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: reactive:otherSpectraStuff [/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$.updateValue
97: ..stacktraceoff..
96: otherSpectraStuff
95: as.data.frame
94: nrow
93: merge.data.frame
92: merge
91: reactive:spectraData [/private/var/folders/2g/ypqf3qpd4ndf9df2q8sss_br0000gn/T/Rtmpwyg3ne/shinyapp9acb6e25fe8d/CloudCal-1e970e8350301ac17770c08d4b0a3ebcd6e924b7/server.R#1727]
90: ..stacktraceon..
89: .func
88: withVisible
87: withCallingHandlers
86: contextFunc
85: env$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: reactive:hotableInputBlank [/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$.updateValue
66: ..stacktraceoff..
65: hotableInputBlank
64: reactive:hotableInput [/private/var/folders/2g/ypqf3qpd4ndf9df2q8sss_br0000gn/T/Rtmpwyg3ne/shinyapp9acb6e25fe8d/CloudCal-1e970e8350301ac17770c08d4b0a3ebcd6e924b7/server.R#2322]
63: ..stacktraceon..
62: .func
61: withVisible
60: withCallingHandlers
59: contextFunc
58: env$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.