Problem consolidating data in add in

[MalteLehmann]

Hey,

I am trying to use an RStudio add-in called phenoptrreports to analyze histological stainings of covid-19 samples. However trying to use the consolidate and summarize add-in I get the following error:

> phenoptrReports:::addin_10_merge()
Loading required package: shiny

Listening on http://127.0.0.1:6169

> phenoptrReports:::addin_20_consolidate()

Listening on http://127.0.0.1:6169
Reading "Merge_cell_seg_data". 
Data is already in microns, no conversion performed
Writing report for "Merge_cell_seg_data". 
Warning: The vignette title specified in \VignetteIndexEntry{} is different from the title in the YAML metadata. The former is "", and the latter is "Cell seg data summary". If that is intentional, you may set options(rmarkdown.html_vignette.check_title = FALSE) to suppress this check.
Joining, by = "Slide ID"
Joining, by = "Slide ID"
Warning: The vignette title specified in \VignetteIndexEntry{} is different from the title in the YAML metadata. The former is "", and the latter is "Cell seg data summary". If that is intentional, you may set options(rmarkdown.html_vignette.check_title = FALSE) to suppress this check.
Warning: Error in split_phenotypes: No positive phenotypes found.
  86: stop
  85: split_phenotypes
  84: function_list[[k]]
  82: freduce
  81: _fseq
  80: eval
  79: eval
  77: %>%
  76: process_one_file
  75: phenoptrReports::consolidate_and_summarize_cell_seg_data
  74: observeEventHandler
   3: shiny::runApp
   2: shiny::runGadget
   1: phenoptrReports:::addin_20_consolidate

> 

I am quite new to R and I dont really get the problem. Is anybody able to help me?

Thank you!

Malte

[EconomiCurtis]

@MalteLehmann

phenoptrReports:::addin_10_merge

Where you are reaching this? I was trying to find documentation for phenoptrReports:::addin_10_merge but can't really find any (just a note about another bug or issue)

I would assume you're following the directions of the documentation site (below), but just in case, that's be a good place to start.

Create reports using Phenoptics data

I may be wrong about this, but I suspect this issue may lie with the addin or R-package that supports it. If that's the case, I'd submit an issue to GitHub - akoyabio/phenoptrReports: Create analysis reports from inForm data.. Be sure to include a reproducible example at aid in diagnosing the issue.