[BioC] golubEsets on Windows/Vista

[Martin Morgan]

Hi Gary -

Gary Lipton wrote:
> 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. 

Your version of golubEsets is 1.0, mine (installed using biocLite this
morning, to R 2.9.1 and a Windows XP machine) is 1.4.5. Have you tried
reinstalling golubEsets (using biocLite('golubEsets'))) or better
updating golubEsets (and other packages), e.g., in a new session

  source('http://bioconductor.org/biocLite.R')
  update.packages(repos=biocinstallRepos(), ask=TRUE)

> 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.

Command line and GUI will generally not differ at all in these kinds of
things -- they are just different interfaces to the same underlying
engine. You are on physically different computers, and most likely they
have different versions of software packages installed. This is why
sessionInfo() can be helpful in tracking down discrepancies.

Martin

> 
> 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 at fhcrc.org
> <mailto:mtmorgan at 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.
>     >
>     >
>     >
>     >
>     ------------------------------------------------------------------------
>     >
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> 
> 
> 
> 
> -- 
> Gary Lipton
> http://www.linkedin.com/in/garylipton
>