Hi there,
I’m just trying to get started with stan programming, but I keep running into pystan installation/stan.build issues. I’ve gone through the previous threads that seem to suggest a similar error, but nothing I’ve tried has worked so far.
My installation process was to activate my desired project-specific conda environment (dissertation) and then install pystan using:
conda install -c conda-forge pystan
The code below was taken from the PyStan documentation page here (PyStan — pystan 3.7.0 documentation) and is what I’ve been using to test the installation.
import stan
import nest_asyncio
nest_asyncio.apply()
schools_code = """
data {
int<lower=0> J; // number of schools
real y[J]; // estimated treatment effects
real<lower=0> sigma[J]; // standard error of effect estimates
}
parameters {
real mu; // population treatment effect
real<lower=0> tau; // standard deviation in treatment effects
vector[J] eta; // unscaled deviation from mu by school
}
transformed parameters {
vector[J] theta = mu + tau * eta; // school treatment effects
}
model {
target += normal_lpdf(eta | 0, 1); // prior log-density
target += normal_lpdf(y | theta, sigma); // log-likelihood
}
"""
schools_data = {"J": 8,
"y": [28, 8, -3, 7, -1, 1, 18, 12],
"sigma": [15, 10, 16, 11, 9, 11, 10, 18]}
posterior = stan.build(schools_code, data=schools_data)
Running the above code continues to yield the following error:
Error handling request
Traceback (most recent call last):
File "/Users/computer/miniconda3/envs/dissertation/lib/python3.10/site-packages/aiohttp/web_protocol.py", line 433, in _handle_request
resp = await request_handler(request)
File "/Users/computer/miniconda3/envs/dissertation/lib/python3.10/site-packages/aiohttp/web_app.py", line 504, in _handle
resp = await handler(request)
File "/Users/computer/miniconda3/envs/dissertation/lib/python3.10/site-packages/httpstan/views.py", line 103, in handle_create_model
_, stanc_warnings = httpstan.compile.compile(program_code, stan_model_name)
File "/Users/computer/miniconda3/envs/dissertation/lib/python3.10/site-packages/httpstan/compile.py", line 37, in compile
completed_process = subprocess.run(run_args, capture_output=True, timeout=1)
File "/Users/computer/miniconda3/envs/dissertation/lib/python3.10/subprocess.py", line 503, in run
with Popen(*popenargs, **kwargs) as process:
File "/Users/computer/miniconda3/envs/dissertation/lib/python3.10/subprocess.py", line 971, in __init__
self._execute_child(args, executable, preexec_fn, close_fds,
File "/Users/computer/miniconda3/envs/dissertation/lib/python3.10/subprocess.py", line 1847, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: PosixPath('/Users/computer/miniconda3/envs/dissertation/lib/python3.10/site-packages/httpstan/stanc')
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
Cell In[4], line 1
----> 1 model = stan.build(model_code, data = data)
File ~/miniconda3/envs/dissertation/lib/python3.10/site-packages/stan/model.py:519, in build(program_code, data, random_seed)
516 return Model(model_name, program_code, data, param_names, constrained_param_names, dims, random_seed)
518 try:
--> 519 return asyncio.run(go())
520 except KeyboardInterrupt:
521 return
File ~/miniconda3/envs/dissertation/lib/python3.10/site-packages/nest_asyncio.py:35, in _patch_asyncio.<locals>.run(main, debug)
33 task = asyncio.ensure_future(main)
34 try:
---> 35 return loop.run_until_complete(task)
36 finally:
37 if not task.done():
File ~/miniconda3/envs/dissertation/lib/python3.10/site-packages/nest_asyncio.py:90, in _patch_loop.<locals>.run_until_complete(self, future)
87 if not f.done():
88 raise RuntimeError(
89 'Event loop stopped before Future completed.')
---> 90 return f.result()
File ~/miniconda3/envs/dissertation/lib/python3.10/asyncio/futures.py:201, in Future.result(self)
199 self.__log_traceback = False
200 if self._exception is not None:
--> 201 raise self._exception.with_traceback(self._exception_tb)
202 return self._result
File ~/miniconda3/envs/dissertation/lib/python3.10/asyncio/tasks.py:232, in Task.__step(***failed resolving arguments***)
228 try:
229 if exc is None:
230 # We use the `send` method directly, because coroutines
231 # don't have `__iter__` and `__next__` methods.
--> 232 result = coro.send(None)
233 else:
234 result = coro.throw(exc)
File ~/miniconda3/envs/dissertation/lib/python3.10/site-packages/stan/model.py:486, in build.<locals>.go()
483 resp = task.result()
485 if resp.status != 201:
--> 486 match = re.search(r"""ValueError\(['"](.*)['"]\)""", resp.json()["message"])
487 if not match: # unknown error, should not happen
488 raise RuntimeError(resp.json()["message"])
File ~/miniconda3/envs/dissertation/lib/python3.10/site-packages/stan/common.py:25, in HTTPResponse.json(self)
23 def json(self) -> dict:
24 # mypy 0.961 complains that simdjson lacks a `loads`.
---> 25 return simdjson.loads(self.content)
File ~/miniconda3/envs/dissertation/lib/python3.10/site-packages/simdjson/__init__.py:52, in loads(s, cls, object_hook, parse_float, parse_int, parse_constant, object_pairs_hook, **kwargs)
43 """
44 Same as the built-in json.loads(), with the following exceptions:
45
(...)
49 - cls is ignored.
50 """
51 parser = Parser()
---> 52 return parser.parse(s, True)
File simdjson/csimdjson.pyx:452, in csimdjson.Parser.parse()
ValueError: The JSON document has an improper structure: missing or superfluous commas, braces, missing keys, etc.
As I said, I’ve found similar issues about the installation and this error being raised, but I haven’t been able to get past my own. Any advice would be appreciated. Let me know if there is any more information that would be helpful.
Thank you for your time.
- Operating System: Mac OS Monterey 12.6, intel i7 processor
- Python Version: python 3.10.8
- PyStan Version: 3.6.0 (httpstan: 4.6.1)
- Compiler/Toolkit: clang version 14.0.6