Dear List, I got an error message in trying to load affycoretools: Hence plotPCA wouldn't work. I am running on a Mac with OS 10.7.5. Error : object ‘l2e’ is not exported by 'namespace:Biobase' In addition: Warning messages: 1: multiple methods tables found for ‘annotation’ 2: multiple methods tables found for ‘annotation<-’ Error: package/namespace load failed for ‘affycoretools Here are relevant excerpts from my session: R version 2.15.2 (2012-10-26) -- "Trick or Treat" Copyright (C) 2012 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: i386-apple-darwin9.8.0/i386 (32-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. [R.app GUI 1.53 (6335) i386-apple-darwin9.8.0] [Workspace restored from /Users/friedman/.RData] [History restored from /Users/friedman/.Rapp.history] > library(affy) Loading required package: BiocGenerics Attaching package: ‘BiocGenerics’ The following object(s) are masked from ‘package:stats’: xtabs The following object(s) are masked from ‘package:base’: anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find, get, intersect, lapply, Map, mapply, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int, rownames, sapply, setdiff, table, tapply, union, unique Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. > library(affyPLM) Loading required package: gcrma Loading required package: preprocessCore > library(affyQCReport) Loading required package: lattice No methods found in "Biobase" for requests: geneNames > library(simpleaffy) Loading required package: genefilter > > library(gcrma) library(limma) > library(arrayQualityMetrics) Warning messages: 1: multiple methods tables found for ‘annotation’ 2: multiple methods tables found for ‘annotation<-’ > library(genefilter) > library(rgl) > library(affycoretools) Loading required package: GO.db Loading required package: AnnotationDbi Loading required package: DBI Loading required package: KEGG.db KEGG.db contains mappings based on older data because the original resource was removed from the the public domain before the most recent update was produced. This package should now be considered deprecated and future versions of Bioconductor may not have it available. One possible alternative to consider is to look at the reactome.db package Error : object ‘l2e’ is not exported by 'namespace:Biobase' In addition: Warning messages: 1: multiple methods tables found for ‘annotation’ 2: multiple methods tables found for ‘annotation<-’ Error: package/namespace load failed for ‘affycoretools’ > sessionInfo() R version 2.15.2 (2012-10-26) Platform: i386-apple-darwin9.8.0/i386 (32-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] mouse4302cdf_2.10.0 KEGG.db_2.8.0 GO.db_2.8.0 [4] RSQLite_0.11.1 DBI_0.2-5 AnnotationDbi_1.20.3 [7] rgl_0.92.880 arrayQualityMetrics_3.14.0 simpleaffy_2.32.0 [10] genefilter_1.38.0 affyQCReport_1.36.0 lattice_0.20-10 [13] affyPLM_1.34.0 preprocessCore_1.20.0 gcrma_2.30.0 [16] affy_1.36.0 Biobase_2.18.0 BiocGenerics_0.4.0 loaded via a namespace (and not attached): [1] affyio_1.24.0 annaffy_1.28.0 annotate_1.34.1 beadarray_2.6.0 [5] BeadDataPackR_1.8.0 BiocInstaller_1.8.3 biomaRt_2.14.0 Biostrings_2.26.2 [9] Cairo_1.5-1 Category_2.22.0 cluster_1.14.3 colorspace_1.1-1 [13] graph_1.34.0 grid_2.15.2 GSEABase_1.18.0 Hmisc_3.9-3 [17] hwriter_1.3 IRanges_1.16.4 latticeExtra_0.6-19 limma_3.12.1 [21] parallel_2.15.2 plyr_1.7.1 RBGL_1.32.1 RColorBrewer_1.0-5 [25] RCurl_1.91-1 reshape2_1.2.1 setRNG_2011.11-2 splines_2.15.2 [29] stats4_2.15.2 stringr_0.6 survival_2.36-14 SVGAnnotation_0.93-1 [33] tools_2.15.2 vsn_3.24.0 XML_3.9-4 xtable_1.7-0 [37] zlibbioc_1.2.0 LATER ON plotPCA(gcnm,,legend=FALSE) Error: could not find function "plotPCA" Thanks and best wishes, Rich Richard A. Friedman, PhD Associate Research Scientist, Biomedical Informatics Shared Resource Herbert Irving Comprehensive Cancer Center (HICCC) Lecturer, Department of Biomedical Informatics (DBMI) Educational Coordinator, Center for Computational Biology and Bioinformatics (C2B2)/ National Center for Multiscale Analysis of Genomic Networks (MAGNet)/ Columbia Initiative in Systems Biology Room 824 Irving Cancer Research Center Columbia University 1130 St. Nicholas Ave New York, NY 10032 (212)851-4765 (voice) friedman@cancercenter.columbia.edu http://cancercenter.columbia.edu/~friedman/ In memoriam, Ray Bradbury [[alternative HTML version deleted]]

Hi Rich, On 12/20/2012 12:57 PM, Richard Friedman wrote: > Dear List, > > I got an error message in trying to load affycoretools: > > Hence plotPCA wouldn't work. I am running on a Mac > with OS 10.7.5. > > Error : object ?l2e? is not exported by 'namespace:Biobase' > In addition: Warning messages: > 1: multiple methods tables found for ?annotation? > 2: multiple methods tables found for ?annotation<-? > Error: package/namespace load failed for ?affycoretools > > > > Here are relevant excerpts from > my session: > > R version 2.15.2 (2012-10-26) -- "Trick or Treat" Right - you are using something called 'Trick or Treat' and you wonder why you have problems? I bet your house has been TP'ed as well. ;-D Anyway, it looks like you have some mixture of old and new packages. Try restarting R, and then library(BiocInstaller) biocLite(character(0)) # <- that's a zero BTW. and answer 'a' to the request to upgrade. If that doesn't help, let us know. Best, Jim > Copyright (C) 2012 The R Foundation for Statistical Computing > ISBN 3-900051-07-0 > Platform: i386-apple-darwin9.8.0/i386 (32-bit) > > R is free software and comes with ABSOLUTELY NO WARRANTY. > You are welcome to redistribute it under certain conditions. > Type 'license()' or 'licence()' for distribution details. > > Natural language support but running in an English locale > > R is a collaborative project with many contributors. > Type 'contributors()' for more information and > 'citation()' on how to cite R or R packages in publications. > > Type 'demo()' for some demos, 'help()' for on-line help, or > 'help.start()' for an HTML browser interface to help. > Type 'q()' to quit R. > > [R.app GUI 1.53 (6335) i386-apple-darwin9.8.0] > > [Workspace restored from /Users/friedman/.RData] > [History restored from /Users/friedman/.Rapp.history] > >> library(affy) > Loading required package: BiocGenerics > > Attaching package: ?BiocGenerics? > > The following object(s) are masked from ?package:stats?: > > xtabs > > The following object(s) are masked from ?package:base?: > > anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find, get, intersect, > lapply, Map, mapply, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, > rbind, Reduce, rep.int, rownames, sapply, setdiff, table, tapply, union, unique > > Loading required package: Biobase > Welcome to Bioconductor > > Vignettes contain introductory material; view with 'browseVignettes()'. To cite > Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. > >> library(affyPLM) > Loading required package: gcrma > Loading required package: preprocessCore >> library(affyQCReport) > Loading required package: lattice > No methods found in "Biobase" for requests: geneNames >> library(simpleaffy) > Loading required package: genefilter >> library(gcrma) > library(limma) >> library(arrayQualityMetrics) > Warning messages: > 1: multiple methods tables found for ?annotation? > 2: multiple methods tables found for ?annotation<-? >> library(genefilter) >> library(rgl) >> library(affycoretools) > Loading required package: GO.db > Loading required package: AnnotationDbi > Loading required package: DBI > > Loading required package: KEGG.db > > KEGG.db contains mappings based on older data because the original resource was removed > from the the public domain before the most recent update was produced. This package > should now be considered deprecated and future versions of Bioconductor may not have it > available. One possible alternative to consider is to look at the reactome.db package > > Error : object ?l2e? is not exported by 'namespace:Biobase' > In addition: Warning messages: > 1: multiple methods tables found for ?annotation? > 2: multiple methods tables found for ?annotation<-? > Error: package/namespace load failed for ?affycoretools? > >> sessionInfo() > R version 2.15.2 (2012-10-26) > Platform: i386-apple-darwin9.8.0/i386 (32-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] mouse4302cdf_2.10.0 KEGG.db_2.8.0 GO.db_2.8.0 > [4] RSQLite_0.11.1 DBI_0.2-5 AnnotationDbi_1.20.3 > [7] rgl_0.92.880 arrayQualityMetrics_3.14.0 simpleaffy_2.32.0 > [10] genefilter_1.38.0 affyQCReport_1.36.0 lattice_0.20-10 > [13] affyPLM_1.34.0 preprocessCore_1.20.0 gcrma_2.30.0 > [16] affy_1.36.0 Biobase_2.18.0 BiocGenerics_0.4.0 > > loaded via a namespace (and not attached): > [1] affyio_1.24.0 annaffy_1.28.0 annotate_1.34.1 beadarray_2.6.0 > [5] BeadDataPackR_1.8.0 BiocInstaller_1.8.3 biomaRt_2.14.0 Biostrings_2.26.2 > [9] Cairo_1.5-1 Category_2.22.0 cluster_1.14.3 colorspace_1.1-1 > [13] graph_1.34.0 grid_2.15.2 GSEABase_1.18.0 Hmisc_3.9-3 > [17] hwriter_1.3 IRanges_1.16.4 latticeExtra_0.6-19 limma_3.12.1 > [21] parallel_2.15.2 plyr_1.7.1 RBGL_1.32.1 RColorBrewer_1.0-5 > [25] RCurl_1.91-1 reshape2_1.2.1 setRNG_2011.11-2 splines_2.15.2 > [29] stats4_2.15.2 stringr_0.6 survival_2.36-14 SVGAnnotation_0.93-1 > [33] tools_2.15.2 vsn_3.24.0 XML_3.9-4 xtable_1.7-0 > [37] zlibbioc_1.2.0 > > LATER ON > > plotPCA(gcnm,,legend=FALSE) > Error: could not find function "plotPCA" > > Thanks and best wishes, > > Rich > > Richard A. Friedman, PhD > Associate Research Scientist, > Biomedical Informatics Shared Resource > Herbert Irving Comprehensive Cancer Center (HICCC) > Lecturer, > Department of Biomedical Informatics (DBMI) > Educational Coordinator, > Center for Computational Biology and Bioinformatics (C2B2)/ > National Center for Multiscale Analysis of Genomic Networks (MAGNet)/ > Columbia Initiative in Systems Biology > Room 824 > Irving Cancer Research Center > Columbia University > 1130 St. Nicholas Ave > New York, NY 10032 > (212)851-4765 (voice) > friedman at cancercenter.columbia.edu > http://cancercenter.columbia.edu/~friedman/ > > In memoriam, Ray Bradbury > > > [[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

Hi Richard, On Thu, Dec 20, 2012 at 12:57 PM, Richard Friedman <friedman at="" cancercenter.columbia.edu=""> wrote: > Dear List, > > I got an error message in trying to load affycoretools: > > Hence plotPCA wouldn't work. I am running on a Mac > with OS 10.7.5. Works for me (running on the same OS, even ;-) What version of affycoretools do you have installed? You can check by punching this into the R console: R> packageVersion("affycoretools") -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact