Message-ID: <258A3382-3287-48A0-909F-592D05EEF65A@stat.berkeley.edu>
Date: 2017-10-23T15:32:44Z
From: Elizabeth Purdom
Subject: [Bioc-devel] How to recreate R CMD BUILD environment in interactive session?
In-Reply-To: <c3631246-b946-b437-cbe5-bc5c825c11d2@roswellpark.org>
>
> 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