3.0.0 beta? I tried one under BioC devel (http://www.bioconductor.org/ packages/2.12/data/annotation/html/BSgenome.Dmelanogaster.UCSC.dm3.htm l), but had no success. > install.packages("BSgenome.Dmelanogaster.UCS C.dm3_1.3.19.tar.gz",repos="null",type="source") Warning: unable to access index for repository null/src/contrib Warning message: package ‘BSgenome.Dmelanogaster.UCSC.dm3_1.3.19.tar.gz’ is not available (for R version 3.0.0 beta) > sessionInfo() R version 3.0.0 beta (2013-03-24 r62395) Platform: x86_64-w64-mingw32/x64 (64-bit)locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_3.0.0 > Thanks, Ying [[alternative HTML version deleted]]

Sorry guys, I got it to work. I had a typo in the install.packages(). I should use repos=NULL instead of repos="null". Ying From: ying_chen@live.com To: bioconductor@r-project.org Date: Wed, 27 Mar 2013 14:49:15 -0400 Subject: [BioC] BSgenome.Dmelanogaster.UCSC.dm3 package for R 3.0.0 beta? Hi guys, Is there a BSgenome.Dmelanogaster.UCSC.dm3 package for R 3.0.0 beta? I tried one under BioC devel (http://www.bioconductor.org/ packages/2.12/data/annotation/html/BSgenome.Dmelanogaster.UCSC.dm3.htm l), but had no success. > install.packages("BSgenome.Dmelanogaster.UCS C.dm3_1.3.19.tar.gz",repos="null",type="source") Warning: unable to access index for repository null/src/contrib Warning message: package ‘BSgenome.Dmelanogaster.UCSC.dm3_1.3.19.tar.gz’ is not available (for R version 3.0.0 beta) > sessionInfo() R version 3.0.0 beta (2013-03-24 r62395) Platform: x86_64-w64-mingw32/x64 (64-bit)locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_3.0.0 > Thanks, Ying [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor@r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]

Hi Ying, On 3/27/2013 2:49 PM, ying chen wrote: > Hi guys, Is there a BSgenome.Dmelanogaster.UCSC.dm3 package for R 3.0.0 beta? I tried one under BioC devel (http://www.bioconductor.org/ packages/2.12/data/annotation/html/BSgenome.Dmelanogaster.UCSC.dm3.htm l), but had no success.> install.packages("BSgenome.Dmelanogaster.UCS C.dm3_1.3.19.tar.gz",repos="null",type="source") > Warning: unable to access index for repository null/src/contrib > Warning message: > package ?BSgenome.Dmelanogaster.UCSC.dm3_1.3.19.tar.gz? is not available (for R version 3.0.0 beta) You have found the correct package on the devel page, so I don't think your question is whether or not one exists. Instead, it appears you are wondering why it didn't install. This is why we tell people (for example here: http://www.bioconductor.org/install/) to do something like |source("http://bioconductor.org/biocLite.R") biocLite("BSgenome.Dmelanogaster.UCSC.dm3") ||| Because a) you don't have to go searching around for the right package and b) it just works. So try installing the package the recommended way, and let us know if you have problems. Best, Jim || >> sessionInfo() > R version 3.0.0 beta (2013-03-24 r62395) > Platform: x86_64-w64-mingw32/x64 (64-bit)locale: > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 > [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 attached base packages: > [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): > [1] tools_3.0.0 > Thanks, Ying > [[alternative HTML version deleted]] > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099