Quarto Notebook not rendering

Hi,

I’m trying to render a quarto document of the model file which I have created but when I’m running the render option via the VScode extension, I was getting this error:

The I was suggested via the support portal to do the following:

Looks like you are on a MacBook. In order to get this working, please do the following.

  1. Restart your Vscode

  2. Command + Shift + P to open command pallette

  3. Type 'open settings" and find User settings.json

  4. Clicking on that should open settings.json in your Vscode

  5. After the last line, make sure there is a comma and then in the next line paste the following

    “terminal.integrated.env.osx”: {
    “QUARTO_JULIA”: “/Applications/Pumas-2.6.0.app/Contents/Resources/julia/bin/julia”,
    “QUARTONOTEBOOKRUNNER_EXEFLAGS”: “["-J/Applications/Pumas-2.6.0.app/Contents/Resources/julia/lib/julia/sys.pumas.dylib"]”
    }

Restart the VSCode and then try to render your quarto document. It should work (It worked for me)

But quarto is still not working, I went ahead and cleared the cache from the quarto installation path, but now I am just getting the following in the terminal without any output:

Starting julia control server process. This might take a while...
Julia server process started.

I’m facing the error issue in Windows machine as well

hi there - can you show us your YAML frontmatter of the .qmd file please.

Hi,

---
title: Model Simulation
engine: julia
---

Thanks @farmacyst

Can you please also provide us the output of quarto --version as well as trying to run quarto with the --execute-debug flag to provide some additional debugging information, e.g.

quarto render path/to/file.qmd --execute-debug

Avoid running the preview command for the time being until we’ve isolated whether single pass render is working correctly. Thanks.

@Michael

quarto --version
1.6.39

after running the execute debug i get the following output:

quarto render brooks-model.qmd --execute-debug
- Transport file /Users/abhimanyu/Library/Caches/quarto/julia/julia_transport.txt exists, reusing server.
- Transport file read successfully.
- Connecting to server at port 8000, pid 1765
- Connecting to server failed, a transport file was reused so it might be stale. Delete transport file and retry.
- Transport file /Users/abhimanyu/Library/Caches/quarto/julia/julia_transport.txt doesn't exist
Starting julia control server process. This might take a while...
The latest version of Julia in the `release` channel is 1.11.2+0.aarch64.apple.darwin14. You currently have `1.10.5+0.aarch64.apple.darwin14` installed. Run:

  juliaup update

in your terminal shell to install Julia 1.11.2+0.aarch64.apple.darwin14 and update the `release` channel to that version.
- Starting detached julia server through julia, once transport file exists, server should be running.
- Transport file did not exist, yet.
- Transport file did not exist, yet.
- Transport file did not exist, yet.
- Transport file did not exist, yet.
- Transport file did not exist, yet.
- Transport file did not exist, yet.
- Transport file read successfully.
Julia server process started.
- Connecting to server at port 8000, pid 1652
- write command "isready" to socket server
- received server response
- Transport file read successfully.
- write command "run" to socket server
- received server response
- received progress update response, listening for further responses
Running [1/7] at line 16:  using Pumas
- received server response
- received progress update response, listening for further responses
Running [2/7] at line 35:  rng = Random.seed!(1234)
- received server response
- received progress update response, listening for further responses
Running [3/7] at line 146:  params = (;
- received server response
- received progress update response, listening for further responses
Running [4/7] at line 175:  xf = XLSX.readdata("clinical patients.xlsx","Sheet1…
- received server response
- received progress update response, listening for further responses
Running [5/7] at line 195:  @rtransform! my_df begin
- received server response
- received progress update response, listening for further responses
Running [6/7] at line 223:  # Making a Population
- received server response
- received progress update response, listening for further responses
Running [7/7] at line 244:  # Simulating
- received server response
ERROR: Julia server returned error after receiving "run" command:
Failed to run notebook: /Users/abhimanyu/Desktop/codespaces/pmx/brooks-model.qmd
ERROR: EvaluationError: Encountered 6 errors during evaluation

Error 1 of 6
@ /Users/abhimanyu/Desktop/codespaces/pmx/brooks-model.qmd:16
ArgumentError: Package Pumas not found in current path.
- Run `import Pkg; Pkg.add("Pumas")` to install the Pumas package.
Stacktrace:
  [1] macro expansion
    @ ./loading.jl:1772 [inlined]
  [2] macro expansion
    @ ./lock.jl:267 [inlined]
  [3] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1753
  [4] #invoke_in_world#3
    @ ./essentials.jl:926 [inlined]
  [5] invoke_in_world
    @ ./essentials.jl:923 [inlined]
  [6] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1746
  [7] eval
    @ ./boot.jl:385 [inlined]
  [8] (::QuartoNotebookWorker.var"#17#18"{Module, Expr})()
    @ QuartoNotebookWorker ~/.julia/packages/QuartoNotebookRunner/eYIiC/src/QuartoNotebookWorker/src/render.jl:222
  [9] (::QuartoNotebookWorker.Packages.IOCapture.var"#5#9"{DataType, QuartoNotebookWorker.var"#17#18"{Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{IOStream}, IOContext{Base.PipeEndpoint}})()
    @ QuartoNotebookWorker.Packages.IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:170
 [10] with_logstate(f::Function, logstate::Any)
    @ Base.CoreLogging ./logging.jl:515
 [11] with_logger
    @ ./logging.jl:627 [inlined]
 [12] capture(f::QuartoNotebookWorker.var"#17#18"{Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer, io_context::Vector{Pair{Symbol, Any}})
    @ QuartoNotebookWorker.Packages.IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:167
 [13] capture
    @ ~/.julia/packages/QuartoNotebookRunner/eYIiC/src/QuartoNotebookWorker/src/render.jl:248 [inlined]
 [14] io_capture(f::Function; cell_options::Dict{String, Any}, kws::@Kwargs{rethrow::DataType, color::Bool, io_context::Vector{Pair{Symbol, Any}}})
    @ QuartoNotebookWorker ~/.julia/packages/QuartoNotebookRunner/eYIiC/src/QuartoNotebookWorker/src/render.jl:250
 [15] io_capture
    @ ~/.julia/packages/QuartoNotebookRunner/eYIiC/src/QuartoNotebookWorker/src/render.jl:246 [inlined]
 [16] include_str(mod::Module, code::String; file::String, line::Int64, cell_options::Dict{String, Any})
    @ QuartoNotebookWorker ~/.julia/packages/QuartoNotebookRunner/eYIiC/src/QuartoNotebookWorker/src/render.jl:201
 [17] #invokelatest#2
    @ ./essentials.jl:894 [inlined]
 [18] invokelatest
    @ ./essentials.jl:889 [inlined]
 [19] #6
    @ ~/.julia/packages/QuartoNotebookRunner/eYIiC/src/QuartoNotebookWorker/src/render.jl:18 [inlined]
 [20] with_inline_display(f::QuartoNotebookWorker.var"#6#7"{String, String, Int64, Dict{String, Any}}, cell_options::Dict{String, Any})
    @ QuartoNotebookWorker ~/.julia/packages/QuartoNotebookRunner/eYIiC/src/QuartoNotebookWorker/src/InlineDisplay.jl:26
 [21] _render_thunk(thunk::Function, code::String, cell_options::Dict{String, Any}, is_expansion_ref::Base.RefValue{Bool}; inline::Bool)
    @ QuartoNotebookWorker ~/.julia/packages/QuartoNotebookRunner/eYIiC/src/QuartoNotebookWorker/src/render.jl:43
 [22] _render_thunk
    @ ~/.julia/packages/QuartoNotebookRunner/eYIiC/src/QuartoNotebookWorker/src/render.jl:35 [inlined]
 [23] #render#5
    @ ~/.julia/packages/QuartoNotebookRunner/eYIiC/src/QuartoNotebookWorker/src/render.jl:15 [inlined]
 [24] render(code::String, file::String, line::Int64, cell_options::Dict{String, Any})
    @ QuartoNotebookWorker ~/.julia/packages/QuartoNotebookRunner/eYIiC/src/QuartoNotebookWorker/src/render.jl:1
 [25] render(::String, ::Vararg{Any}; kwargs::@Kwargs{})
    @ Main ~/.julia/packages/QuartoNotebookRunner/eYIiC/src/worker.jl:30
 [26] top-level scope
    @ none:1

Error 2 of 6
@ /Users/abhimanyu/Desktop/codespaces/pmx/brooks-model.qmd:35
UndefVarError: `Random` not defined
Stacktrace:
 [1] top-level scope
   @ ~/Desktop/codespaces/pmx/brooks-model.qmd:36

Error 3 of 6
@ /Users/abhimanyu/Desktop/codespaces/pmx/brooks-model.qmd:175
UndefVarError: `XLSX` not defined
Stacktrace:
 [1] top-level scope
   @ ~/Desktop/codespaces/pmx/brooks-model.qmd:176

Error 4 of 6
@ /Users/abhimanyu/Desktop/codespaces/pmx/brooks-model.qmd:195
LoadError: UndefVarError: `@rtransform!` not defined
in expression starting at /Users/abhimanyu/Desktop/codespaces/pmx/brooks-model.qmd:196

Error 5 of 6
@ /Users/abhimanyu/Desktop/codespaces/pmx/brooks-model.qmd:223
UndefVarError: `nrow` not defined
Stacktrace:
 [1] top-level scope
   @ ~/Desktop/codespaces/pmx/brooks-model.qmd:225

Error 6 of 6
@ /Users/abhimanyu/Desktop/codespaces/pmx/brooks-model.qmd:244
UndefVarError: `rng` not defined
Stacktrace:
 [1] top-level scope
   @ ~/Desktop/codespaces/pmx/brooks-model.qmd:246

ERROR: Internal julia server error

Stack trace:
    at writeJuliaCommand (file:///Applications/quarto/bin/quarto.js:41406:19)
    at eventLoopTick (ext:core/01_core.js:175:7)
    at async executeJulia (file:///Applications/quarto/bin/quarto.js:41300:22)
    at async Object.execute (file:///Applications/quarto/bin/quarto.js:41037:20)
    at async renderExecute (file:///Applications/quarto/bin/quarto.js:85757:27)
    at async renderFileInternal (file:///Applications/quarto/bin/quarto.js:85925:43)
    at async renderFiles (file:///Applications/quarto/bin/quarto.js:85793:17)
    at async render (file:///Applications/quarto/bin/quarto.js:90695:21)
    at async Command.actionHandler (file:///Applications/quarto/bin/quarto.js:90843:32)
    at async Command.execute (file:///Applications/quarto/bin/quarto.js:8111:13)

Thanks, might be related to this output:

The latest version of Julia in the `release` channel is 1.11.2+0.aarch64.apple.darwin14. You currently have `1.10.5+0.aarch64.apple.darwin14` installed. Run:

  juliaup update

in your terminal shell to install Julia 1.11.2+0.aarch64.apple.darwin14 and update the `release` channel to that version.

Are you running this quarto command in a vscode terminal panel, or is it a separate terminal window? By the looks of the juliaup related output the QUARTO_JULIA command isn’t being picked up. What is the full contents of your settings.json in vscode?

Hi,

I have updated my julia version. I have now tried running quarto using both VScode terminal and separate terminal window. But now I am getting the follow output:

quarto render /Users/abhimanyu/Desktop/codespaces/pmx/brooks-model.qmd --to html
ERROR: Julia server returned error after receiving "run" command:
Failed to run notebook: /Users/abhimanyu/Desktop/codespaces/pmx/brooks-model.qmd
ERROR: ArgumentError: `startpath` must be non-empty
Stacktrace:
  [1] evaluate_raw_cells!(f::QuartoNotebookRunner.File, chunks::Vector{Any}, options::Dict{String, Any}; showprogress::Bool, chunk_callback::QuartoNotebookRunner.var"#chunk_callback#67"{TCPSocket})
    @ QuartoNotebookRunner ~/.julia/packages/QuartoNotebookRunner/eYIiC/src/server.jl:629
  [2] evaluate!(f::QuartoNotebookRunner.File, output::Nothing; showprogress::Bool, options::Dict{String, Any}, chunk_callback::Function, markdown::String)
    @ QuartoNotebookRunner ~/.julia/packages/QuartoNotebookRunner/eYIiC/src/server.jl:152
  [3] evaluate!
    @ ~/.julia/packages/QuartoNotebookRunner/eYIiC/src/server.jl:137 [inlined]
  [4] (::QuartoNotebookRunner.var"#32#36"{Nothing, String, Bool, Dict{String, Any}, QuartoNotebookRunner.var"#chunk_callback#67"{TCPSocket}, Server})(file::QuartoNotebookRunner.File)
    @ QuartoNotebookRunner ~/.julia/packages/QuartoNotebookRunner/eYIiC/src/server.jl:1113
  [5] (::QuartoNotebookRunner.var"#42#45"{Bool, QuartoNotebookRunner.var"#32#36"{Nothing, String, Bool, Dict{String, Any}, QuartoNotebookRunner.var"#chunk_callback#67"{TCPSocket}, Server}, Server, String})()
    @ QuartoNotebookRunner ~/.julia/packages/QuartoNotebookRunner/eYIiC/src/server.jl:1185
  [6] lock(f::QuartoNotebookRunner.var"#42#45"{Bool, QuartoNotebookRunner.var"#32#36"{Nothing, String, Bool, Dict{String, Any}, QuartoNotebookRunner.var"#chunk_callback#67"{TCPSocket}, Server}, Server, String}, l::ReentrantLock)
    @ Base ./lock.jl:229
  [7] borrow_file!(f::QuartoNotebookRunner.var"#32#36"{Nothing, String, Bool, Dict{String, Any}, QuartoNotebookRunner.var"#chunk_callback#67"{TCPSocket}, Server}, server::Server, path::String; optionally_create::Bool, options::Dict{String, Any})
    @ QuartoNotebookRunner ~/.julia/packages/QuartoNotebookRunner/eYIiC/src/server.jl:1178
  [8] borrow_file!
    @ ~/.julia/packages/QuartoNotebookRunner/eYIiC/src/server.jl:1139 [inlined]
  [9] #run!#31
    @ ~/.julia/packages/QuartoNotebookRunner/eYIiC/src/server.jl:1108 [inlined]
 [10] _handle_response(socket::TCPSocket, notebooks::Server, request::@NamedTuple{type::String, content::Union{Dict{String, Any}, String}}, showprogress::Bool)
    @ QuartoNotebookRunner ~/.julia/packages/QuartoNotebookRunner/eYIiC/src/socket.jl:273
 [11] (::QuartoNotebookRunner.var"#59#66"{Bool, Base.RefValue{Bool}, Server, Base.UUID})()
    @ QuartoNotebookRunner ~/.julia/packages/QuartoNotebookRunner/eYIiC/src/socket.jl:201
ERROR: Internal julia server error

Stack trace:
    at writeJuliaCommand (file:///Applications/quarto/bin/quarto.js:41406:19)
    at eventLoopTick (ext:core/01_core.js:175:7)
    at async executeJulia (file:///Applications/quarto/bin/quarto.js:41300:22)
    at async Object.execute (file:///Applications/quarto/bin/quarto.js:41037:20)
    at async renderExecute (file:///Applications/quarto/bin/quarto.js:85757:27)
    at async renderFileInternal (file:///Applications/quarto/bin/quarto.js:85925:43)
    at async renderFiles (file:///Applications/quarto/bin/quarto.js:85793:17)
    at async render (file:///Applications/quarto/bin/quarto.js:90695:21)
    at async Command.actionHandler (file:///Applications/quarto/bin/quarto.js:90843:32)
    at async Command.execute (file:///Applications/quarto/bin/quarto.js:8111:13)

These are the settings.json file:

{
    "julia.executablePath": "/Applications/Pumas-2.6.0.app/Contents/Resources/julia/bin/julia",
    "terminal.integrated.commandsToSkipShell": [
        "language-julia.interrupt"
    ],
    "julia.additionalArgs": ["-J/Applications/Pumas-2.6.0.app/Contents/Resources/julia/lib/julia/sys.pumas.dylib"],
    "julia.environmentPath": "~/.julia/environments/Pumas_v2.6/",
    "julia.symbolCacheDownload": true,
    "julia.enableTelemetry": false,
    "terminal.integrated.env.osx": {
        "QUARTO_JULIA": "/Applications/Pumas-2.6.0.app/Contents/Resources/julia/bin/julia",
        "QUARTONOTEBOOKRUNNER_EXEFLAGS": "[\"-J/Applications/Pumas-2.6.0.app/Contents/Resources/julia/lib/julia/sys.pumas.dylib\"]"
    }
}

The previous time I’ve seen this kind of error show up was due to removal of the directory that originally was used to run quarto from. Had you removed any directories between individual runs of quarto render by any chance?

No, I don’t think so. But now do I need to remove and reinstall Quarto or is there any other way to resolve this issue?

Ideally you should not need to. See whether just doing a reboot helps, sometimes old processes don’t get correctly terminated. Restarting your system might help that. If not then let me know and I’m happy to have a live debugging session with you to work out the cause of this.

Cross-referencing the newly opened issue: Quarto Notebook not rendering · Issue #222 · PumasAI/QuartoNotebookRunner.jl · GitHub

@farmacyst, would be best to either use this thread or that issue, but not both, since we’ll end up with information spread out over several places which will make debugging this harder.


julia> s = Server()
Server(Dict{String, QuartoNotebookRunner.File}(), ReentrantLock(nothing, 0x00000000, 0x00, Base.GenericCondition{Base.Threads.SpinLock}(Base.IntrusiveLinkedList{Task}(nothing, nothing), Base.Threads.SpinLock(0)), (2, 5169072480, 4511137552)), Base.RefValue{Function}(identity))

julia> run!(s, "trial.qmd")
  License Type:.....................................Time Limited
  Status:.................................................Active
  Trial:...................................................false
  Activated offline:.......................................false
  Times Activated (out of):................................2 (2)
  Expiration Date:....................................2025-01-31
  Days Remaining:.............................................52┌ Warning: Module QuartoNotebookWorkerPlotlyBaseExt with build ID ffffffff-ffff-ffff-0000-01f366394e78 is missing from the cache.
│ This may mean QuartoNotebookWorkerPlotlyBaseExt [b62a409d-317b-51f2-b01d-bd64667fbf9e] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:1948
┌ Error: Error during loading of extension QuartoNotebookWorkerPlotlyBaseExt of QuartoNotebookWorker, use `Base.retry_load_extensions()` to retry.
│   exception =
│    1-element ExceptionStack:
│    Declaring __precompile__(false) is not allowed in files that are being precompiled.
│    Stacktrace:
│      [1] _require(pkg::Base.PkgId, env::Nothing)
│        @ Base /Applications/Pumas-2.6.0.app/Contents/Resources/julia/lib/julia/sys.pumas.dylib:-1
│      [2] __require_prelocked(uuidkey::Base.PkgId, env::Nothing)
│        @ Base /Applications/Pumas-2.6.0.app/Contents/Resources/julia/lib/julia/sys.pumas.dylib:-1
│      [3] run_extension_callbacks(extid::Base.ExtensionId)
│        @ Base /Applications/Pumas-2.6.0.app/Contents/Resources/julia/lib/julia/sys.pumas.dylib:-1
│      [4] run_extension_callbacks(pkgid::Base.PkgId)
│        @ Base /Applications/Pumas-2.6.0.app/Contents/Resources/julia/lib/julia/sys.pumas.dylib:-1
│      [5] run_package_callbacks(modkey::Base.PkgId)
│        @ Base /Applications/Pumas-2.6.0.app/Contents/Resources/julia/lib/julia/sys.pumas.dylib:-1
│      [6] __require_prelocked(uuidkey::Base.PkgId, env::String)
│        @ Base /Applications/Pumas-2.6.0.app/Contents/Resources/julia/lib/julia/sys.pumas.dylib:-1
│      [7] __require(into::Module, mod::Symbol)
│        @ Base /Applications/Pumas-2.6.0.app/Contents/Resources/julia/lib/julia/sys.pumas.dylib:-1
│      [8] require(into::Module, mod::Symbol)
│        @ Base /Applications/Pumas-2.6.0.app/Contents/Resources/julia/lib/julia/sys.pumas.dylib:-1
│      [9] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
│        @ Base /Applications/Pumas-2.6.0.app/Contents/Resources/julia/lib/julia/sys.pumas.dylib:-1
│     [10] _include(mapexpr::Function, mod::Module, _path::String)
│        @ Base /Applications/Pumas-2.6.0.app/Contents/Resources/julia/lib/julia/sys.pumas.dylib:-1
│     [11] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::String)
│        @ Base /Applications/Pumas-2.6.0.app/Contents/Resources/julia/lib/julia/sys.pumas.dylib:-1
│     [12] top-level scope
│        @ stdin:3
│     [13] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
│        @ Base /Applications/Pumas-2.6.0.app/Contents/Resources/julia/lib/julia/sys.pumas.dylib:-1
│     [14] exec_options(opts::Base.JLOptions)
│        @ Base /Applications/Pumas-2.6.0.app/Contents/Resources/julia/lib/julia/sys.pumas.dylib:-1
│     [15] _start()
│        @ Base /Applications/Pumas-2.6.0.app/Contents/Resources/julia/lib/julia/sys.pumas.dylib:-1
└ @ Base loading.jl:1301

During a debug call we ran the notebook directly through QuartoNotebookRunner.jl and found the following output. Appears to be package extension interaction with the system image causing this for some reason.

While we continue to track down the root cause of this @farmacyst has been shown how to run and render qmds via QuartoNotebookRunner.jl directly.

We’ll reply in this thread once we have tracked this down more clearly.

@farmacyst, good morning. Can you please try adjusting your settings JSON file to include the following terminal.integrated.env.osx setting instead of the previous one used:

    "terminal.integrated.env.osx": {
        "QUARTO_JULIA": "/Applications/Pumas-2.6.0.app/Contents/Resources/julia/bin/julia",
        "QUARTONOTEBOOKRUNNER_EXEFLAGS": "[\"--project=~/.julia/environments/Pumas_v2.6/\", \"-J/Applications/Pumas-2.6.0.app/Contents/Resources/julia/lib/julia/sys.pumas.dylib\"]"
    }

Hi @Michael

Quarto seems to be working properly now. I am able to directly execute a render from CLI, as well as the Preview option in VScode is also working.

quarto render brooks-model.qmd          
Running [ 1/10] at line 14:  using Pumas
Running [ 2/10] at line 32:  rng = Random.seed!(1234)
Running [ 3/10] at line 181:  params = (;
Running [ 4/10] at line 211:  xf = XLSX.readdata("clinical patients.xlsx","Sheet1","B1:H183")
Running [ 5/10] at line 232:  app_df = my_df
Running [ 6/10] at line 253:  @rtransform! app_df begin
Running [ 7/10] at line 266:  clinic_pop_40 = map(
Running [ 8/10] at line 286:  clinic_sim_40 = simobs(brooks_model,clinic_pop_40,params;obstimes = 0:0.5:100,rng)
Running [ 9/10] at line 297:  clinic_sim_40_df = DataFrame(clinic_sim_40)
Running [10/10] at line 311:  sim_plot(brooks_model,
pandoc 
  to: html
  output-file: brooks-model.html
  standalone: true
  section-divs: true
  html-math-method: mathjax
  wrap: none
  default-image-extension: png
  
metadata
  document-css: false
  link-citations: true
  date-format: long
  lang: en
  title: Brooks Fludarabine Model Simulations
  subtitle: Simulating with our Patient Data
  author: Abhimanyu Thakur
  
Output created: brooks-model.html
quarto preview /Users/farmacyst/Desktop/pmx/brooks-model.qmd --no-browser --no-watch-inputs
farmacyst@Abhimanyus-MacBook-Air pmx % quarto preview /Users/farmacyst/Desktop/pmx/brooks-model.qmd --no-browser --no-watch-inputs
Running [ 1/10] at line 14:  using Pumas
Running [ 2/10] at line 32:  rng = Random.seed!(1234)
Running [ 3/10] at line 181:  params = (;
Running [ 4/10] at line 211:  xf = XLSX.readdata("clinical patients.xlsx","Sheet1","B1:H183")
Running [ 5/10] at line 232:  app_df = my_df
Running [ 6/10] at line 253:  @rtransform! app_df begin
Running [ 7/10] at line 266:  clinic_pop_40 = map(
Running [ 8/10] at line 286:  clinic_sim_40 = simobs(brooks_model,clinic_pop_40,params;obstimes = 0:0.5:100,rng)
Running [ 9/10] at line 297:  clinic_sim_40_df = DataFrame(clinic_sim_40)
Running [10/10] at line 311:  sim_plot(brooks_model,
pandoc 
  to: html
  output-file: brooks-model.html
  standalone: true
  section-divs: true
  html-math-method: mathjax
  wrap: none
  default-image-extension: png
  
metadata
  document-css: false
  link-citations: true
  date-format: long
  lang: en
  title: Brooks Fludarabine Model Simulations
  subtitle: Simulating with our Patient Data
  author: Abhimanyu Thakur
  
Output created: brooks-model.html

Watching files for changes
Browse at http://localhost:4524/

Thanks for confirming for me.

Summary for future readers. The --project flag, as well as the -J are required for it to run quarto render correctly. The next release of PumasDesktop installers for Windows and macOS will include this setting automatically. In the interim users will need to copy the above setting into their settings.json file manually.

Hi @Michael what do I put in the User JSON in windows vscode?