Hi, received these messagages when trying to install SNPlocs.Hsapiens.dbSNP.20090506 Any tips? Thanks, Dan > source("http://bioconductor.org/biocLite.R") Warning messages: 1: In safeSource() : Redefining ?biocinstall? 2: In safeSource() : Redefining ?biocinstallPkgGroups? 3: In safeSource() : Redefining ?biocinstallRepos? > biocLite("SNPlocs.Hsapiens.dbSNP.20090506") Using R version 2.10.0, biocinstall version 2.5.10. Installing Bioconductor version 2.5 packages: [1] "SNPlocs.Hsapiens.dbSNP.20090506" Please wait... Warning message: In getDependencies(pkgs, dependencies, available, lib) : package ?SNPlocs.Hsapiens.dbSNP.20090506? is not available > sessionInfo() R version 2.10.0 (2009-10-26) i386-pc-mingw32 locale: [1] LC_COLLATE=English_Canada.1252 LC_CTYPE=English_Canada.1252 LC_MONETARY=English_Canada.1252 LC_NUMERIC=C [5] LC_TIME=English_Canada.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BSgenome_1.14.2 Biostrings_2.14.10 IRanges_1.4.9 org.Hs.eg.db_2.3.6 RSQLite_0.8-1 DBI_0.2-5 AnnotationDbi_1.8.0 [8] Biobase_2.6.0 loaded via a namespace (and not attached): [1] tools_2.10.0

Hi Dan, Dan Strumpf wrote: > Hi, > received these messagages when trying to install > > SNPlocs.Hsapiens.dbSNP.20090506 > > Any tips? Where do you get that package name? I only see versions from 2007 and 2008: > suppressMessages(library(Biobase)) > z <- biocReposList() > a <- available.packages(paste(a[2], "/src/contrib", sep ="")) > grep("SNPlocs.Hsapiens", row.names(a), value = TRUE) [1] "SNPlocs.Hsapiens.dbSNP.20071016" "SNPlocs.Hsapiens.dbSNP.20080617" > sessionInfo() R version 2.10.0 Patched (2009-11-05 r50317) i386-pc-mingw32 locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] Biobase_2.6.1 loaded via a namespace (and not attached): [1] tools_2.10.0 Best, Jim > > Thanks, > > Dan > > > source("http://bioconductor.org/biocLite.R") > Warning messages: > 1: In safeSource() : Redefining ?biocinstall? > 2: In safeSource() : Redefining ?biocinstallPkgGroups? > 3: In safeSource() : Redefining ?biocinstallRepos? > > biocLite("SNPlocs.Hsapiens.dbSNP.20090506") > Using R version 2.10.0, biocinstall version 2.5.10. > Installing Bioconductor version 2.5 packages: > [1] "SNPlocs.Hsapiens.dbSNP.20090506" > Please wait... > > Warning message: > In getDependencies(pkgs, dependencies, available, lib) : > package ?SNPlocs.Hsapiens.dbSNP.20090506? is not available > > > sessionInfo() > R version 2.10.0 (2009-10-26) > i386-pc-mingw32 > > locale: > [1] LC_COLLATE=English_Canada.1252 LC_CTYPE=English_Canada.1252 > LC_MONETARY=English_Canada.1252 LC_NUMERIC=C > [5] LC_TIME=English_Canada.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] BSgenome_1.14.2 Biostrings_2.14.10 IRanges_1.4.9 > org.Hs.eg.db_2.3.6 RSQLite_0.8-1 DBI_0.2-5 AnnotationDbi_1.8.0 > [8] Biobase_2.6.0 > > loaded via a namespace (and not attached): > [1] tools_2.10.0 > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues