Yes, that works fine. > library(Biobase) ... > library(arrayQualityMetrics) Creating a generic function for ‘hist’ from package ‘graphics’ in package ‘affyPLM’ > library(affyPLM) Loading required package: affy Loading required package: gcrma Loading required package: preprocessCore So the affyPLM NAMESPACE file needs to declare the dependency; importFrom(Biobase, "addVigs2WinMenu"). cheers, Marcus On Mon, Sep 3, 2012 at 5:05 PM, Martin Morgan <mtmorgan@fhcrc.org> wrote: > On 09/02/2012 07:17 PM, Marcus Davy wrote: > >> This more informative error is from another fresh test >> >> ## Fresh Install of R-2.15.1 >> >>> source("http://www.**bioconductor.org/biocLite.R<http: www.biocon="" ductor.org="" bioclite.r=""> >>> ") >>> biocLite("arrayQualityMetrics"**) >>> >> ... >> >> library(arrayQualityMetrics) >>> >> Creating a generic function for ‘boxplot’ from package ‘graphics’ in >> package ‘affyPLM’ >> Creating a generic function for ‘hist’ from package ‘graphics’ in package >> ‘affyPLM’ >> Error : .onLoad failed in loadNamespace() for 'affyPLM', details: >> call: fun(libname, pkgname) >> error: could not find function "addVigs2WinMenu" >> Error: package/namespace load failed for ‘arrayQualityMetrics’ >> > > affyPLM should importFrom(Biobase, addVigs2WinMenu). I think you can work > around this by first loading Biobase > > library(Biobase) > library(arrayQualityMetrics) > > Martin > > >> Marcus >> >> On Mon, Sep 3, 2012 at 1:50 PM, Marcus Davy <mdavy86@gmail.com> wrote: >> >> Hi, >>> I have a script which works fine under R-2.14.1 on windows (and previous >>> versions), but is throwing an error when loading the library on a fresh >>> build with R-2.15.1. From a bioC thread recently about >>> arrayQualityMetrics >>> It looks like it is working on other platforms. The error looks like it >>> is >>> a namespace dependency issue with affyPLM and Biobase::addVigs2WinMenu. >>> >>> cheers, >>> >>> Marcus >>> >>> library(arrayQualityMetrics) >>>> >>> Error in loadNamespace(i[[1L]], c(lib.loc, .libPaths())) : >>> there is no package called ‘affyPLM’ >>> Error: package/namespace load failed for ‘arrayQualityMetrics’ >>> >>>> sessionInfo() >>>> >>> R version 2.15.1 (2012-06-22) >>> Platform: i386-pc-mingw32/i386 (32-bit) >>> >>> locale: >>> [1] LC_COLLATE=English_New Zealand.1252 LC_CTYPE=English_New >>> Zealand.1252 LC_MONETARY=English_New Zealand.1252 >>> [4] LC_NUMERIC=C LC_TIME=English_New >>> Zealand.1252 >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] BiocInstaller_1.5.12 Biobase_2.17.7 BiocGenerics_0.3.1 >>> >>> loaded via a namespace (and not attached): >>> [1] affy_1.35.1 affyio_1.25.0 preprocessCore_1.19.0 >>> tools_2.15.1 zlibbioc_1.3.0 >>> >>> >>> >> [[alternative HTML version deleted]] >> >> >> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.e="" thz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: http://news.gmane.org/gmane.** >> science.biology.informatics.**conductor<http: news.gmane.org="" gmane="" .science.biology.informatics.conductor=""> >> >> > > -- > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M1 B861 > Phone: (206) 667-2793 > [[alternative HTML version deleted]]