When I try to load up the simpleaffy package, at the end it generates an error message: 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")'. Loading required package: affy Loading required package: genefilter Loading required package: gcrma No methods found in "Biobase" for requests: geneNames I can reproduce this on both Linux and OS X, using 2.15.2, 2.15.3, 3.0.0 and 3.0.1. It looks like the simpleaffy package attaches (as does Biobase): R> sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-apple-darwin12.3.0 (64-bit) locale: [1] C attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] simpleaffy_2.36.0 gcrma_2.32.0 genefilter_1.42.0 affy_1.38.1 [5] Biobase_2.20.0 BiocGenerics_0.6.0 loaded via a namespace (and not attached): [1] AnnotationDbi_1.22.5 BiocInstaller_1.10.1 Biostrings_2.28.0 [4] DBI_0.2-7 IRanges_1.18.1 RSQLite_0.11.4 [7] XML_3.96-1.1 affyio_1.28.0 annotate_1.38.0 [10] preprocessCore_1.22.0 splines_3.0.1 stats4_3.0.1 [13] survival_2.37-4 xtable_1.7-1 zlibbioc_1.6.0 I'm checking to see if there's any functionality that breaks because of this, but at the moment I'm not aware of any problems. Does this mean that the error can be ignored? I found a link that suggested updating the bioconductor install, but even after doing that the error still persists. -Mike -- Michael Steeves (steeves at raingods.net)

On 06/04/2013 10:26 AM, Michael Steeves wrote: > When I try to load up the simpleaffy package, at the end it generates an > error message: > > 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")'. > > Loading required package: affy > Loading required package: genefilter > Loading required package: gcrma > No methods found in "Biobase" for requests: geneNames > > I can reproduce this on both Linux and OS X, using 2.15.2, 2.15.3, 3.0.0 > and 3.0.1. It looks like the simpleaffy package attaches (as does Biobase): > > R> sessionInfo() > R version 3.0.1 (2013-05-16) > Platform: x86_64-apple-darwin12.3.0 (64-bit) > > locale: > [1] C > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] simpleaffy_2.36.0 gcrma_2.32.0 genefilter_1.42.0 affy_1.38.1 > [5] Biobase_2.20.0 BiocGenerics_0.6.0 > > loaded via a namespace (and not attached): > [1] AnnotationDbi_1.22.5 BiocInstaller_1.10.1 Biostrings_2.28.0 > [4] DBI_0.2-7 IRanges_1.18.1 RSQLite_0.11.4 > [7] XML_3.96-1.1 affyio_1.28.0 annotate_1.38.0 > [10] preprocessCore_1.22.0 splines_3.0.1 stats4_3.0.1 > [13] survival_2.37-4 xtable_1.7-1 zlibbioc_1.6.0 > > I'm checking to see if there's any functionality that breaks because of > this, but at the moment I'm not aware of any problems. Does this mean > that the error can be ignored? I found a link that suggested updating > the bioconductor install, but even after doing that the error still > persists. Thanks Mike for the report; this is fixed in simpleaffy 2.36.1, which should be available via biocLite Wednesday after about 10am Seattle time; eventually you would have encountered code that used geneNames, and it would have failed. Martin > > > > > -Mike > -- 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