Error in zip files starting the code (= no results at the end) and FCS export missing in cytofkit2

[Manu1007]

Hi,

Thank you very much for this.
I was using cytofkit before a lot in the past and stopped using once it was not supported anymore. I started to see some issue as for example the tSNE results were not reflecting any changes in the settings etc. I have now tried to run cytofkit2 but I was unable as I found two problems:

1. I have noticed that cytofkit2 does not allow you to save and export the results as new FCS files. Why? Is there a way to be able to do it even manually by coding?Am I missing anything? The instructions are not updated (refer to cytofkit1) and many links are empty.
   2 )Once I start the run with cytofkit2 the run seams to stop without saving the results and the gives me the following error. The first error with zip files has been reported already, but no solution yet. In addition, the GUI/shinyAPP interface disappears as well and I can only force quit R.

Can anyone please help?

Thank you very much in advance.

The error is below:

Warning: Error in zip: 'files' must a character vector specifying one or more filepaths
[No stack trace available]
Input arguments:

• Project Name: cytofkit3_k50_Functional
• Input FCS files for analysis:
  .....
• Markers:
  ....
• Data merging method: all
• 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...
68955 x 55 data was extracted!
Dimension reduction...
Running t-SNE...with seed 42 DONE
Run clustering...
Running PhenoGraph...Run Rphenograph starts:
-Input data of 68955 rows and 30 columns
-k is set to 50
Finding nearest neighbors...DONE ~ 299.39 s
Compute jaccard coefficient between nearest-neighbor sets...DONE ~ 108.56 s
Build undirected graph from the weighted links...DONE ~ 27.75 s
Run louvain clustering on the graph ...DONE ~ 33.5 s
Run Rphenograph DONE, took a total of 469.2s.
Return a community class
-Modularity value: 0.764057
-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 cytofkit3_k50_Functional.RData
THIS R OBJECT IS THE INPUT OF SHINY APP!
Warning: Removed 38691 rows containing missing values (geom_point).
Warning: Error in if: missing value where TRUE/FALSE needed
2: shiny::runApp
1: cytofkit_shiny_dashboard

[raman91]

Hi, we have fixed this. Please check if it is working. Thanks