cmdstanpy: Command "make build" failed in CmdStanInstall

Summary:

Cannot rebuild nor install cmdstan via cmdstanpy. CmdStan from Github compiles without issues.

Description:

Weird bug - cmdstan stopped working with:

INFO:cmdstanpy:compiling stan file /Users/jerzybaranowski/GitHub/KAIR-ISZ/isz/src/python/laboratoria/stan4.stan to exe file /Users/jerzybaranowski/GitHub/KAIR-ISZ/isz/src/python/laboratoria/stan4
WARNING:cmdstanpy:CmdStan's precompiled header (PCH) files may need to be rebuilt.If your model failed to compile please run cmdstanpy.rebuild_cmdstan().
If the issue persists please open a bug report

I attempted rebuild_cmdstan()

Compiling:  (01:06) | ████▉      | make: ** ... stansummary] Error 1
---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)
File /opt/anaconda3/envs/DA2022/lib/python3.10/site-packages/cmdstanpy/install_cmdstan.py:117, in build(verbose, progress, cores)
    [116]()[     progress_hook: Any = _wrap_build_progress_hook()
--> ]()[117]()[     do_command(cmd, fd_out=None, pbar=progress_hook)
    ]()[118]()[ else:

File /opt/anaconda3/envs/DA2022/lib/python3.10/site-packages/cmdstanpy/utils.py:1089, in do_command(cmd, cwd, fd_out, pbar)
   ]()[1086]()[             msg = 'Command {}\n\t{} {}'.format(
   ]()[1087]()[                 cmd, returncode_msg(proc.returncode), serror
   ]()[1088]()[             )
-> ]()[1089]()[             raise RuntimeError(msg)
   ]()[1090]()[ except OSError as e:

RuntimeError: Command ['make', 'build', '-j1']
	error during processing No such file or directory

During handling of the above exception, another exception occurred:

CmdStanInstallError                       Traceback (most recent call last)
/Users/jerzybaranowski/GitHub/KAIR-ISZ/isz/src/python/laboratoria/lab2a.ipynb Cell 29' in <module>
----> ]()[1]()[ rebuild_cmdstan()

File /opt/anaconda3/envs/DA2022/lib/python3.10/site-packages/cmdstanpy/install_cmdstan.py:223, in rebuild_cmdstan(verbose, progress, cores)
    ]()[221]()[     with pushd(cmdstan_path()):
    ]()[222]()[         clean_all(verbose)
--> ]()[223]()[         build(verbose, progress, cores)
    ]()[224]()[         compile_example(verbose)
    ]()[225]()[ except ValueError as e:

File /opt/anaconda3/envs/DA2022/lib/python3.10/site-packages/cmdstanpy/install_cmdstan.py:123, in build(verbose, progress, cores)
    ]()[119]()[         do_command(cmd, fd_out=None)
    ]()[121]()[ except RuntimeError as e:
    ]()[122]()[     # pylint: disable=raise-missing-from
--> ]()[123]()[     raise CmdStanInstallError(f'Command "make build" failed\n{str(e)}')
    ]()[124]()[ if not os.path.exists(os.path.join('bin', 'stansummary' + EXTENSION)):
    ]()[125]()[     raise CmdStanInstallError(
    ]()[126]()[         f'bin/stansummary{EXTENSION} not found'
    ]()[127]()[         ', please rebuild or report a bug!'
    ]()[128]()[     )

CmdStanInstallError: Command "make build" failed
Command ['make', 'build', '-j1']
	error during processing No such file or directory]()

install_cmdstan gave similar results

Installing CmdStan version: 2.29.1
Install directory: /Users/jerzybaranowski/.cmdstan
Downloading CmdStan version 2.29.1
Download successful, file: /var/folders/96/_4tl8xsx4tx9rj0ykk82715h0000gn/T/tmpyd5u5ghr
Extracting distribution
Unpacked download as cmdstan-2.29.1
Building version cmdstan-2.29.1, may take several minutes, depending on your system.
Command "make build" failed
Command ['make', 'build', '-j1']
	error during processing No such file or directory
---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)
File /opt/anaconda3/envs/DA2022/lib/python3.10/site-packages/cmdstanpy/install_cmdstan.py:119, in build(verbose, progress, cores)
    [118]()[     else:
--> ]()[119]()[         do_command(cmd, fd_out=None)
    ]()[121]()[ except RuntimeError as e:
    ]()[122]()[     # pylint: disable=raise-missing-from

File /opt/anaconda3/envs/DA2022/lib/python3.10/site-packages/cmdstanpy/utils.py:1089, in do_command(cmd, cwd, fd_out, pbar)
   ]()[1086]()[             msg = 'Command {}\n\t{} {}'.format(
   ]()[1087]()[                 cmd, returncode_msg(proc.returncode), serror
   ]()[1088]()[             )
-> ]()[1089]()[             raise RuntimeError(msg)
   ]()[1090]()[ except OSError as e:

RuntimeError: Command ['make', 'build', '-j1']
	error during processing No such file or directory

During handling of the above exception, another exception occurred:

CmdStanInstallError                       Traceback (most recent call last)
File /opt/anaconda3/envs/DA2022/lib/python3.10/site-packages/cmdstanpy/install_cmdstan.py:529, in main(args)
    ]()[528]()[     retrieve_version(version, progress)
--> ]()[529]()[     install_version(
    ]()[530]()[         cmdstan_version=cmdstan_version,
    ]()[531]()[         overwrite=args['overwrite'],
    ]()[532]()[         verbose=args['verbose'],
    ]()[533]()[         progress=progress,
    ]()[534]()[         cores=args['cores'],
    ]()[535]()[     )
    ]()[536]()[ except RuntimeError as e:

File /opt/anaconda3/envs/DA2022/lib/python3.10/site-packages/cmdstanpy/install_cmdstan.py:259, in install_version(cmdstan_version, overwrite, verbose, progress, cores)
    ]()[258]()[     print('Rebuilding version {}'.format(cmdstan_version))
--> ]()[259]()[ build(verbose, progress=progress, cores=cores)
    ]()[260]()[ print('Test model compilation')

File /opt/anaconda3/envs/DA2022/lib/python3.10/site-packages/cmdstanpy/install_cmdstan.py:123, in build(verbose, progress, cores)
    ]()[121]()[ except RuntimeError as e:
    ]()[122]()[     # pylint: disable=raise-missing-from
--> ]()[123]()[     raise CmdStanInstallError(f'Command "make build" failed\n{str(e)}')
    ]()[124]()[ if not os.path.exists(os.path.join('bin', 'stansummary' + EXTENSION)):

CmdStanInstallError: Command "make build" failed
Command ['make', 'build', '-j1']
	error during processing No such file or directory

During handling of the above exception, another exception occurred:

SystemExit                                Traceback (most recent call last)
    [... skipping hidden 1 frame]

/Users/jerzybaranowski/GitHub/KAIR-ISZ/isz/src/python/laboratoria/lab2a.ipynb Cell 30' in <module>
      ]()[1]()[ from cmdstanpy import install_cmdstan
----> ]()[2]()[ install_cmdstan()

File /opt/anaconda3/envs/DA2022/lib/python3.10/site-packages/cmdstanpy/utils.py:1303, in install_cmdstan(version, dir, overwrite, compiler, progress, verbose, cores)
   ]()[1301]()[     from .install_cmdstan import main
-> ]()[1303]()[     main(args)
   ]()[1304]()[ # pylint: disable=broad-except

File /opt/anaconda3/envs/DA2022/lib/python3.10/site-packages/cmdstanpy/install_cmdstan.py:538, in main(args)
    ]()[537]()[         print(e)
--> ]()[538]()[         sys.exit(3)
    ]()[539]()[ else:

SystemExit: 3

During handling of the above exception, another exception occurred:

AssertionError                            Traceback (most recent call last)
    [... skipping hidden 1 frame]

File /opt/anaconda3/envs/DA2022/lib/python3.10/site-packages/IPython/core/interactiveshell.py:1927, in showtraceback(self, exc_tuple, filename, tb_offset, exception_only, running_compiled_code)
   ]()[1926]()[ def show_usage_error(self, exc):
-> ]()[1927]()[     """Show a short message for UsageErrors
   ]()[1928]()[ 
   ]()[1929]()[     These are special exceptions that shouldn't show a traceback.
   ]()[1930]()[     """
   ]()[1931]()[     print("UsageError: %s" % exc, file=sys.stderr)

File /opt/anaconda3/envs/DA2022/lib/python3.10/site-packages/IPython/core/ultratb.py:578, in ListTB.get_exception_only(self, etype, value)
    ]()[570]()[ def get_exception_only(self, etype, value):
    ]()[571]()[     """Only print the exception type and message, without a traceback.
    ]()[572]()[ 
    ]()[573]()[     Parameters
   (...)
    ]()[576]()[     value : exception value
    ]()[577]()[     """
--> ]()[578]()[     return ListTB.structured_traceback(self, etype, value)

File /opt/anaconda3/envs/DA2022/lib/python3.10/site-packages/IPython/core/ultratb.py:436, in ListTB.structured_traceback(self, etype, evalue, etb, tb_offset, context)
    ]()[433]()[     chained_exc_ids.add(id(exception[1]))
    ]()[434]()[     chained_exceptions_tb_offset = 0
    ]()[435]()[     out_list = (
--> ]()[436]()[         self.structured_traceback(
    ]()[437]()[             etype, evalue, (etb, chained_exc_ids),
    ]()[438]()[             chained_exceptions_tb_offset, context)
    ]()[439]()[         + chained_exception_message
    ]()[440]()[         + out_list)
    ]()[442]()[ return out_list

File /opt/anaconda3/envs/DA2022/lib/python3.10/site-packages/IPython/core/ultratb.py:1105, in AutoFormattedTB.structured_traceback(self, etype, value, tb, tb_offset, number_of_lines_of_context)
   ]()[1103]()[ else:
   ]()[1104]()[     self.tb = tb
-> ]()[1105]()[ return FormattedTB.structured_traceback(
   ]()[1106]()[     self, etype, value, tb, tb_offset, number_of_lines_of_context)

File /opt/anaconda3/envs/DA2022/lib/python3.10/site-packages/IPython/core/ultratb.py:999, in FormattedTB.structured_traceback(self, etype, value, tb, tb_offset, number_of_lines_of_context)
    ]()[996]()[ mode = self.mode
    ]()[997]()[ if mode in self.verbose_modes:
    ]()[998]()[     # Verbose modes need a full traceback
--> ]()[999]()[     return VerboseTB.structured_traceback(
   ]()[1000]()[         self, etype, value, tb, tb_offset, number_of_lines_of_context
   ]()[1001]()[     )
   ]()[1002]()[ elif mode == 'Minimal':
   ]()[1003]()[     return ListTB.get_exception_only(self, etype, value)

File /opt/anaconda3/envs/DA2022/lib/python3.10/site-packages/IPython/core/ultratb.py:852, in VerboseTB.structured_traceback(self, etype, evalue, etb, tb_offset, number_of_lines_of_context)
    ]()[850]()[ """Return a nice text document describing the traceback."""
    ]()[851]()[ assert etb is not None
--> ]()[852]()[ formatted_exception = self.format_exception_as_a_whole(etype, evalue, etb, number_of_lines_of_context,
    ]()[853]()[                                                        tb_offset)
    ]()[855]()[ colors = self.Colors  # just a shorthand + quicker name lookup
    ]()[856]()[ colorsnormal = colors.Normal  # used a lot

File /opt/anaconda3/envs/DA2022/lib/python3.10/site-packages/IPython/core/ultratb.py:786, in VerboseTB.format_exception_as_a_whole(self, etype, evalue, etb, number_of_lines_of_context, tb_offset)
    ]()[784]()[ assert isinstance(tb_offset, int)
    ]()[785]()[ head = self.prepare_header(etype, self.long_header)
--> ]()[786]()[ records = self.get_records(etb, number_of_lines_of_context, tb_offset)
    ]()[788]()[ frames = []
    ]()[789]()[ skipped = 0

File /opt/anaconda3/envs/DA2022/lib/python3.10/site-packages/IPython/core/ultratb.py:840, in VerboseTB.get_records(self, etb, number_of_lines_of_context, tb_offset)
    ]()[834]()[ options = stack_data.Options(
    ]()[835]()[     before=before,
    ]()[836]()[     after=after,
    ]()[837]()[     pygments_formatter=formatter,
    ]()[838]()[ )
    ]()[839]()[ assert etb is not None
--> ]()[840]()[ return list(stack_data.FrameInfo.stack_data(etb, options=options))[tb_offset:]

File /opt/anaconda3/envs/DA2022/lib/python3.10/site-packages/stack_data/core.py:546, in FrameInfo.stack_data(cls, frame_or_tb, options, collapse_repeated_frames)
    ]()[530]()[ @classmethod
    ]()[531]()[ def stack_data(
    ]()[532]()[         cls,
   (...)
    ]()[536]()[         collapse_repeated_frames: bool = True
    ]()[537]()[ ) -> Iterator[Union['FrameInfo', RepeatedFrames]]:
    ]()[538]()[     """
    ]()[539]()[     An iterator of FrameInfo and RepeatedFrames objects representing
    ]()[540]()[     a full traceback or stack. Similar consecutive frames are collapsed into RepeatedFrames
   (...)
    ]()[544]()[     and optionally an Options object to configure.
    ]()[545]()[     """
--> ]()[546]()[     stack = list(iter_stack(frame_or_tb))
    ]()[548]()[     # Reverse the stack from a frame so that it's in the same order
    ]()[549]()[     # as the order from a traceback, which is the order of a printed
    ]()[550]()[     # traceback when read top to bottom (most recent call last)
    ]()[551]()[     if is_frame(frame_or_tb):

File /opt/anaconda3/envs/DA2022/lib/python3.10/site-packages/stack_data/utils.py:98, in iter_stack(frame_or_tb)
     ]()[96]()[ while frame_or_tb:
     ]()[97]()[     yield frame_or_tb
---> ]()[98]()[     if is_frame(frame_or_tb):
     ]()[99]()[         frame_or_tb = frame_or_tb.f_back
    ]()[100]()[     else:

File /opt/anaconda3/envs/DA2022/lib/python3.10/site-packages/stack_data/utils.py:91, in is_frame(frame_or_tb)
     ]()[90]()[ def is_frame(frame_or_tb: Union[FrameType, TracebackType]) -> bool:
---> ]()[91]()[     assert_(isinstance(frame_or_tb, (types.FrameType, types.TracebackType)))
     ]()[92]()[     return isinstance(frame_or_tb, (types.FrameType,))

File /opt/anaconda3/envs/DA2022/lib/python3.10/site-packages/stack_data/utils.py:172, in assert_(condition, error)
    ]()[170]()[ if isinstance(error, str):
    ]()[171]()[     error = AssertionError(error)
--> ]()[172]() raise error

AssertionError:

cmdstan from sources compiles proprly but does not cooperate with cmdstanpy.

Additional Information:

Everything is on Mac OS Monterey 12.2.1 M1 mac mini.

Tried :

• reinstallation of xcode command line tools
• new conda environment
• reinstallation of cmdstanpy
• building cmdstan from sources

Current Version:

cmdstanpy-1.0.1