Hi Wolfgang Thank you for your message. That has resolved both issues, my apologies, I thought I had upgraded but it must have been on a different machine. Thanks for the detailed suggestions. With regards, Lavinia. Lavinia Gordon Senior Research Officer Quantitative Sciences Core, Bioinformatics Murdoch Childrens Research Institute The Royal Children's Hospital Flemington Road Parkville Victoria 3052 Australia T 03 8341 6221 www.mcri.edu.au -----Original Message----- From: Wolfgang Huber [mailto:whuber@embl.de] Sent: Monday, 26 November 2012 7:37 PM To: Lavinia Gordon Cc: bioconductor at r-project.org Subject: Re: [BioC] arrayQualityMetrics and lumi - failure to load in R2.15.1 windows Dear Lavinia could it be that your installation of Bioconductor packages is incoherent? Have you tried running source("http://bioconductor.org/biocLite.R") biocLite("BiocUpgrade") biocLite("arrayQualityMetrics") from a clean new R 2.15.2? As is described e.g. here: http://www.bioconductor.org/install . To see whether what you experience might be a problem with the package(s) in general, or one with your computer in particular, you could check the 'daily package check reports' on the Bioc build server at http://bioconductor.org/checkResults/release/bioc-LATEST . Here you will see that no problem is currently reported for arrayQualityMetrics or lumi, which suggests that the latter is the case. Hope this helps, best wishes Wolfgang Il giorno Nov 26, 2012, alle ore 3:56 AM, Lavinia Gordon <lavinia.gordon at="" mcri.edu.au=""> ha scritto: > Dear All, > The package arrayQualityMetrics fails to load in R2.15.1: > >> library(arrayQualityMetrics) > Error : object 'geneNames' is not exported by 'namespace:Biobase' > Error: package/namespace load failed for 'arrayQualityMetrics' > > The library lumi also fails: >> library(lumi) > Loading required package: methylumi > Loading required package: scales > Loading required package: reshape2 > Loading required package: ggplot2 > Find out what's changed in ggplot2 with news(Version == "0.9.2.1", > package = "ggplot2") Loading required package: nleqslv Error : object > 'get_xsbasetypes_conversion_lookup' is not exported by > 'namespace:Biostrings' > In addition: Warning messages: > 1: found methods to import for function 'eapply' but not the generic > itself > 2: replacing previous import 'image' when loading 'graphics' > 3: package 'nleqslv' was built under R version 2.15.2 > Error: package/namespace load failed for 'lumi' > >> sessionInfo() > R version 2.15.1 (2012-06-22) > Platform: i386-pc-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252 > LC_MONETARY=English_Australia.1252 > [4] LC_NUMERIC=C LC_TIME=English_Australia.1252 > > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > > other attached packages: > [1] nleqslv_1.9.4 methylumi_2.2.0 ggplot2_0.9.2.1 > reshape2_1.2.1 scales_0.2.2 > [6] Biobase_2.18.0 BiocGenerics_0.4.0 > > loaded via a namespace (and not attached): > [1] affy_1.36.0 affyio_1.26.0 annotate_1.36.0 > AnnotationDbi_1.20.2 BiocInstaller_1.8.3 > [6] Biostrings_2.26.2 colorspace_1.2-0 DBI_0.2-5 > dichromat_1.2-4 digest_0.6.0 > [11] GenomicRanges_1.10.3 grid_2.15.1 gtable_0.1.1 > IRanges_1.16.4 labeling_0.2 > [16] lattice_0.20-11 MASS_7.3-22 memoise_0.1 > munsell_0.4 parallel_2.15.1 > [21] plyr_1.7.1 preprocessCore_1.20.0 proto_0.3-9.2 > RColorBrewer_1.0-5 RCurl_1.95-3 > [26] RSQLite_0.11.2 stats4_2.15.1 stringr_0.6.1 > XML_3.95-0.1 xtable_1.7-1 > [31] zlibbioc_1.4.0 > > With regards, > Lavinia Gordon. > > > Senior Research Officer > Quantitative Sciences Core, Bioinformatics > > Murdoch Childrens Research Institute > The Royal Children's Hospital > Flemington Road Parkville Victoria 3052 Australia T 03 8341 6221 > www.mcri.edu.au > > ______________________________________________________________________ > This email has been scanned by the Symantec Email Security.cloud service. > For more information please visit http://www.symanteccloud.com > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor ______________________________________________________________________ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com If you have any question, please contact MCRI IT Helpdesk for further assistance. ______________________________________________________________________ ______________________________________________________________________ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com