[BioC] Problem when loading simpleaffy package

[Martin Morgan]

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
>


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