Running examples in ‘patPRO-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: patproPlotThree
> ### Title: Generate Patient Profile of Three Plots.
> ### Aliases: patproPlotThree
> ### Keywords: package
> 
> ### ** Examples
> 
> # Plot individual patient
> data("PatProAlphaDiv",package="patPRO")
> data("PatProMap",package="patPRO")
> data("PatProOTU",package="patPRO")
> data("PatProBacLoad",package="patPRO")
> # Alpha Diversity
> mergedMapAlpha <- mergeMapMetaData(map.file=PatProMap, 
+   merging.file=PatProAlphaDiv, 
+   map.sub.id="SubjectID", 
+   map.tmpt="Time_point", 
+   map.smpl.id="SampleID", 
+   sample.id.col="SampleID")
> testNormAlphaDiv <- normalizeAlphaDiv(mergedMapAlpha, c("chao1","shannon"), 1)
No id variables; using all as measure variables
> alphaDivPlot <- plotNormalizedAlphaDiv(testNormAlphaDiv, 
+   c("chao1","shannon"), 
+   plot.title="Subject One Diversity", 
+   color.brewer.set="Set2", 
+   legend.text.size = 12)
> # Bacterial Load
> mergedMapBacLoad <- mergeMapMetaData(map.file=PatProMap, 
+   merging.file=PatProBacLoad, 
+   map.sub.id="SubjectID", 
+   map.tmpt="Time_point", 
+   map.smpl.id="SampleID", 
+   sample.id.col="SampleID")
> bacLoad <- plotBacterialLoad(mergedMapBacLoad, 
+   1, 
+   bac.load.col="Num_Bacteria", 
+   plot.title="Subject One Bacterial Load")
> # Taxa Relative Abundance
> transTestRelAbund <- transposeRelAbund(PatProOTU)
> mergedMapTransRA <- mergeMapMetaData(map.file=PatProMap, 
+   merging.file=transTestRelAbund, 
+   map.sub.id="SubjectID", 
+   map.tmpt="Time_point", 
+   map.smpl.id="SampleID", 
+   sample.id.col="SampleID")
> top5RelAbund <- topRelAbundDataFrame(x=mergedMapTransRA, top.taxa.num=5)
Using SampleID as id variables
> topTaxa <- plotTopTaxa(top5RelAbund, 
+   1, 
+   plot.title="Subject One Taxonomy", 
+   color.brewer.set="Set2", 
+   mark.events=TRUE, 
+   mark.times=c(2,6), 
+   mark.text="Surgery", 
+   legend.text.size=8)
Warning: Ignoring unknown aesthetics: width
> # Plot three
> patproPlotThree(alphaDivPlot, bacLoad, topTaxa, "Subject One Profile")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: patproPlotThree ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted