Saving result doesn't finish

[chuancn]

I run PhenoGraph and generate tnse and UMAP plots. There is a problem saving the data (see below). Shiny disappears and I have to manually stop R run. Although most of the useful data including RData, csv and PDFs have been saved under the temp folder and I'm able to retrieve them.

Another irrelevant small issue: tsne seems to run no matter I choose it or not.

* Data merging method: 
ceil

* Data transformation method: 
cytofAsinh

* Dimensionality reduction method: 
tsne

* Data clustering method(s): 
Rphenograph

* Data visualization method(s): 
tsne

* Subset progression analysis method: 
NULL


Extract expression data...
  3000 x 50 data was extracted!

Dimension reduction...
  Running t-SNE...with seed42
  DONE

Run clustering...
  Running PhenoGraph...
Run Rphenograph starts:
  -Input data of 3000 rows and 15 columns
  -k is set to 30
  Finding nearest neighbors...
DONE ~0.0600000000049477s
 Compute jaccard coefficient between nearest-neighbor sets...
DONE ~0.779999999998836s
 Build undirected graph from the weighted links...
DONE ~0.260000000002037s
 Run louvain clustering on the graph ...
DONE ~0.0899999999965075s

Run Rphenograph DONE, took a total of 1.19000000000233s.
  Return a community class
  -Modularity value:0.868095729618385

  -Number of clusters:20
 DONE!

Progression analysis...
Listing markers used for dimension reduction...
Stashing sample names...
Wrapping results...
Analysis DONE, saving the results...
R object is saved in test.RData

  **THIS R OBJECT IS THE INPUT OF SHINY APP!**  
Save to file:C:/Users/AGPRIL~1/AppData/Local/Temp/Rtmp6bccem/a2cfb30ea83cea06319ee239/09-MBL-071-comp.fcs

Warning: Error in [[: subscript out of bounds
  2: shiny::runApp
  1: cytofkit_shiny_dashboard