[Bioc-devel] How to recreate R CMD BUILD environment in interactive session?

[Elizabeth Purdom]

> 
> I can reproduce the error with
> 
> clusterExperiment/vignettes master$ R_DEFAULT_PACKAGES= LC_COLLATE=C R -f clusterExperimentTutorial.R
> 
> leading to
> 
> > ## ----recallRSEC------------------------------------------------------------
> > rsecFluidigm<-RSEC(rsecFluidigm,isCount=TRUE,combineProportion=0.6,mergeMethod="JC",mergeCutoff=0.05)
> Error in validObject(.Object) :
>  invalid class "ClusterExperiment" object: merge_nodeMerge must be data.frame with 4 columns and column names equal to: 'Node','Contrast','isMerged','mergeClusterId'
> Calls: RSEC ... .local -> new -> initialize -> initialize -> validObject
> Execution halted
> 
> and then for work inside R
> 
> 
> clusterExperiment/vignettes$ R_DEFAULT_PACKAGES= LC_COLLATE=C R
> Bioconductor version 3.6 (BiocInstaller 1.27.7), ?biocLite for help
> > source("clusterExperimentTutorial.R", echo=TRUE, max=Inf)
> 
> Does that set you down the right path?
> 
> Martin
> 

Yes, thank you!!! I can get it in the interactive session now.
Elizabeth