[BioC] Problem when loading simpleaffy package

Michael Steeves steeves at raingods.net
Tue Jun 4 19:26:41 CEST 2013

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)

[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

Michael Steeves (steeves at raingods.net)

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