Martin:
Here is my session info. I have tried using golubEsets 1.4.5 with the
Golub_Train name, but I get the same result. As you can see from the output
of data(package="golubEsets"), the data set is in fact named golubTrain, not
Golub_Train.

It seems to be a difference between the command-line version of R (actually,
I was using Mac OS X, not Linux) and the GUI version. The command-line
version works exactly as expected.

Gary

> sessionInfo()
R version 2.9.1 (2009-06-26)
i386-pc-mingw32

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=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_1.0 Biobase_2.4.1


On Sun, Jul 5, 2009 at 3:15 PM, Martin Morgan <mtmorgan@fhcrc.org> wrote:

> 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)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> States.1252;LC_MONETARY=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.
> >
> >
> >
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>


-- 
Gary Lipton
http://www.linkedin.com/in/garylipton

	[[alternative HTML version deleted]]

