">Could you please send the entire source for your report?"
Sure thing:

library(ggplot2)
library(reshape2)
library(plotly)
library(htmlwidgets)

# this (fix Pandoc error)
Sys.setenv(RSTUDIO_PANDOC='C:/Program Files (x86)/Pandoc')

run<-as.data.frame(labkey.data)
#print(head(run))

data<-run[c(1,50,8:48)]

colnames(data)[colnames(data) == "specimenid"] <- "Name"
#print(dim(data))
#print(reshape2::melt(data$Name))

data<-aggregate(data[c(2:42)], list(data$Name), mean)
rownames(data) <- data$Group.1

data_melt<-reshape2::melt(data)

colnames(data_melt)[colnames(data_melt) == "Group.1"] <- "Condition"
colnames(data_melt)[colnames(data_melt) == "variable"] <- "Analyte"

# Create heatmap with ggplot2
ggp <- ggplot(data_melt, aes(Condition, Analyte)) +                           
              geom_tile(aes(fill = value)) +
               theme(axis.text.x = element_text( 
                   angle = 90, 
                   size=6)) +
             scale_x_discrete(breaks = data_melt$Condition)

# Save ggplotly as widget in file test.html -  fails ... permission?
#saveWidget(ggplotly(ggp), file = paste(labkey.url.base, labkey.url.path, "test.html", sep='')) 

# report doesn't show - now I get "Failed to retrieve report results"
# "output.html" saved to temp and is desired interactive plotly
#saveWidget(ggplotly(ggp), file = "test.html")
#rawHTML <- paste(readLines("test.html"),collapse="\n") 
## ${htmlout:output}
#write(rawHTML, file="output")

# "Failed to retrieve report results" writes "output" in temp location, 
# looks like html, but wont display in browser
#saveWidget(ggplotly(ggp), file = "output")
## ${htmlout:output}
#write(ggplotly(ggp), file="output")

# works, but not auto-sized, not interactive
ggsave("${imgout:labkeyl_png}",plot=ggp,device="png",width=5, height=8)

">When you saved the file to a temp location, did the interactive heatmap work as you wanted?"
yes, when writing raw HTML

">When using the "saveWidget" did you experience any issues with that function not being found?"
No, but there was a Pandoc error. It was in the system path but wasn't being seen by the report/script

">Are you using the ggplot2 library? or What packages/libraries are you using?"
yes, ggplot2

Disclosure: I am on an older version of labkey (18.2) - my next step was to create an installation with the latest LabKey and test it there. But it'd be helpful to know if you think it should work or not.