[BioC] Does old workspace work?

[Loren Engrav]

Ok, I will get my stuff modern
One more question
Those old saved workspaces and histories might be 32bit from before I went
to 64bit
If they are 32bit workspaces will they work in 64bit (save for the
deprecated stuff)


> From: Robert Gentleman <rgentlem at fhcrc.org>
> Date: Mon, 27 Oct 2008 22:31:21 -0700
> To: Loren Engrav <engrav at u.washington.edu>
> Cc: "bioconductor at stat.math.ethz.ch" <bioconductor at stat.math.ethz.ch>
> Subject: Re: [BioC] Does old workspace work?
> 
> Hi,
> 
> Loren Engrav wrote:
>>> sessionInfo()
>> R version 2.8.0 Patched (2008-10-26 r46783)
>> i386-apple-darwin9.5.0
>> 
>> locale:
>> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>> 
>> attached base packages:
>> [1] splines   tools     stats     graphics  grDevices utils     datasets
>> methods   base  
>> 
>> other attached packages:
>> [1] simpleaffy_2.18.0  genefilter_1.22.0  survival_2.34-1    affyio_1.10.0
>> porcinecdf_2.3.0   gcrma_2.14.0       matchprobes_1.14.0 affy_1.20.0
>> Biobase_2.2.0   
>> 
>> loaded via a namespace (and not attached):
>> [1] AnnotationDbi_1.4.0  DBI_0.2-4            RSQLite_0.7-1
>> annotate_1.20.0      preprocessCore_1.4.0
>> 
>> ==============
>> A year or so ago I ran 64bit R on Mac PPC and saved various workspaces
>> 
>> Now am running 64bit R on Intel 2x3.2 QuadCore and MacOS 10.5.5
>> 
>> I load up the old workspaces
>> and I enter
>> 
>>> write.exprs(ABeset_gcrma, file="ABeset_gcrma081028orig.txt")
>> Where ABeset_gcrma is an old file
>> 
>> and I get
>> Error in function (classes, fdef, mtable)  :
>> unable to find an inherited method for function "write.exprs", for signature
>> "exprSet"
>> 
>    It was probably more than a year ago - the exprSet class was
> deprecated and subsequently made defunct.
> 
>    You could try to do:
>   library(Biobase)
> 
>    updateObject(ABeset_gcrma)
> 
>   failing that, you can try something like
>    write.table(ABeset_gcrma at exprs,
> file="ABeset_gcrma081028orig.txt",uote = FALSE, sep = "\t",
>          col.names = NA)
> 
>   or something like that.
> 
>> And I enter
>>> exprs2excel(ABeset_gcrma, file="ABeset_gcrma081028v2.csv")
>> 
>> And I get
>> Error: could not find function "exprs2excel"
> 
>    That function has been made defunct.
>> 
>> Am I doing something wrong?
> 
>    No, you just can't expect that things won't change.
> 
>   best wishes
>     Robert
> 
>> 
>> Thank you
>> 
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> 
> -- 
> Robert Gentleman, PhD
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M2-B876
> PO Box 19024
> Seattle, Washington 98109-1024
> 206-667-7700
> rgentlem at fhcrc.org