[BioC] Error in .nextMethod(e1, e2) working with R2.0. in Windows

[Martin Morgan]

Hi Lauro and others --

To emphasize, the following involves the DEVELOPMENT version of
Biobase; users of the released version DO NOT have these problems.

My solution (using biocLite) is not correct, for the moment -- the
Biobase 'fix' requires the R change, but our build machines do not
yet have the updated version of R and so cannot perform the steps to
make Biobase available.

In theory, the solutions are to use versions of R-devel and Biobase
that predate the change, or to use the R-alpha (R-devel has now
'branched' in preparation for the October release) and an svn version
of Biobase that post-date the change. Realizing the second option
(R-alpha + Biobase from svn) requires the ability to build R and R
packages from source.

Working combinations of R-alpha and Biobase accessible using biocLite are
at least a day away.

Martin

Martin Morgan <mtmorgan at fhcrc.org> writes:

> Hi Lauro --
>
> This was a change in the development version of R over the weekend
> (r32748, 2007-09-04 02:33:30 -0700, I think) and was fixed in the
> development version of Biobase the same day (r26853, 2007-09-04
> 16:08:07 -0700; Biobase version 1.15.31). Unfortunately, your machines
> captured the combination of R and Biobase during the approx. 14 hours
> when things were not working!
>
> The solution is to update Biobase, e.g.,
>
>> source('http://bioconductor.org/biocLite.R')
>> biocLite('Biobase')
>
> As you found out, using development versions of R and Biobase can have
> very unfortunate consequences. When offering courses, we try to
> identify an R snapshot that seems to work, and to use facilities like
> building and installing packages and course material (and hence
> building vignettes and exercising the packages on the version of R we
> will use) to make sure that things will work.
>
> Sorry that this happened at such an inopportune time.
>
> Martin
>
> "Lauro Sumoy Van Dyck" <lauro.sumoy at crg.es> writes:
>
>> Hello,
>
>> While conducting a workshop on Bioconductor arrayQC we have
>> encountered the following error but not on all machines.
>>  
>> Error in .nextMethod(e1, e2) : 
>>   comparison of these types is not implemented
>>  
>> This error is generated upon trying to generate new objects.
>>  
>> Could you please help solve this issue? I am told -I am not an R
>> expert- that there must be a problem associated to handling S4 class
>> objects.
>>  
>> Thank you,
>>  
>> Lauro
>>  
>> In my particular case this is the session info:
>>> sessionInfo()
>> R version 2.6.0 Under development (unstable) (2007-09-04 r42752) 
>> i386-pc-mingw32 
>> locale:
>> LC_COLLATE=Spanish_Spain.1252;LC_CTYPE=Spanish_Spain.1252;LC_MONETARY=Spanish_Spain.1252;LC_NUMERIC=C;LC_TIME=Spanish_Spain.1252
>> attached base packages:
>> [1] splines   tools     stats     graphics  grDevices utils     datasets  methods   base     
>> other attached packages:
>>  [1] arrayQualityMetrics_1.0.17 CCl4_1.0.5                 limma_2.11.11              simpleaffy_2.13.01         affyPLM_1.13.6            
>>  [6] gcrma_2.9.1                matchprobes_1.9.10         affydata_1.11.3            RColorBrewer_1.0-1         vsn_3.0.14                
>> [11] affy_1.15.7                preprocessCore_0.99.12     affyio_1.5.8               genefilter_1.15.11         survival_2.32             
>> [16] geneplotter_1.15.9         lattice_0.16-4             annotate_1.15.6            AnnotationDbi_0.1.12       RSQLite_0.6-0             
>> [21] DBI_0.2-3                  Biobase_1.15.30           
>> loaded via a namespace (and not attached):
>> [1] grid_2.6.0         KernSmooth_2.22-21
>>
>> Commands that generated the same type of error:
>>> object<-new("AffyBatch")
>> Error in .nextMethod(e1, e2) : 
>>   comparison of these types is not implemented
>>> object<-new("NChannelSet")
>> Error in .nextMethod(e1, e2) : 
>>   comparison of these types is not implemented
>>  
>>  
>> Lauro Sumoy
>> Microarray Laboratory
>> Bioinformatics and Genomics Program
>> Center for Genomic Regulation (CRG)
>> Dr. Aiguader 88
>> 08003 Barcelona
>> Spain
>> Office Phone: +34-93-316-0125
>> CRG Fax: +34-93-316-0099
>> e-mail: lauro.sumoy at crg.es
>> http://www.crg.es <http://www.crg.es/>  
>> ---------------------------
>> Microarray Laboratory Phone: +34-93-316-0126
>> Microarray Services Office: +34-93-316-0272
>> Microarray Bioinformatics Office: +34-93-316-0238
>> Program Secretarial Office: +34-93-316-0110
>>
>> 	[[alternative HTML version deleted]]
>>
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>
> -- 
> Martin Morgan
> Bioconductor / Computational Biology
> http://bioconductor.org
>
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-- 
Martin Morgan
Bioconductor / Computational Biology
http://bioconductor.org