[BioC] golubEsets on Windows/Vista

Martin Morgan mtmorgan at fhcrc.org
Sun Jul 5 21:15:54 CEST 2009

Hi Gary --

Gary Lipton wrote:
> I would like to use golubEsets on the Windows version of R (2.9.1) under
> Vista. I have no difficulty running under Linux. Here is what I get in
> Windows:
>> library(golubEsets)
> Loading required package: Biobase
> Welcome to Bioconductor
>   Vignettes contain introductory material. To view, type
>   'openVignette()'. To cite Bioconductor, see
>   'citation("Biobase")' and for packages 'citation(pkgname)'.
>> data(golubTrain)
> Warning message:
> In data(golubTrain) : *data set 'golubTrain' not found*

I get

> data(golubTrain)
Warning message:
'golubTrain' is deprecated.
Use 'Golub_Train' instead.
See help("Deprecated")

which means that, in the 2.9.1 version of golubEsets, 'golubTrain' is
marked as deprecated and will, in 2.10.0, disappear in favor of
'Golub_Train'. So my speculation is that your Windows installation has
an incorrect version of the golubEsets package (and perhaps others?)
installed. This is not a good situation, and if true it would pay to
identify how this has occurred (perhaps you set up a library path that
is, inadvertently, shared by all R installations?) and correcting.

Here's my session info, what's yours?

> sessionInfo()
R version 2.9.1 (2009-06-26)

LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] golubEsets_1.4.5 Biobase_2.4.1

loaded via a namespace (and not attached):
[1] tools_2.9.1

> If I give the command
>> data(package="golubEsets")
> I get:
> Data sets in package ‘golubEsets’:
> golubMerge (golubMerge.rda)
>                         Combined Test and Training Sets from the Golub
>                         Paper
> golubTest (golubTest.rda)
>                         Test Set Data from the Golub Paper
> *golubTrain (golubTrain.rda)*
>                         Training Set from the Golub Paper
> Thank you.
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