quarto preview quarto-book/ does not work

[kae-vm]

I tried to run the command quarto preview quarto-book/, but it's throwing an error. What do I do?

Preparing to preview
[ 1/10] index.qmd
[ 2/10] intro.qmd
[ 3/10] random-variables.qmd

Starting python3 kernel...Done

Executing 'random-variables.ipynb'
  Cell 1/11: ''...Done
  Cell 2/11: ''...

An error occurred while executing the following cell:
------------------
model = CmdStanModel(stan_file = "stan/flip.stan")
------------------


---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
Cell In[2], line 1
----> 1 model = CmdStanModel(stan_file = "stan/flip.stan")

File ~\AppData\Local\Programs\Python\Python312\Lib\site-packages\cmdstanpy\model.py:215, in CmdStanModel.__init__(self, model_name, stan_file, exe_file, force_compile, stanc_options, cpp_options, user_header, compile)
    211 if not cmdstan_version_before(
    212     2, 27
    213 ):  # unknown end of version range
    214     try:
--> 215         model_info = self.src_info()
    216         if 'parameters' in model_info:
    217             self._fixed_param |= len(model_info['parameters']) == 0

File ~\AppData\Local\Programs\Python\Python312\Lib\site-packages\cmdstanpy\model.py:321, in CmdStanModel.src_info(self)
    319 if self.stan_file is None or cmdstan_version_before(2, 27):
    320     return {}
--> 321 return compilation.src_info(str(self.stan_file), self._compiler_options)

File ~\AppData\Local\Programs\Python\Python312\Lib\site-packages\cmdstanpy\compilation.py:348, in src_info(stan_file, compiler_options)
    338 def src_info(
    339     stan_file: str, compiler_options: CompilerOptions
    340 ) -> Dict[str, Any]:
    341     """
    342     Get source info for Stan program file.
    343
    344     This function is used in the implementation of
    345     :meth:`CmdStanModel.src_info`, and should not be called directly.
    346     """
    347     cmd = (
--> 348         [os.path.join(cmdstan_path(), 'bin', 'stanc' + EXTENSION)]
    349         # handle include-paths, allow-undefined etc
    350         + compiler_options.compose_stanc(None)
    351         + ['--info', str(stan_file)]
    352     )
    353     proc = subprocess.run(cmd, capture_output=

[mitzimorris]

do you have CmdStanPy and CommandStan installed? cf: https://mc-stan.org/cmdstanpy/installation.html

[kae-vm]

I installed them, then this error is showing

Preparing to preview
[1/8] random-variables.qmd

Starting python3 kernel...Done

Executing 'random-variables.ipynb'
  Cell 1/11: ''...Done
  Cell 2/11: ''...

An error occurred while executing the following cell:
------------------
model = CmdStanModel(stan_file = "stan/flip.stan")
------------------


---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
Cell In[2], line 1
----> 1 model = CmdStanModel(stan_file = "stan/flip.stan")

File ~\AppData\Local\Programs\Python\Python312\Lib\site-packages\cmdstanpy\model.py:260, in CmdStanModel.__init__(self, model_name, stan_file, exe_file, force_compile, stanc_options, cpp_options, user_header, compile)
    257         get_logger().debug("TBB already found in load path")
    259 if compile and self._exe_file is None:
--> 260     self.compile(force=str(compile).lower() == 'force', _internal=True)

File ~\AppData\Local\Programs\Python\Python312\Lib\site-packages\cmdstanpy\model.py:513, in CmdStanModel.compile(self, force, stanc_options, cpp_options, user_header, override_options, _internal)
    510         else:
    511             self._compiler_options.add(compiler_options)
--> 513 self._exe_file = compilation.compile_stan_file(
    514     str(self.stan_file),
    515     force=force,
    516     stanc_options=self._compiler_options.stanc_options,
    517     cpp_options=self._compiler_options.cpp_options,
    518     user_header=self._compiler_options.user_header,
    519 )

File ~\AppData\Local\Programs\Python\Python312\Lib\site-packages\cmdstanpy\compilation.py:475, in compile_stan_file(src, force, stanc_options, cpp_options, user_header)
    468     if 'PCH' in console or 'precompiled header' in console:
    469         get_logger().warning(
    470             "CmdStan's precompiled header (PCH) files "
    471             "may need to be rebuilt."
    472             "Please run cmdstanpy.rebuild_cmdstan().\

[bob-carpenter]

Can you do some simpler diagnostics:

1. Can you run a notebook of whatever kind you're running without including Stan?
2. Can you run Stan not in a notebook setting?

It looks like the problem may be that you need to rebuild cmdstan. Try this from within Python:

> import cmdstanpy as csp
> csp.rebuild_cmdstan()

CmdStan needs to be rebuilt whenever the binary in the back end changes, which if you'e on a Mac, is pretty much every time Xcode updates if you haven't plugged in a custom C++ toolchain.

[kae-vm]

Can you elaborate on what you mean by not in a notebook setting? I tried running those commands within Python, and it still seems to be throwing me an error.

Python 3.12.2 (tags/v3.12.2:6abddd9, Feb  6 2024, 21:26:36) [MSC v.1937 64 bit (AMD64)] on win32
Type "help", "copyright", "credits" or "license" for more information.
>>> import cmdstanpy as csp
>>> csp.rebuild_cmdstan()
Traceback (most recent call last):
  File "C:\Users\keval\AppData\Local\Programs\Python\Python312\Lib\site-packages\cmdstanpy\utils\command.py", line 42, in do_command
    proc = subprocess.Popen(
           ^^^^^^^^^^^^^^^^^
  File "C:\Users\keval\AppData\Local\Programs\Python\Python312\Lib\subprocess.py", line 1026, in __init__
    self._execute_child(args, executable, preexec_fn, close_fds,
  File "C:\Users\keval\AppData\Local\Programs\Python\Python312\Lib\subprocess.py", line 1538, in _execute_child
    hp, ht, pid, tid = _winapi.CreateProcess(executable, args,
                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
FileNotFoundError: [WinError 2] The system cannot find the file specified

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "C:\Users\keval\AppData\Local\Programs\Python\Python312\Lib\site-packages\cmdstanpy\install_cmdstan.py", line 252, in clean_all
    do_command(cmd, fd_out=None)
  File "C:\Users\keval\AppData\Local\Programs\Python\Python312\Lib\site-packages\cmdstanpy\utils\command.py", line 79, in do_command
    raise RuntimeError(msg) from e
RuntimeError: Command: ['mingw32-make', 'clean-all']
failed with error [WinError 2] The system cannot find the file specified


During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "C:\Users\keval\AppData\Local\Programs\Python\Python312\Lib\site-packages\cmdstanpy\install_cmdstan.py", line 388, in rebuild_cmdstan
    clean_all(verbose)
  File "C:\Users\keval\AppData\Local\Programs\Python\Python312\Lib\site-packages\cmdstanpy\install_cmdstan.py", line 256, in clean_all
    raise CmdStanInstallError(f'Command "make clean-all" failed\n{str(e)}')
cmdstanpy.install_cmdstan.CmdStanInstallError: Command "make clean-all" failed
Command: ['mingw32-make', 'clean-all']
failed with error [WinError 2] The system cannot find the file specified

>>>

I am on Windows, btw