Dear List, I just istalled the R 2.13.0 and Bioconductor 2.8. When loading the latest arrayQualityMetrics package it failed because there was no 'affyPLM' package. I then re-installed 'affyPLM' but received the message "package ‘affyPLM’ is not available (for R version 2.13.0)". I seeing some of the discussion recently on new features in arrayQualityMetrics, I am looking forward to checking them out. The error messages and sessionInfo are pasted below. Thanks for any assistance! Eric Error in loadNamespace(i[[1L]], c(lib.loc, .libPaths())) : there is no package called 'affyPLM' Error: package/namespace load failed for 'arrayQualityMetrics' > utils:::menuInstallPkgs() Error in install.packages(NULL, .libPaths()[1L], dependencies = NA, type = type) : no packages were specified > utils:::menuInstallPkgs() Error in install.packages(NULL, .libPaths()[1L], dependencies = NA, type = type) : no packages were specified > biocLite("affyPLM") Using R version 2.13.0, biocinstall version 2.8.3. Installing Bioconductor version 2.8 packages: [1] "affyPLM" Please wait... Warning message: In getDependencies(pkgs, dependencies, available, lib) : package ‘affyPLM’ is not available (for R version 2.13.0) > > sessionInfo() R version 2.13.0 (2011-04-13) Platform: i386-pc-mingw32/i386 (32-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 other attached packages: [1] affy_1.30.0 Biobase_2.12.0 loaded via a namespace (and not attached): [1] affyio_1.20.0 preprocessCore_1.14.0 tools_2.13.0 -- Eric Bremer, PhD Chief Scientific Officer Precision Biomarker Resources, Inc. 820 Davis St., Suite 216 Evanston, Illinois 60201 Office: 847.866.0406 Mobile: 708.267.2052 Skype: egbremer www.precisionbiomarker.com [[alternative HTML version deleted]]

Hello Eric, Thanks for reporting this problem. It will be fixed in tomorrow's builds (around noon Seattle time) Dan On Thu, Apr 14, 2011 at 4:23 PM, Eric Bremer <egbremer at="" precisionbiomarker.com=""> wrote: > Dear List, > I just istalled the R 2.13.0 and Bioconductor 2.8. ?When loading the latest > arrayQualityMetrics package it failed because there was no 'affyPLM' > package. ?I then re-installed 'affyPLM' but received the message "package > ?affyPLM? is not available (for R version 2.13.0)". ?I seeing some of the > discussion recently on new features in arrayQualityMetrics, I am looking > forward to checking them out. The error messages and sessionInfo are pasted > below. > Thanks for any assistance! > Eric > > Error in loadNamespace(i[[1L]], c(lib.loc, .libPaths())) : > ?there is no package called 'affyPLM' > Error: package/namespace load failed for 'arrayQualityMetrics' >> utils:::menuInstallPkgs() > Error in install.packages(NULL, .libPaths()[1L], dependencies = NA, type = > type) : > ?no packages were specified >> utils:::menuInstallPkgs() > Error in install.packages(NULL, .libPaths()[1L], dependencies = NA, type = > type) : > ?no packages were specified >> biocLite("affyPLM") > Using R version 2.13.0, biocinstall version 2.8.3. > Installing Bioconductor version 2.8 packages: > [1] "affyPLM" > Please wait... > > Warning message: > In getDependencies(pkgs, dependencies, available, lib) : > ?package ?affyPLM? is not available (for R version 2.13.0) >> > > >> sessionInfo() > R version 2.13.0 (2011-04-13) > Platform: i386-pc-mingw32/i386 (32-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 > > other attached packages: > [1] affy_1.30.0 ? ?Biobase_2.12.0 > > loaded via a namespace (and not attached): > [1] affyio_1.20.0 ? ? ? ? preprocessCore_1.14.0 tools_2.13.0 > > > -- > Eric Bremer, PhD > Chief Scientific Officer > Precision Biomarker Resources, Inc. > 820 Davis St., ?Suite 216 > Evanston, Illinois ?60201 > > Office: 847.866.0406 > Mobile: 708.267.2052 > Skype: egbremer > > www.precisionbiomarker.com > > ? ? ? ?[[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 >