[Bioc-devel] Recent / forthcoming changes to Biobase

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.

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"



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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.

Hi,

Some data packages are available at
http://www.bioconductor.org/packages/1.9/data/annotation/ for testing.
Version number is 1.13.0. Both source and windows binaries are there.
They were built by using R 2.4.0 alpha, AnnBuilder 1.11.11 and GO
1.13.0. Annotation data was downloaded from public databases on Aug 25
and from chip manufactures on Aug 29: