CloudCal counts not loading or showing up

[jmillhauser]

Hi,

I'm running CloudCal using R 4.3.2 on a Mac. I have uploaded a set of 20 CSV files that I created from PDZ files using S1PXRF and following your recommendation to select 'Replace duration with live time.' I tried uploading PDZ files instead of CSV files, but they don't work (I get an error message stating that the readPDZ24 file is missing), so I've just worked with the CSV.

I'm trying to work my way through the next steps, but the video tutorial seems to be for an older version of CloudCal. If there's a newer tutorial available that solves this problem please let me know (and sorry for not being able to find it in my own).

When I move to the counts tab, I see a blank table with no data (screenshot attached)

When I click "confirm elements" for the pre-filled elements or for any others I add, the screen goes grey and nothing happens.

Is there a critical step that I have missed?

Thank you!

I'll note that I get some warnings when I upload the CSV files in the R console.

| 0 % ~calculating Warning in csvFrame(filepath = inFile[x, "datapath"], filename = inFile[x, : NAs introduced by coercion Warning in csvFrame(filepath = inFile[x, "datapath"], filename = inFile[x, : NAs introduced by coercion |+++++++++++++++++ | 33% ~00s Warning in csvFrame(filepath = inFile[x, "datapath"], filename = inFile[x, : NAs introduced by coercion Warning in csvFrame(filepath = inFile[x, "datapath"], filename = inFile[x, : NAs introduced by coercion |++++++++++++++++++++++++++++++++++ | 67% ~00s Warning in csvFrame(filepath = inFile[x, "datapath"], filename = inFile[x, : NAs introduced by coercion Warning in csvFrame(filepath = inFile[x, "datapath"], filename = inFile[x, : NAs introduced by coercion |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s
Warning in data.frame(Energy = as.numeric(gsub("X", "", colnames(data)))[-1], : NAs introduced by coercion

I also see the following when I select "confirm elements" in the R consol

| | 0 % ~calculating
| | 0 % ~calculating
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=01s Warning: Error in fix.by: 'by' must specify a uniquely valid column 118: h 117: .handleSimpleError 116: stop 115: fix.by 114: merge.data.frame 113: merge 112: [/private/var/folders/2g/ypqf3qpd4ndf9df2q8sss_br0000gn/T/Rtmpwyg3ne/shinyapp9acb6e25fe8d/CloudCal-1e970e8350301ac17770c08d4b0a3ebcd6e924b7/server.R#1707] 111: ..stacktraceon.. 110: .func 109: withVisible 108: withCallingHandlers 107: contextFunc 106: env$runWith 105: force 104: domain$wrapSync 103: promises::with_promise_domain 102: withReactiveDomain 101: domain$wrapSync 100: promises::with_promise_domain 99: ctx$run 98: self$.updateValue 97: ..stacktraceoff.. 96: otherSpectraStuff 95: as.data.frame 94: nrow 93: merge.data.frame 92: merge 91: [/private/var/folders/2g/ypqf3qpd4ndf9df2q8sss_br0000gn/T/Rtmpwyg3ne/shinyapp9acb6e25fe8d/CloudCal-1e970e8350301ac17770c08d4b0a3ebcd6e924b7/server.R#1727] 90: ..stacktraceon.. 89: .func 88: withVisible 87: withCallingHandlers 86: contextFunc 85: env$runWith 84: force 83: domain$wrapSync 82: promises::with_promise_domain 81: withReactiveDomain 80: domain$wrapSync 79: promises::with_promise_domain 78: ctx$run 77: self$.updateValue 76: ..stacktraceoff.. 75: spectraData 74: observe [/private/var/folders/2g/ypqf3qpd4ndf9df2q8sss_br0000gn/T/Rtmpwyg3ne/shinyapp9acb6e25fe8d/CloudCal-1e970e8350301ac17770c08d4b0a3ebcd6e924b7/server.R#1826] 73: <observer:observeEvent(input$linecommit)> 72: valueFunc 71: ..stacktraceon.. 70: contextFunc 69: env$runWith 68: force 67: domain$wrapSync 66: promises::with_promise_domain 65: withReactiveDomain 64: domain$wrapSync 63: promises::with_promise_domain 62: ctx$run 61: ..stacktraceoff.. 60: isolate 59: func 58: withVisible 57: f 56: Reduce 55: withCallingHandlers 54: domain$wrapSync 53: promises::with_promise_domain 52: captureStackTraces 51: doTryCatch 50: tryCatchOne 49: tryCatchList 48: tryCatch 47: do 46: hybrid_chain 45: observeEvent(input$linecommit) 44: contextFunc 43: env$runWith 42: force 41: domain$wrapSync 40: promises::with_promise_domain 39: withReactiveDomain 38: domain$wrapSync 37: promises::with_promise_domain 36: ctx$run 35: run 34: withCallingHandlers 33: domain$wrapSync 32: promises::with_promise_domain 31: captureStackTraces 30: withCallingHandlers 29: shinyCallingHandlers 28: force 27: withVisible 26: withCallingHandlers 25: domain$wrapSync 24: promises::with_promise_domain 23: captureStackTraces 22: doTryCatch 21: tryCatchOne 20: tryCatchList 19: tryCatch 18: do 17: hybrid_chain 16: flushCallback 15: FUN 14: lapply 13: ctx$executeFlushCallbacks 12: .getReactiveEnvironment()$flush 11: flushReact 10: serviceApp 9: ..stacktracefloor.. 8: withCallingHandlers 7: domain$wrapSync 6: promises::with_promise_domain 5: captureStackTraces 4: ..stacktraceoff.. 3: runApp 2: runUrl 1: shiny::runGitHub |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s
Warning: Error in [: incorrect number of dimensions 84: h 83: .handleSimpleError 82: data.frame 81: [/private/var/folders/2g/ypqf3qpd4ndf9df2q8sss_br0000gn/T/Rtmpwyg3ne/shinyapp9acb6e25fe8d/CloudCal-1e970e8350301ac17770c08d4b0a3ebcd6e924b7/server.R#2229] 80: ..stacktraceon.. 79: .func 78: withVisible 77: withCallingHandlers 76: contextFunc 75: env$runWith 74: force 73: domain$wrapSync 72: promises::with_promise_domain 71: withReactiveDomain 70: domain$wrapSync 69: promises::with_promise_domain 68: ctx$run 67: self$.updateValue 66: ..stacktraceoff.. 65: hotableInputBlank 64: [/private/var/folders/2g/ypqf3qpd4ndf9df2q8sss_br0000gn/T/Rtmpwyg3ne/shinyapp9acb6e25fe8d/CloudCal-1e970e8350301ac17770c08d4b0a3ebcd6e924b7/server.R#2322] 63: ..stacktraceon.. 62: .func 61: withVisible 60: withCallingHandlers 59: contextFunc 58: env$runWith 57: force 56: domain$wrapSync 55: promises::with_promise_domain 54: withReactiveDomain 53: domain$wrapSync 52: promises::with_promise_domain 51: ctx$run 50: self$.updateValue 49: ..stacktraceoff.. 48: hotableInput 47: observe [/private/var/folders/2g/ypqf3qpd4ndf9df2q8sss_br0000gn/T/Rtmpwyg3ne/shinyapp9acb6e25fe8d/CloudCal-1e970e8350301ac17770c08d4b0a3ebcd6e924b7/server.R#2340] 46: 45: ..stacktraceon.. 44: contextFunc 43: env$runWith 42: force 41: domain$wrapSync 40: promises::with_promise_domain 39: withReactiveDomain 38: domain$wrapSync 37: promises::with_promise_domain 36: ctx$run 35: run 34: withCallingHandlers 33: domain$wrapSync 32: promises::with_promise_domain 31: captureStackTraces 30: withCallingHandlers 29: shinyCallingHandlers 28: force 27: withVisible 26: withCallingHandlers 25: domain$wrapSync 24: promises::with_promise_domain 23: captureStackTraces 22: doTryCatch 21: tryCatchOne 20: tryCatchList 19: tryCatch 18: do 17: hybrid_chain 16: flushCallback 15: FUN 14: lapply 13: ctx$executeFlushCallbacks 12: .getReactiveEnvironment()$flush 11: flushReact 10: serviceApp 9: ..stacktracefloor.. 8: withCallingHandlers 7: domain$wrapSync 6: promises::with_promise_domain 5: captureStackTraces 4: ..stacktraceoff.. 3: runApp 2: runUrl 1: shiny::runGitHub

Describe the bug A clear and concise description of what the bug is.

To Reproduce Steps to reproduce the behavior:

1. Go to '...'
2. Click on '....'
3. Scroll down to '....'
4. See error

Expected behavior A clear and concise description of what you expected to happen.

Screenshots If applicable, add screenshots to help explain your problem.

Desktop (please complete the following information):

• OS: [e.g. iOS]
• Browser [e.g. chrome, safari]
• Version [e.g. 22]

Smartphone (please complete the following information):

• Device: [e.g. iPhone6]
• OS: [e.g. iOS8.1]
• Browser [e.g. stock browser, safari]
• Version [e.g. 22]

Additional context Add any other context about the problem here.

[leedrake5]

I've got a a separate repo (https://github.com/leedrake5/rpdz) to handle PDZ files. From your description it sounds like this has not been installed. Can you try the following:

remotes::install_github("leedrake5/rPDZ")

And let me know if PDZ files then work? Either PDZ 25 or PDZ 24 should work, though still working through bugs with how some files are set up.

It's hard to tell what the issue is, but it looks like it may be in the CSV files since it sounds like there is missing data.