Hi Robert and others, Your new book looks great, and I can't wait until I can get a copy - literally. About a month ago, I downloaded all the packages using getMonograph(), version 1.2.2, although I then got so busy I couldn't check it out. I just now tried running through an R script from the first chapter, and ran into the same problem that was posted on the list serve on July 25, 2005, but there was no response: > library("RbcBook1") Error in open.connection(con, "rb") : unable to open connection In addition: Warning message: cannot open compressed file 'C:/PROGRA~1/R/rw2011/library/RbcBook1/R/all.rda' Error in library("RbcBook1") : .First.lib failed for 'RbcBook1' > sessionInfo() R version 2.1.1, 2005-06-20, i386-pc-mingw32 attached base packages: [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" [7] "datasets" "base" other attached packages: RColorBrewer SpikeInSubset affy reposTools Biobase "0.2-3" "1.0.1" "1.6.7" "1.5.19" "1.5.12" I also have R 2.2 and Bioconductor 1.7, so today I tried using getMonograph(), version 1.3 to download the newest versions of the packages. However, most of the packages are no longer available from the specified repositories: > source("http://www.bioconductor.org/getMonograph.R") > getMonograph() Running getMonograph version 1.3.0 with R version 2.2.0 Warning: unable to access index for repository http://www.bioconductor.org/packages/bioc/stable/bin/windows/contrib/2 .2 Warning: unable to access index for repository http://www.bioconductor.org/packages/data/experiment/stable/bin/window s/contrib/2.2 Warning: unable to access index for repository http://www.bioconductor.org/packages/omegahat/stable/bin/windows/contr ib/2.2 Warning: unable to access index for repository http://www.bioconductor.org/packages/lindsey/stable/bin/windows/contri b/2.2 Warning: unable to access index for repository http://www.bioconductor.org/packages/monograph/1.1/bin/windows/contrib /2.2 dependencies ''affycomp'' are not availabledependencies ''affydata'' are not availabledependencies ''affypdnn'' are not availabledependencies ''affyPLM'' are not availabledependencies ''ALL'' are not availabledependencies ''ALLMLL'' are not availabledependencies ''AmpAffyExample'' are not availabledependencies ''annaffy'' are not availabledependencies ''AnnBuilder'' are not availabledependencies ''annotate'' are not availabledependencies ''arrayMagic'' are not availabledependencies ''arrayQuality'' are not availabledependencies ''beta7'' are not availabledependencies ''Biobase'' are not availabledependencies ''bioDist'' are not availabledependencies ''Biostrings'' are not availabledependencies ''CoCiteStats'' are not availabledependencies ''convert'' are not availabledependencies ''edd'' are not availabledependencies ''estrogen'' are not availabledependencies ''facsDorit'' are not availabledependencies ''factDesign'' are not availabledependencies ''gcrma'' are not availabledependencies ''geneplotter'' are not availabledependencies ''golubEsets'' are not availabledependencies ''GOstats'' are not availabledependencies ''graph'' are not availabledependencies ''hexbin'' are not availabledependencies ''hgu2beta7'' are not availabledependencies ''KEGGSOAP'' are not availabledependencies ''kidpack'' are not availabledependencies ''LogitBoost'' are not availabledependencies ''matchprobes'' are not availabledependencies ''MLInterfaces'' are not availabledependencies ''prada'' are not availabledependencies ''PROcess'' are not availabledependencies ''ProData'' are not availabledependencies ''RbcBook1'' are not availabledependencies ''RBGL'' are not availabledependencies ''RCurl'' are not availabledependencies ''reposTools'' are not availabledependencies ''Rgraphviz'' are not availabledependencies ''simpleaffy'' are not availabledependencies ''SpikeInSubset'' are not availabledependencies ''SSOAP'' are not availabledependencies ''vsn'' are not availabledependencies ''yeastExpData'' are not available > sessionInfo() R version 2.2.0, 2005-10-06, i386-pc-mingw32 attached base packages: [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" [7] "datasets" "base" other attached packages: RColorBrewer affy Biobase RWinEdt hgu133acdf "0.2-3" "1.8.1" "1.8.0" "1.7-3" "1.5.1" Is this a problem related to the new release of Bioconductor? What can be done to get getMonograph() to work? Thanks, Jenny Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist W.M. Keck Center for Comparative and Functional Genomics Roy J. Carver Biotechnology Center University of Illinois, Urbana-Champaign 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 USA ph: 217-244-7355 fax: 217-265-5066 e-mail: drnevich at uiuc.edu

Hi Jenny, Thanks for the report. We are working on rebuilding the monograph repository for the latest release and should have something available sometime tomorrow. Best, + seth