ShinyApps Surivival analysis breaking

[selkamand]

Test with edge and multiple users

[selkamand]

Survival analysis timing out when using edge. Not replicable on MAC. Reported to also happen on local version of CRUX

[selkamand]

It happens on some macs too. Both in offline version and online version.

My guess it requires some sort of obscure system dependency to render the results (e.g. a particular font installed)

I can't reproduce it on any system I own (windows/mac/linux), which has made it really painful to debug. Will have to try dropping visualization and seeing if the bug dissapears

[selkamand]

Testing further, I'm suspecting the cause is the trycatch. When the error happens we see the message 1 but not message two. I'm wondering if the validate is not appropriate here. Maybe we should try forcing an error here and see if we can replicate the issue

     message('[1] Running maftools::survGroup')
      result = tryCatch(
        expr = { 
          maftools::survGroup(
            maf = maf(), 
            top = input$in_num_genes_to_include, 
            geneSetSize = input$in_num_geneset_size, 
            minSamples = input$in_num_minsamples, 
            time = column_time_to_event(), 
            Status = column_event_status()
          ) 
        },
        error = function(err){
          # I think this is throwing a problem on some devices
          validate(paste0("Couldn't run survival analysis. This usually means either the wrong `event` or `time` columns were selected, or these columns are formatted incorrectly. Please see the manual for examples. \nFull Error Message: ",as.character(err)))
        }
      )

      message('[2] Finished running maftools::survGroup')

[selkamand]

Note plots use col = "gray70" for abline, which is NOT web safe (see maftools::run_surv())

[selkamand]

Could reproduce on the following setup using browserling