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


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