[BioC] Error: package/namespace load failed for ‘affycoretools
James W. MacDonald
jmacdon at uw.edu
Thu Dec 20 19:35:38 CET 2012
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
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> [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
>
>
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>
>
>
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--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
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