[BioC] Does old workspace work?

[Robert Gentleman]

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Loren Engrav wrote:
> 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)

  Currently that is the case.  But I am not sure how long it will remain
so, as it means that R cannot be truly 64bit, so likely in the next year
or so some change will be needed.  Of course, one will always be able to
read 32 bit workspaces in 64bits, but the converse will not likely hold
for very much longer

  Robert


> 
> 
>> 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
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
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>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
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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
> 
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> 

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