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

[Martin Morgan]

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]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

-- 
Martin Morgan
Bioconductor / Computational Biology
http://bioconductor.org