[Bioc-devel] Problem loading Biobase in newest R2.4 for windows

James W. MacDonald jmacdon at med.umich.edu
Fri Sep 8 15:43:37 CEST 2006

Oosting, J. (PATH) wrote:
> When I try to load Biobase 1.11.32 in the latest versions of R (from
> about 3 sep onwards) I get the following error message. I'm not sure
> whether this is a R problem or a Biobase problem. This doesn't happen
> to a july version of R2.4, and looking at the check page for 1.9 it
> doesn't happen with the aug 31 version either. I have now tried it on
> different systems and a few versions (even compiled R for windows on
> the latest src snapshot). It does not happen on a linux system with
> the latest R.

This is because of some changes in S4 objects in R-devel. You can't just 
use the win32 binaries from BioC right now (the release 1.9 binaries 
that is) because they have to be rebuilt using a newer version of 
R-devel that has the changes (which are still being made AFAIK). If you 
can build source packages on your windows box, you can always use

biocLite("packagename", type = "source")

which will download and install the source packages, which will then 
work. Unfortunately this doesn't work for certain packages because they 
need special babying on windows (XML, RCurl, RMySQL, maybe some others). 
These have to be installed by hand.



>> library(Biobase)
> Loading required package: tools Error in loadNamespace(package,
> c(which.lib.loc, lib.loc), keep.source = keep.source) : in 'Biobase'
> methods for export not found: [, [[, $, abstract,
> addVarMetadataEntry, aggenv, aggfun, annotatedDataFrameFrom,
> annotation, coerce, combine, content, convertVarLabels, description,
> dims, eList, experimentData, expinfo, exprs, exprs2excel,
> featureNames, featureData, featureData<-, geneNames, getExpData,
> getUnits, getVarMetadata, hybridizations, initfun, iter, length,
> locked, normControls, ncol, notes, otherInfo, pData, phenoData,
> preproc, sampleNames, samples, se.exprs, split, storageMode,
> update2MIAME, varLabels, varMetadata, reporterInfo, annotation<-,
> description<-, eList<-, experimentData<-, exprs<-, featureNames<-,
> geneNames<-, notes<-, pData<-, phenoData<-, sampleNames<-,
> varLabels<-, varMetadata<-, assayData<-, reporterInfo<-, se.exprs<-,
> storageMode<-, write.exprs, as.data.frame.exprSet, dim, dimLabels,
> assayData, reporterNames, pubMedIds, pubMedIds<-, isVersioned,
> isCurrent, c Error: package/namespace load failed for 'Biobase'
>> library(Biobase)
> Error in formals(contents) : object "contents" not found Error:
> .onLoad failed in 'loadNamespace' for 'Biobase' Error:
> package/namespace load failed for 'Biobase'
>> sessionInfo()
> R version 2.4.0 alpha (2006-09-05 r39134) i386-pc-mingw32
> locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> States.1252;LC_MONETARY=English_United
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
> attached base packages: [1] "tools"     "methods"   "stats"
> "graphics"  "grDevices" "utils" [7] "datasets"  "base"
> [[alternative HTML version deleted]]
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James W. MacDonald, M.S.
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

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