[GH-ISSUE #104] Module Not Found Error #98

Closed
opened 2026-02-26 12:20:29 +03:00 by kerem · 12 comments
Owner

Originally created by @rcolpo on GitHub (Jun 8, 2020).
Original GitHub issue: https://github.com/brentvollebregt/auto-py-to-exe/issues/104

I'm trying to make an executable file out of the python code below:

import cobra
import _libsbml
print(1)

However, I keep receiving the error message
ModuleNotFoundError: No module named '_libsbml'

Any ideas on how to solve this?
The line "import _libsbml" was not in my original code. I added it while trying to solve this problem. I also added "_libsbml" on the "--hiddenimport" advanced field, but without results.

Originally created by @rcolpo on GitHub (Jun 8, 2020). Original GitHub issue: https://github.com/brentvollebregt/auto-py-to-exe/issues/104 I'm trying to make an executable file out of the python code below: ``` import cobra import _libsbml print(1) ``` However, I keep receiving the error message `ModuleNotFoundError: No module named '_libsbml' ` Any ideas on how to solve this? The line "import _libsbml" was not in my original code. I added it while trying to solve this problem. I also added "_libsbml" on the "--hiddenimport" advanced field, but without results.
kerem closed this issue 2026-02-26 12:20:29 +03:00
Author
Owner

@brentvollebregt commented on GitHub (Jun 9, 2020):

What is the "Current Command" that auto-py-to-exe displayed when you packaged your script?

<!-- gh-comment-id:641029315 --> @brentvollebregt commented on GitHub (Jun 9, 2020): What is the "Current Command" that auto-py-to-exe displayed when you packaged your script?
Author
Owner

@rcolpo commented on GitHub (Jun 9, 2020):

Current Command:
pyinstaller --noconfirm --onedir --nowindowed "C:/phd/Eric/SBMLComp-master/Scripts/exePythonTest.py"

Output:

Running auto-py-to-exe v2.7.4
Building directory: C:\Users\colpoama\AppData\Local\Temp\tmp_xijgwf9
Provided command: pyinstaller --noconfirm --onedir --nowindowed  "C:/phd/Eric/SBMLComp-master/Scripts/exePythonTest.py"
Recursion Limit is set to 5000
Executing: pyinstaller --noconfirm --onedir --nowindowed C:/phd/Eric/SBMLComp-master/Scripts/exePythonTest.py --distpath C:\Users\colpoama\AppData\Local\Temp\tmp_xijgwf9\application --workpath C:\Users\colpoama\AppData\Local\Temp\tmp_xijgwf9\build --specpath C:\Users\colpoama\AppData\Local\Temp\tmp_xijgwf9

139942 INFO: PyInstaller: 3.6
139950 INFO: Python: 3.7.6
139956 INFO: Platform: Windows-10-10.0.18362-SP0
139972 INFO: wrote C:\Users\colpoama\AppData\Local\Temp\tmp_xijgwf9\exePythonTest.spec
139983 INFO: UPX is not available.
139994 INFO: Extending PYTHONPATH with paths
['C:\\phd\\Eric\\SBMLComp-master\\Scripts',
 'C:\\Users\\colpoama\\AppData\\Local\\Temp\\tmp_xijgwf9']
140001 INFO: checking Analysis
140009 INFO: Building Analysis because Analysis-00.toc is non existent
140014 INFO: Initializing module dependency graph...
140026 INFO: Caching module graph hooks...
140051 INFO: Analyzing base_library.zip ...
143365 INFO: Caching module dependency graph...
143451 INFO: running Analysis Analysis-00.toc
143477 INFO: Adding Microsoft.Windows.Common-Controls to dependent assemblies of final executable
  required by c:\users\colpoama\appdata\local\programs\python\python37\python.exe
143551 INFO: Analyzing C:\phd\Eric\SBMLComp-master\Scripts\exePythonTest.py
145649 INFO: Processing pre-find module path hook   distutils
145658 INFO: distutils: retargeting to non-venv dir 'c:\\users\\colpoama\\appdata\\local\\programs\\python\\python37\\lib'
149752 INFO: Processing pre-find module path hook   site
149763 INFO: site: retargeting to fake-dir 'c:\\users\\colpoama\\appdata\\local\\programs\\python\\python37\\lib\\site-packages\\PyInstaller\\fake-modules'
150847 INFO: Processing pre-safe import module hook   setuptools.extern.six.moves
159006 INFO: Processing pre-safe import module hook   six.moves
163760 INFO: Processing pre-safe import module hook   urllib3.packages.six.moves
196661 INFO: Processing pre-safe import module hook   win32com
205317 INFO: Processing module hooks...
205325 INFO: Loading module hook "hook-certifi.py"...
205339 INFO: Loading module hook "hook-distutils.py"...
205352 INFO: Loading module hook "hook-encodings.py"...
205540 INFO: Loading module hook "hook-gevent.py"...
205960 INFO: Determining a mapping of distributions to packages...
228000 WARNING: Unable to find package for requirement greenlet from package gevent.
228009 WARNING: Unable to find package for requirement zope.event from package gevent.
228020 WARNING: Unable to find package for requirement zope.interface from package gevent.
228028 INFO: Packages required by gevent:
['setuptools', 'cffi']
229760 INFO: Loading module hook "hook-importlib_metadata.py"...
229773 INFO: Loading module hook "hook-IPython.py"...
230770 INFO: Excluding import 'gtk'
230786 INFO: Excluding import 'PyQt4'
230800 INFO:   Removing import of PyQt4 from module IPython.external.qt_loaders
230808 INFO: Excluding import 'PyQt5'
230824 INFO:   Removing import of PyQt5 from module IPython.external.qt_loaders
230832 INFO: Excluding import 'tkinter'
230847 INFO:   Removing import of tkinter from module IPython.lib.clipboard
230857 INFO: Excluding import 'matplotlib'
230872 INFO:   Removing import of matplotlib from module IPython.core.pylabtools
230879 INFO:   Removing import of matplotlib._pylab_helpers from module IPython.core.pylabtools
230891 INFO:   Removing import of matplotlib.pyplot from module IPython.core.pylabtools
230899 INFO:   Removing import of matplotlib.figure from module IPython.core.pylabtools
230909 INFO:   Removing import of matplotlib from module IPython.lib.latextools
230917 INFO:   Removing import of matplotlib.mathtext from module IPython.lib.latextools
230927 INFO: Excluding import 'PySide'
230944 INFO:   Removing import of PySide from module IPython.external.qt_loaders
230953 INFO: Loading module hook "hook-jedi.py"...
231219 INFO: Loading module hook "hook-jinja2.py"...
231251 INFO: Loading module hook "hook-jsonschema.py"...
231271 INFO: Loading module hook "hook-lib2to3.py"...
231297 INFO: Loading module hook "hook-matplotlib.backends.py"...
232343 INFO:   Matplotlib backend "GTK3Agg": ignored
    cairo backend requires that pycairo>=1.11.0 or cairocffiis installed
232723 INFO:   Matplotlib backend "GTK3Cairo": ignored
    cairo backend requires that pycairo>=1.11.0 or cairocffiis installed
233315 INFO:   Matplotlib backend "MacOSX": ignored
    cannot import name '_macosx' from 'matplotlib.backends' (C:\Users\colpoama\AppData\Roaming\Python\Python37\site-packages\matplotlib\backends\__init__.py)
234315 INFO:   Matplotlib backend "nbAgg": added
234853 INFO:   Matplotlib backend "Qt4Agg": ignored
    Failed to import any qt binding
235307 INFO:   Matplotlib backend "Qt4Cairo": ignored
    cairo backend requires that pycairo>=1.11.0 or cairocffiis installed
235854 INFO:   Matplotlib backend "Qt5Agg": ignored
    Failed to import any qt binding
236303 INFO:   Matplotlib backend "Qt5Cairo": ignored
    cairo backend requires that pycairo>=1.11.0 or cairocffiis installed
237022 INFO:   Matplotlib backend "TkAgg": added
237612 INFO:   Matplotlib backend "TkCairo": ignored
    cairo backend requires that pycairo>=1.11.0 or cairocffiis installed
238218 INFO:   Matplotlib backend "WebAgg": added
238758 INFO:   Matplotlib backend "WX": ignored
    No module named 'wx'
239197 INFO:   Matplotlib backend "WXAgg": ignored
    No module named 'wx'
239576 INFO:   Matplotlib backend "WXCairo": ignored
    No module named 'wx'
239963 INFO:   Matplotlib backend "agg": added
240398 INFO:   Matplotlib backend "cairo": ignored
    cairo backend requires that pycairo>=1.11.0 or cairocffiis installed
240872 INFO:   Matplotlib backend "pdf": added
241410 INFO:   Matplotlib backend "pgf": added
241783 INFO:   Matplotlib backend "ps": added
242179 INFO:   Matplotlib backend "svg": added
242708 INFO:   Matplotlib backend "template": added
242980 INFO: Loading module hook "hook-matplotlib.py"...
243368 INFO: Loading module hook "hook-nbconvert.py"...
243415 INFO: Loading module hook "hook-nbformat.py"...
243442 INFO: Loading module hook "hook-notebook.py"...
244936 INFO: Loading module hook "hook-numpy.core.py"...
245039 INFO: Loading module hook "hook-numpy.py"...
245053 INFO: Loading module hook "hook-pandas.py"...
246259 INFO: Loading module hook "hook-pkg_resources.py"...
246944 INFO: Excluding import '__main__'
246960 INFO:   Removing import of __main__ from module pkg_resources
246970 INFO: Loading module hook "hook-pycparser.py"...
246988 INFO: Loading module hook "hook-pydoc.py"...
247003 INFO: Loading module hook "hook-pygments.py"...
249125 INFO: Loading module hook "hook-pytest.py"...
250026 INFO: Loading module hook "hook-pythoncom.py"...
250491 INFO: Loading module hook "hook-pytz.py"...
250617 INFO: Loading module hook "hook-pywintypes.py"...
251079 INFO: Loading module hook "hook-scipy.io.matlab.py"...
251100 INFO: Loading module hook "hook-scipy.linalg.py"...
251121 INFO: Loading module hook "hook-scipy.py"...
251153 INFO: Loading module hook "hook-scipy.sparse.csgraph.py"...
251175 INFO: Loading module hook "hook-scipy.special._ellip_harm_2.py"...
251195 INFO: Loading module hook "hook-scipy.special._ufuncs.py"...
251214 INFO: Loading module hook "hook-setuptools.py"...
252012 INFO: Loading module hook "hook-sqlite3.py"...
252202 INFO: Loading module hook "hook-sysconfig.py"...
252218 INFO: Loading module hook "hook-win32com.py"...
252808 INFO: Loading module hook "hook-xml.dom.domreg.py"...
252824 INFO: Loading module hook "hook-xml.etree.cElementTree.py"...
252844 INFO: Loading module hook "hook-xml.py"...
252862 INFO: Loading module hook "hook-zmq.py"...
253766 INFO: Loading module hook "hook-_tkinter.py"...
254107 INFO: checking Tree
254125 INFO: Building Tree because Tree-00.toc is non existent
254143 INFO: Building Tree Tree-00.toc
254304 INFO: checking Tree
254318 INFO: Building Tree because Tree-01.toc is non existent
254340 INFO: Building Tree Tree-01.toc
254721 INFO: Looking for ctypes DLLs
254992 INFO: Analyzing run-time hooks ...
255049 INFO: Including run-time hook 'pyi_rth_win32comgenpy.py'
255076 INFO: Including run-time hook 'pyi_rth_multiprocessing.py'
255102 INFO: Including run-time hook 'pyi_rth__tkinter.py'
255127 INFO: Including run-time hook 'pyi_rth_traitlets.py'
255151 INFO: Including run-time hook 'pyi_rth_certifi.py'
255179 INFO: Including run-time hook 'pyi_rth_mplconfig.py'
255204 INFO: Including run-time hook 'pyi_rth_mpldata.py'
255228 INFO: Including run-time hook 'pyi_rth_pkgres.py'
255335 INFO: Looking for dynamic libraries
256609 WARNING: lib not found: libzmq.cp37-win_amd64.pyd dependency of C:\Users\colpoama\AppData\Roaming\Python\Python37\site-packages\zmq\backend\cython\context.cp37-win_amd64.pyd
256633 WARNING: lib not found: libzmq.cp37-win_amd64.pyd dependency of C:\Users\colpoama\AppData\Roaming\Python\Python37\site-packages\zmq\backend\cython\utils.cp37-win_amd64.pyd
256661 WARNING: lib not found: libzmq.cp37-win_amd64.pyd dependency of C:\Users\colpoama\AppData\Roaming\Python\Python37\site-packages\zmq\backend\cython\message.cp37-win_amd64.pyd
256685 WARNING: lib not found: libzmq.cp37-win_amd64.pyd dependency of C:\Users\colpoama\AppData\Roaming\Python\Python37\site-packages\zmq\backend\cython\_device.cp37-win_amd64.pyd
256711 WARNING: lib not found: libzmq.cp37-win_amd64.pyd dependency of C:\Users\colpoama\AppData\Roaming\Python\Python37\site-packages\zmq\backend\cython\_proxy_steerable.cp37-win_amd64.pyd
256737 WARNING: lib not found: libzmq.cp37-win_amd64.pyd dependency of C:\Users\colpoama\AppData\Roaming\Python\Python37\site-packages\zmq\backend\cython\socket.cp37-win_amd64.pyd
256763 WARNING: lib not found: libzmq.cp37-win_amd64.pyd dependency of C:\Users\colpoama\AppData\Roaming\Python\Python37\site-packages\zmq\backend\cython\error.cp37-win_amd64.pyd
256795 WARNING: lib not found: libzmq.cp37-win_amd64.pyd dependency of C:\Users\colpoama\AppData\Roaming\Python\Python37\site-packages\zmq\backend\cython\_version.cp37-win_amd64.pyd
256825 WARNING: lib not found: libzmq.cp37-win_amd64.pyd dependency of C:\Users\colpoama\AppData\Roaming\Python\Python37\site-packages\zmq\backend\cython\_poll.cp37-win_amd64.pyd
258558 INFO: Looking for eggs
258573 INFO: Using Python library c:\users\colpoama\appdata\local\programs\python\python37\python37.dll
258595 INFO: Found binding redirects: 
[]
258673 INFO: Warnings written to C:\Users\colpoama\AppData\Local\Temp\tmp_xijgwf9\build\exePythonTest\warn-exePythonTest.txt
259380 INFO: Graph cross-reference written to C:\Users\colpoama\AppData\Local\Temp\tmp_xijgwf9\build\exePythonTest\xref-exePythonTest.html
259731 INFO: checking PYZ
259749 INFO: Building PYZ because PYZ-00.toc is non existent
259766 INFO: Building PYZ (ZlibArchive) C:\Users\colpoama\AppData\Local\Temp\tmp_xijgwf9\build\exePythonTest\PYZ-00.pyz
268190 INFO: Building PYZ (ZlibArchive) C:\Users\colpoama\AppData\Local\Temp\tmp_xijgwf9\build\exePythonTest\PYZ-00.pyz completed successfully.
268352 INFO: checking PKG
268369 INFO: Building PKG because PKG-00.toc is non existent
268390 INFO: Building PKG (CArchive) PKG-00.pkg
268490 INFO: Building PKG (CArchive) PKG-00.pkg completed successfully.
268510 INFO: Bootloader c:\users\colpoama\appdata\local\programs\python\python37\lib\site-packages\PyInstaller\bootloader\Windows-64bit\run.exe
268531 INFO: checking EXE
268552 INFO: Building EXE because EXE-00.toc is non existent
268572 INFO: Building EXE from EXE-00.toc
268596 INFO: Appending archive to EXE C:\Users\colpoama\AppData\Local\Temp\tmp_xijgwf9\build\exePythonTest\exePythonTest.exe
268662 INFO: Building EXE from EXE-00.toc completed successfully.
268689 INFO: checking COLLECT
268707 INFO: Building COLLECT because COLLECT-00.toc is non existent
268729 INFO: Building COLLECT COLLECT-00.toc
292586 INFO: Building COLLECT COLLECT-00.toc completed successfully.

Moving project to: C:\Users\colpoama\AppData\Local\Programs\Python\Python37\Scripts\output
Complete.

This is the complete error message I got when I try running the newly created executable file:

Traceback (most recent call last):
  File "libsbml\__init__.py", line 21, in swig_import_helper
  File "importlib\__init__.py", line 127, in import_module
  File "<frozen importlib._bootstrap>", line 1006, in _gcd_import
  File "<frozen importlib._bootstrap>", line 983, in _find_and_load
  File "<frozen importlib._bootstrap>", line 965, in _find_and_load_unlocked
ModuleNotFoundError: No module named '_libsbml'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "exePythonTest.py", line 1, in <module>
  File "c:\users\colpoama\appdata\local\programs\python\python37\lib\site-packages\PyInstaller\loader\pyimod03_importers.py", line 623, in exec_module
    exec(bytecode, module.__dict__)
  File "cobra\__init__.py", line 40, in <module>
  File "c:\users\colpoama\appdata\local\programs\python\python37\lib\site-packages\PyInstaller\loader\pyimod03_importers.py", line 623, in exec_module
    exec(bytecode, module.__dict__)
  File "cobra\io\__init__.py", line 8, in <module>
  File "c:\users\colpoama\appdata\local\programs\python\python37\lib\site-packages\PyInstaller\loader\pyimod03_importers.py", line 623, in exec_module
    exec(bytecode, module.__dict__)
  File "cobra\io\sbml.py", line 41, in <module>
  File "c:\users\colpoama\appdata\local\programs\python\python37\lib\site-packages\PyInstaller\loader\pyimod03_importers.py", line 623, in exec_module
    exec(bytecode, module.__dict__)
  File "libsbml\__init__.py", line 24, in <module>
  File "libsbml\__init__.py", line 23, in swig_import_helper
  File "importlib\__init__.py", line 127, in import_module
ModuleNotFoundError: No module named '_libsbml'
[14724] Failed to execute script exePythonTest
<!-- gh-comment-id:641194433 --> @rcolpo commented on GitHub (Jun 9, 2020): Current Command: `pyinstaller --noconfirm --onedir --nowindowed "C:/phd/Eric/SBMLComp-master/Scripts/exePythonTest.py"` Output: ``` Running auto-py-to-exe v2.7.4 Building directory: C:\Users\colpoama\AppData\Local\Temp\tmp_xijgwf9 Provided command: pyinstaller --noconfirm --onedir --nowindowed "C:/phd/Eric/SBMLComp-master/Scripts/exePythonTest.py" Recursion Limit is set to 5000 Executing: pyinstaller --noconfirm --onedir --nowindowed C:/phd/Eric/SBMLComp-master/Scripts/exePythonTest.py --distpath C:\Users\colpoama\AppData\Local\Temp\tmp_xijgwf9\application --workpath C:\Users\colpoama\AppData\Local\Temp\tmp_xijgwf9\build --specpath C:\Users\colpoama\AppData\Local\Temp\tmp_xijgwf9 139942 INFO: PyInstaller: 3.6 139950 INFO: Python: 3.7.6 139956 INFO: Platform: Windows-10-10.0.18362-SP0 139972 INFO: wrote C:\Users\colpoama\AppData\Local\Temp\tmp_xijgwf9\exePythonTest.spec 139983 INFO: UPX is not available. 139994 INFO: Extending PYTHONPATH with paths ['C:\\phd\\Eric\\SBMLComp-master\\Scripts', 'C:\\Users\\colpoama\\AppData\\Local\\Temp\\tmp_xijgwf9'] 140001 INFO: checking Analysis 140009 INFO: Building Analysis because Analysis-00.toc is non existent 140014 INFO: Initializing module dependency graph... 140026 INFO: Caching module graph hooks... 140051 INFO: Analyzing base_library.zip ... 143365 INFO: Caching module dependency graph... 143451 INFO: running Analysis Analysis-00.toc 143477 INFO: Adding Microsoft.Windows.Common-Controls to dependent assemblies of final executable required by c:\users\colpoama\appdata\local\programs\python\python37\python.exe 143551 INFO: Analyzing C:\phd\Eric\SBMLComp-master\Scripts\exePythonTest.py 145649 INFO: Processing pre-find module path hook distutils 145658 INFO: distutils: retargeting to non-venv dir 'c:\\users\\colpoama\\appdata\\local\\programs\\python\\python37\\lib' 149752 INFO: Processing pre-find module path hook site 149763 INFO: site: retargeting to fake-dir 'c:\\users\\colpoama\\appdata\\local\\programs\\python\\python37\\lib\\site-packages\\PyInstaller\\fake-modules' 150847 INFO: Processing pre-safe import module hook setuptools.extern.six.moves 159006 INFO: Processing pre-safe import module hook six.moves 163760 INFO: Processing pre-safe import module hook urllib3.packages.six.moves 196661 INFO: Processing pre-safe import module hook win32com 205317 INFO: Processing module hooks... 205325 INFO: Loading module hook "hook-certifi.py"... 205339 INFO: Loading module hook "hook-distutils.py"... 205352 INFO: Loading module hook "hook-encodings.py"... 205540 INFO: Loading module hook "hook-gevent.py"... 205960 INFO: Determining a mapping of distributions to packages... 228000 WARNING: Unable to find package for requirement greenlet from package gevent. 228009 WARNING: Unable to find package for requirement zope.event from package gevent. 228020 WARNING: Unable to find package for requirement zope.interface from package gevent. 228028 INFO: Packages required by gevent: ['setuptools', 'cffi'] 229760 INFO: Loading module hook "hook-importlib_metadata.py"... 229773 INFO: Loading module hook "hook-IPython.py"... 230770 INFO: Excluding import 'gtk' 230786 INFO: Excluding import 'PyQt4' 230800 INFO: Removing import of PyQt4 from module IPython.external.qt_loaders 230808 INFO: Excluding import 'PyQt5' 230824 INFO: Removing import of PyQt5 from module IPython.external.qt_loaders 230832 INFO: Excluding import 'tkinter' 230847 INFO: Removing import of tkinter from module IPython.lib.clipboard 230857 INFO: Excluding import 'matplotlib' 230872 INFO: Removing import of matplotlib from module IPython.core.pylabtools 230879 INFO: Removing import of matplotlib._pylab_helpers from module IPython.core.pylabtools 230891 INFO: Removing import of matplotlib.pyplot from module IPython.core.pylabtools 230899 INFO: Removing import of matplotlib.figure from module IPython.core.pylabtools 230909 INFO: Removing import of matplotlib from module IPython.lib.latextools 230917 INFO: Removing import of matplotlib.mathtext from module IPython.lib.latextools 230927 INFO: Excluding import 'PySide' 230944 INFO: Removing import of PySide from module IPython.external.qt_loaders 230953 INFO: Loading module hook "hook-jedi.py"... 231219 INFO: Loading module hook "hook-jinja2.py"... 231251 INFO: Loading module hook "hook-jsonschema.py"... 231271 INFO: Loading module hook "hook-lib2to3.py"... 231297 INFO: Loading module hook "hook-matplotlib.backends.py"... 232343 INFO: Matplotlib backend "GTK3Agg": ignored cairo backend requires that pycairo>=1.11.0 or cairocffiis installed 232723 INFO: Matplotlib backend "GTK3Cairo": ignored cairo backend requires that pycairo>=1.11.0 or cairocffiis installed 233315 INFO: Matplotlib backend "MacOSX": ignored cannot import name '_macosx' from 'matplotlib.backends' (C:\Users\colpoama\AppData\Roaming\Python\Python37\site-packages\matplotlib\backends\__init__.py) 234315 INFO: Matplotlib backend "nbAgg": added 234853 INFO: Matplotlib backend "Qt4Agg": ignored Failed to import any qt binding 235307 INFO: Matplotlib backend "Qt4Cairo": ignored cairo backend requires that pycairo>=1.11.0 or cairocffiis installed 235854 INFO: Matplotlib backend "Qt5Agg": ignored Failed to import any qt binding 236303 INFO: Matplotlib backend "Qt5Cairo": ignored cairo backend requires that pycairo>=1.11.0 or cairocffiis installed 237022 INFO: Matplotlib backend "TkAgg": added 237612 INFO: Matplotlib backend "TkCairo": ignored cairo backend requires that pycairo>=1.11.0 or cairocffiis installed 238218 INFO: Matplotlib backend "WebAgg": added 238758 INFO: Matplotlib backend "WX": ignored No module named 'wx' 239197 INFO: Matplotlib backend "WXAgg": ignored No module named 'wx' 239576 INFO: Matplotlib backend "WXCairo": ignored No module named 'wx' 239963 INFO: Matplotlib backend "agg": added 240398 INFO: Matplotlib backend "cairo": ignored cairo backend requires that pycairo>=1.11.0 or cairocffiis installed 240872 INFO: Matplotlib backend "pdf": added 241410 INFO: Matplotlib backend "pgf": added 241783 INFO: Matplotlib backend "ps": added 242179 INFO: Matplotlib backend "svg": added 242708 INFO: Matplotlib backend "template": added 242980 INFO: Loading module hook "hook-matplotlib.py"... 243368 INFO: Loading module hook "hook-nbconvert.py"... 243415 INFO: Loading module hook "hook-nbformat.py"... 243442 INFO: Loading module hook "hook-notebook.py"... 244936 INFO: Loading module hook "hook-numpy.core.py"... 245039 INFO: Loading module hook "hook-numpy.py"... 245053 INFO: Loading module hook "hook-pandas.py"... 246259 INFO: Loading module hook "hook-pkg_resources.py"... 246944 INFO: Excluding import '__main__' 246960 INFO: Removing import of __main__ from module pkg_resources 246970 INFO: Loading module hook "hook-pycparser.py"... 246988 INFO: Loading module hook "hook-pydoc.py"... 247003 INFO: Loading module hook "hook-pygments.py"... 249125 INFO: Loading module hook "hook-pytest.py"... 250026 INFO: Loading module hook "hook-pythoncom.py"... 250491 INFO: Loading module hook "hook-pytz.py"... 250617 INFO: Loading module hook "hook-pywintypes.py"... 251079 INFO: Loading module hook "hook-scipy.io.matlab.py"... 251100 INFO: Loading module hook "hook-scipy.linalg.py"... 251121 INFO: Loading module hook "hook-scipy.py"... 251153 INFO: Loading module hook "hook-scipy.sparse.csgraph.py"... 251175 INFO: Loading module hook "hook-scipy.special._ellip_harm_2.py"... 251195 INFO: Loading module hook "hook-scipy.special._ufuncs.py"... 251214 INFO: Loading module hook "hook-setuptools.py"... 252012 INFO: Loading module hook "hook-sqlite3.py"... 252202 INFO: Loading module hook "hook-sysconfig.py"... 252218 INFO: Loading module hook "hook-win32com.py"... 252808 INFO: Loading module hook "hook-xml.dom.domreg.py"... 252824 INFO: Loading module hook "hook-xml.etree.cElementTree.py"... 252844 INFO: Loading module hook "hook-xml.py"... 252862 INFO: Loading module hook "hook-zmq.py"... 253766 INFO: Loading module hook "hook-_tkinter.py"... 254107 INFO: checking Tree 254125 INFO: Building Tree because Tree-00.toc is non existent 254143 INFO: Building Tree Tree-00.toc 254304 INFO: checking Tree 254318 INFO: Building Tree because Tree-01.toc is non existent 254340 INFO: Building Tree Tree-01.toc 254721 INFO: Looking for ctypes DLLs 254992 INFO: Analyzing run-time hooks ... 255049 INFO: Including run-time hook 'pyi_rth_win32comgenpy.py' 255076 INFO: Including run-time hook 'pyi_rth_multiprocessing.py' 255102 INFO: Including run-time hook 'pyi_rth__tkinter.py' 255127 INFO: Including run-time hook 'pyi_rth_traitlets.py' 255151 INFO: Including run-time hook 'pyi_rth_certifi.py' 255179 INFO: Including run-time hook 'pyi_rth_mplconfig.py' 255204 INFO: Including run-time hook 'pyi_rth_mpldata.py' 255228 INFO: Including run-time hook 'pyi_rth_pkgres.py' 255335 INFO: Looking for dynamic libraries 256609 WARNING: lib not found: libzmq.cp37-win_amd64.pyd dependency of C:\Users\colpoama\AppData\Roaming\Python\Python37\site-packages\zmq\backend\cython\context.cp37-win_amd64.pyd 256633 WARNING: lib not found: libzmq.cp37-win_amd64.pyd dependency of C:\Users\colpoama\AppData\Roaming\Python\Python37\site-packages\zmq\backend\cython\utils.cp37-win_amd64.pyd 256661 WARNING: lib not found: libzmq.cp37-win_amd64.pyd dependency of C:\Users\colpoama\AppData\Roaming\Python\Python37\site-packages\zmq\backend\cython\message.cp37-win_amd64.pyd 256685 WARNING: lib not found: libzmq.cp37-win_amd64.pyd dependency of C:\Users\colpoama\AppData\Roaming\Python\Python37\site-packages\zmq\backend\cython\_device.cp37-win_amd64.pyd 256711 WARNING: lib not found: libzmq.cp37-win_amd64.pyd dependency of C:\Users\colpoama\AppData\Roaming\Python\Python37\site-packages\zmq\backend\cython\_proxy_steerable.cp37-win_amd64.pyd 256737 WARNING: lib not found: libzmq.cp37-win_amd64.pyd dependency of C:\Users\colpoama\AppData\Roaming\Python\Python37\site-packages\zmq\backend\cython\socket.cp37-win_amd64.pyd 256763 WARNING: lib not found: libzmq.cp37-win_amd64.pyd dependency of C:\Users\colpoama\AppData\Roaming\Python\Python37\site-packages\zmq\backend\cython\error.cp37-win_amd64.pyd 256795 WARNING: lib not found: libzmq.cp37-win_amd64.pyd dependency of C:\Users\colpoama\AppData\Roaming\Python\Python37\site-packages\zmq\backend\cython\_version.cp37-win_amd64.pyd 256825 WARNING: lib not found: libzmq.cp37-win_amd64.pyd dependency of C:\Users\colpoama\AppData\Roaming\Python\Python37\site-packages\zmq\backend\cython\_poll.cp37-win_amd64.pyd 258558 INFO: Looking for eggs 258573 INFO: Using Python library c:\users\colpoama\appdata\local\programs\python\python37\python37.dll 258595 INFO: Found binding redirects: [] 258673 INFO: Warnings written to C:\Users\colpoama\AppData\Local\Temp\tmp_xijgwf9\build\exePythonTest\warn-exePythonTest.txt 259380 INFO: Graph cross-reference written to C:\Users\colpoama\AppData\Local\Temp\tmp_xijgwf9\build\exePythonTest\xref-exePythonTest.html 259731 INFO: checking PYZ 259749 INFO: Building PYZ because PYZ-00.toc is non existent 259766 INFO: Building PYZ (ZlibArchive) C:\Users\colpoama\AppData\Local\Temp\tmp_xijgwf9\build\exePythonTest\PYZ-00.pyz 268190 INFO: Building PYZ (ZlibArchive) C:\Users\colpoama\AppData\Local\Temp\tmp_xijgwf9\build\exePythonTest\PYZ-00.pyz completed successfully. 268352 INFO: checking PKG 268369 INFO: Building PKG because PKG-00.toc is non existent 268390 INFO: Building PKG (CArchive) PKG-00.pkg 268490 INFO: Building PKG (CArchive) PKG-00.pkg completed successfully. 268510 INFO: Bootloader c:\users\colpoama\appdata\local\programs\python\python37\lib\site-packages\PyInstaller\bootloader\Windows-64bit\run.exe 268531 INFO: checking EXE 268552 INFO: Building EXE because EXE-00.toc is non existent 268572 INFO: Building EXE from EXE-00.toc 268596 INFO: Appending archive to EXE C:\Users\colpoama\AppData\Local\Temp\tmp_xijgwf9\build\exePythonTest\exePythonTest.exe 268662 INFO: Building EXE from EXE-00.toc completed successfully. 268689 INFO: checking COLLECT 268707 INFO: Building COLLECT because COLLECT-00.toc is non existent 268729 INFO: Building COLLECT COLLECT-00.toc 292586 INFO: Building COLLECT COLLECT-00.toc completed successfully. Moving project to: C:\Users\colpoama\AppData\Local\Programs\Python\Python37\Scripts\output Complete. ``` This is the complete error message I got when I try running the newly created executable file: ``` Traceback (most recent call last): File "libsbml\__init__.py", line 21, in swig_import_helper File "importlib\__init__.py", line 127, in import_module File "<frozen importlib._bootstrap>", line 1006, in _gcd_import File "<frozen importlib._bootstrap>", line 983, in _find_and_load File "<frozen importlib._bootstrap>", line 965, in _find_and_load_unlocked ModuleNotFoundError: No module named '_libsbml' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "exePythonTest.py", line 1, in <module> File "c:\users\colpoama\appdata\local\programs\python\python37\lib\site-packages\PyInstaller\loader\pyimod03_importers.py", line 623, in exec_module exec(bytecode, module.__dict__) File "cobra\__init__.py", line 40, in <module> File "c:\users\colpoama\appdata\local\programs\python\python37\lib\site-packages\PyInstaller\loader\pyimod03_importers.py", line 623, in exec_module exec(bytecode, module.__dict__) File "cobra\io\__init__.py", line 8, in <module> File "c:\users\colpoama\appdata\local\programs\python\python37\lib\site-packages\PyInstaller\loader\pyimod03_importers.py", line 623, in exec_module exec(bytecode, module.__dict__) File "cobra\io\sbml.py", line 41, in <module> File "c:\users\colpoama\appdata\local\programs\python\python37\lib\site-packages\PyInstaller\loader\pyimod03_importers.py", line 623, in exec_module exec(bytecode, module.__dict__) File "libsbml\__init__.py", line 24, in <module> File "libsbml\__init__.py", line 23, in swig_import_helper File "importlib\__init__.py", line 127, in import_module ModuleNotFoundError: No module named '_libsbml' [14724] Failed to execute script exePythonTest ```
Author
Owner

@brentvollebregt commented on GitHub (Jun 9, 2020):

Are you sure you added _libsbml to the hidden import field? That current command you have provided does not have it in there which hints that you didn't add it. (Or that field is broken)

<!-- gh-comment-id:641201283 --> @brentvollebregt commented on GitHub (Jun 9, 2020): Are you sure you added `_libsbml` to the hidden import field? That current command you have provided does not have it in there which hints that you didn't add it. (Or that field is broken)
Author
Owner

@rcolpo commented on GitHub (Jun 9, 2020):

Thank you for your reply.

I also tried the "Current Command"

pyinstaller --noconfirm --onedir --nowindowed --hiddenimport "libsbml" "C:/phd/Eric/SBMLComp-master/Scripts/exePythonTest3.py"

and

pyinstaller --noconfirm --onedir --nowindowed --hiddenimport "_libsbml" "C:/phd/Eric/SBMLComp-master/Scripts/exePythonTest2.py"

but got the same error in both scenarios (same error as in my previous message):
ModuleNotFoundError: No module named '_libsbml'

When I try
pyinstaller --noconfirm --onedir --nowindowed --hiddenimport "_libsbml" --hiddenimport "libsbml" "C:/phd/Eric/SBMLComp-master/Scripts/exePythonTest.py"
the "Converting..." step never ends and the executable file is not generated.

<!-- gh-comment-id:641297916 --> @rcolpo commented on GitHub (Jun 9, 2020): Thank you for your reply. I also tried the "Current Command" `pyinstaller --noconfirm --onedir --nowindowed --hiddenimport "libsbml" "C:/phd/Eric/SBMLComp-master/Scripts/exePythonTest3.py"` and `pyinstaller --noconfirm --onedir --nowindowed --hiddenimport "_libsbml" "C:/phd/Eric/SBMLComp-master/Scripts/exePythonTest2.py"` but got the same error in both scenarios (same error as in my previous message): `ModuleNotFoundError: No module named '_libsbml'` When I try `pyinstaller --noconfirm --onedir --nowindowed --hiddenimport "_libsbml" --hiddenimport "libsbml" "C:/phd/Eric/SBMLComp-master/Scripts/exePythonTest.py"` the "Converting..." step never ends and the executable file is not generated.
Author
Owner

@brentvollebregt commented on GitHub (Jun 10, 2020):

If you try to execute pyinstaller --noconfirm --onedir --nowindowed --hidden-import "_libsbml" "C:/phd/Eric/SBMLComp-master/Scripts/exePythonTest2.py" in cmd, will it output a working executable in the dist folder or at least give a different error?

It's interesting to see that --hiddenimport is now being used instead of --hidden-import.

<!-- gh-comment-id:641656366 --> @brentvollebregt commented on GitHub (Jun 10, 2020): If you try to execute `pyinstaller --noconfirm --onedir --nowindowed --hidden-import "_libsbml" "C:/phd/Eric/SBMLComp-master/Scripts/exePythonTest2.py"` in cmd, will it output a working executable in the dist folder or at least give a different error? It's interesting to see that `--hiddenimport` is now being used instead of `--hidden-import`.
Author
Owner

@rcolpo commented on GitHub (Jun 10, 2020):

Yes, the error changed.

I tried to make an executable file from two different python files:

import cobra
print(1)

and

import cobra
import _libsbml
print(1)

Using the commands
pyinstaller --noconfirm --onedir --nowindowed --hidden-import "_libsbml" "C:/phd/Eric/SBMLComp-master/Scripts/exePythonTest2.py"
and
pyinstaller --noconfirm --onedir --nowindowed "C:/phd/Eric/SBMLComp-master/Scripts/exePythonTest2.py"

and on the 4 attempts I got the same error:

.
.
.
Line 1750: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\site-packages\PyInstaller\depend\analysis.py", line 382, in _safe_import_module
Line 1751: module_basename, module_name, parent_package)
Line 1752: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\site-packages\PyInstaller\lib\modulegraph\modulegraph.py", line 2055, in _safe_import_module
Line 1753: module_name, file_handle, pathname, metadata)
Line 1754: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\site-packages\PyInstaller\lib\modulegraph\modulegraph.py", line 2159, in _load_module
Line 1755: self._scan_code(m, co, co_ast)
Line 1756: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\site-packages\PyInstaller\lib\modulegraph\modulegraph.py", line 2643, in _scan_code
Line 1757: self._process_imports(module)
Line 1758: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\site-packages\PyInstaller\lib\modulegraph\modulegraph.py", line 2842, in _process_imports
Line 1759: target_module = self._safe_import_hook(*import_info, **kwargs)[0]
Line 1760: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\site-packages\PyInstaller\lib\modulegraph\modulegraph.py", line 2298, in _safe_import_hook
Line 1761: target_attr_names=None, level=level, edge_attr=edge_attr)
Line 1762: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\site-packages\PyInstaller\lib\modulegraph\modulegraph.py", line 1482, in import_hook
Line 1763: target_module = self._load_tail(target_package, target_module_partname)
Line 1764: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\site-packages\PyInstaller\lib\modulegraph\modulegraph.py", line 1701, in _load_tail
Line 1765: submodule = self._safe_import_module(head, mname, submodule)
Line 1766: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\site-packages\PyInstaller\depend\analysis.py", line 382, in _safe_import_module
Line 1767: module_basename, module_name, parent_package)
Line 1768: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\site-packages\PyInstaller\lib\modulegraph\modulegraph.py", line 2055, in _safe_import_module
Line 1769: module_name, file_handle, pathname, metadata)
Line 1770: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\site-packages\PyInstaller\lib\modulegraph\modulegraph.py", line 2159, in _load_module
Line 1771: self._scan_code(m, co, co_ast)
Line 1772: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\site-packages\PyInstaller\lib\modulegraph\modulegraph.py", line 2631, in _scan_code
Line 1773: self._scan_ast(module, module_code_object_ast)
Line 1774: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\site-packages\PyInstaller\lib\modulegraph\modulegraph.py", line 2660, in _scan_ast
Line 1775: visitor.visit(module_code_object_ast)
Line 1776: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\ast.py", line 271, in visit
Line 1777: return visitor(node)
Line 1778: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\ast.py", line 279, in generic_visit
Line 1779: self.visit(item)
Line 1780: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\ast.py", line 271, in visit
Line 1781: return visitor(node)
Line 1782: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\site-packages\PyInstaller\lib\modulegraph\modulegraph.py", line 1036, in visit_FunctionDef
Line 1783: self.generic_visit(node)
Line 1784: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\ast.py", line 279, in generic_visit
Line 1785: self.visit(item)
Line 1786: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\ast.py", line 271, in visit
Line 1787: return visitor(node)
Line 1788: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\site-packages\PyInstaller\lib\modulegraph\modulegraph.py", line 1036, in visit_FunctionDef
Line 1789: self.generic_visit(node)
Line 1790: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\ast.py", line 279, in generic_visit
Line 1791: self.visit(item)
Line 1792: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\ast.py", line 271, in visit
Line 1793: return visitor(node)
Line 1794: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\site-packages\PyInstaller\lib\modulegraph\modulegraph.py", line 1036, in visit_FunctionDef
Line 1795: self.generic_visit(node)
Line 1796: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\ast.py", line 279, in generic_visit
Line 1797: self.visit(item)
Line 1798: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\ast.py", line 271, in visit
Line 1799: return visitor(node)
Line 1800: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\site-packages\PyInstaller\lib\modulegraph\modulegraph.py", line 1043, in visit_Try
Line 1801: self.generic_visit(node)
Line 1802: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\ast.py", line 279, in generic_visit
Line 1803: self.visit(item)
Line 1804: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\ast.py", line 271, in visit
Line 1805: return visitor(node)
Line 1806: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\ast.py", line 279, in generic_visit
Line 1807: self.visit(item)
Line 1808: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\ast.py", line 271, in visit
Line 1809: return visitor(node)
Line 1810: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\ast.py", line 281, in generic_visit
Line 1811: self.visit(value)
Line 1812: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\ast.py", line 271, in visit
Line 1813: return visitor(node)
Line 1814: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\ast.py", line 275, in generic_visit
Line 1815: for field, value in iter_fields(node):
Line 1816: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\ast.py", line 188, in iter_fields
Line 1817: yield field, getattr(node, field)
Line 1818: RecursionError: maximum recursion depth exceeded while calling a Python object
<!-- gh-comment-id:641926889 --> @rcolpo commented on GitHub (Jun 10, 2020): Yes, the error changed. I tried to make an executable file from two different python files: ``` import cobra print(1) ``` and ``` import cobra import _libsbml print(1) ``` Using the commands `pyinstaller --noconfirm --onedir --nowindowed --hidden-import "_libsbml" "C:/phd/Eric/SBMLComp-master/Scripts/exePythonTest2.py" ` and `pyinstaller --noconfirm --onedir --nowindowed "C:/phd/Eric/SBMLComp-master/Scripts/exePythonTest2.py"` and on the 4 attempts I got the same error: ``` . . . Line 1750: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\site-packages\PyInstaller\depend\analysis.py", line 382, in _safe_import_module Line 1751: module_basename, module_name, parent_package) Line 1752: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\site-packages\PyInstaller\lib\modulegraph\modulegraph.py", line 2055, in _safe_import_module Line 1753: module_name, file_handle, pathname, metadata) Line 1754: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\site-packages\PyInstaller\lib\modulegraph\modulegraph.py", line 2159, in _load_module Line 1755: self._scan_code(m, co, co_ast) Line 1756: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\site-packages\PyInstaller\lib\modulegraph\modulegraph.py", line 2643, in _scan_code Line 1757: self._process_imports(module) Line 1758: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\site-packages\PyInstaller\lib\modulegraph\modulegraph.py", line 2842, in _process_imports Line 1759: target_module = self._safe_import_hook(*import_info, **kwargs)[0] Line 1760: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\site-packages\PyInstaller\lib\modulegraph\modulegraph.py", line 2298, in _safe_import_hook Line 1761: target_attr_names=None, level=level, edge_attr=edge_attr) Line 1762: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\site-packages\PyInstaller\lib\modulegraph\modulegraph.py", line 1482, in import_hook Line 1763: target_module = self._load_tail(target_package, target_module_partname) Line 1764: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\site-packages\PyInstaller\lib\modulegraph\modulegraph.py", line 1701, in _load_tail Line 1765: submodule = self._safe_import_module(head, mname, submodule) Line 1766: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\site-packages\PyInstaller\depend\analysis.py", line 382, in _safe_import_module Line 1767: module_basename, module_name, parent_package) Line 1768: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\site-packages\PyInstaller\lib\modulegraph\modulegraph.py", line 2055, in _safe_import_module Line 1769: module_name, file_handle, pathname, metadata) Line 1770: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\site-packages\PyInstaller\lib\modulegraph\modulegraph.py", line 2159, in _load_module Line 1771: self._scan_code(m, co, co_ast) Line 1772: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\site-packages\PyInstaller\lib\modulegraph\modulegraph.py", line 2631, in _scan_code Line 1773: self._scan_ast(module, module_code_object_ast) Line 1774: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\site-packages\PyInstaller\lib\modulegraph\modulegraph.py", line 2660, in _scan_ast Line 1775: visitor.visit(module_code_object_ast) Line 1776: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\ast.py", line 271, in visit Line 1777: return visitor(node) Line 1778: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\ast.py", line 279, in generic_visit Line 1779: self.visit(item) Line 1780: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\ast.py", line 271, in visit Line 1781: return visitor(node) Line 1782: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\site-packages\PyInstaller\lib\modulegraph\modulegraph.py", line 1036, in visit_FunctionDef Line 1783: self.generic_visit(node) Line 1784: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\ast.py", line 279, in generic_visit Line 1785: self.visit(item) Line 1786: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\ast.py", line 271, in visit Line 1787: return visitor(node) Line 1788: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\site-packages\PyInstaller\lib\modulegraph\modulegraph.py", line 1036, in visit_FunctionDef Line 1789: self.generic_visit(node) Line 1790: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\ast.py", line 279, in generic_visit Line 1791: self.visit(item) Line 1792: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\ast.py", line 271, in visit Line 1793: return visitor(node) Line 1794: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\site-packages\PyInstaller\lib\modulegraph\modulegraph.py", line 1036, in visit_FunctionDef Line 1795: self.generic_visit(node) Line 1796: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\ast.py", line 279, in generic_visit Line 1797: self.visit(item) Line 1798: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\ast.py", line 271, in visit Line 1799: return visitor(node) Line 1800: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\site-packages\PyInstaller\lib\modulegraph\modulegraph.py", line 1043, in visit_Try Line 1801: self.generic_visit(node) Line 1802: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\ast.py", line 279, in generic_visit Line 1803: self.visit(item) Line 1804: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\ast.py", line 271, in visit Line 1805: return visitor(node) Line 1806: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\ast.py", line 279, in generic_visit Line 1807: self.visit(item) Line 1808: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\ast.py", line 271, in visit Line 1809: return visitor(node) Line 1810: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\ast.py", line 281, in generic_visit Line 1811: self.visit(value) Line 1812: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\ast.py", line 271, in visit Line 1813: return visitor(node) Line 1814: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\ast.py", line 275, in generic_visit Line 1815: for field, value in iter_fields(node): Line 1816: File "c:\users\colpoama\appdata\local\programs\python\python37\lib\ast.py", line 188, in iter_fields Line 1817: yield field, getattr(node, field) Line 1818: RecursionError: maximum recursion depth exceeded while calling a Python object ```
Author
Owner

@brentvollebregt commented on GitHub (Jun 10, 2020):

Are you using auto-py-to-exe to do this? If not, this issue is no longer associated with this tool.

I believe I added a fix for this problem quite a while ago in the tool which is applied automatically.

<!-- gh-comment-id:642208092 --> @brentvollebregt commented on GitHub (Jun 10, 2020): Are you using auto-py-to-exe to do this? If not, this issue is no longer associated with this tool. I believe I added a fix for this problem quite a while ago in the tool which is applied automatically.
Author
Owner

@rcolpo commented on GitHub (Jun 10, 2020):

I misunderstood your instruction. I'm very sorry.

I tried to create an executable file using the following Current Command:
pyinstaller --noconfirm --onedir --console --hidden-import "_libsbml" "C:/phd/Eric/SBMLComp-master/Scripts/exePythonTest2.py"

Trying to run the file created I got the error
ModuleNotFoundError: No module named 'pkg_resources.py2_warn'
The error changed!

Then I changed the Current Command to
pyinstaller --noconfirm --onedir --console --hidden-import "_libsbml" --hidden-import "pkg_resources.py2_warn" "C:/phd/Eric/SBMLComp-master/Scripts/exePythonTest2.py"

And got the error
ModuleNotFoundError: No module named '_libsbml'
which is the same error I got when I did not include "_libsbml" on the hidden-import field.

Maybe it could not handle two hidden-import parameters simultaneously?

<!-- gh-comment-id:642305940 --> @rcolpo commented on GitHub (Jun 10, 2020): I misunderstood your instruction. I'm very sorry. I tried to create an executable file using the following Current Command: `pyinstaller --noconfirm --onedir --console --hidden-import "_libsbml" "C:/phd/Eric/SBMLComp-master/Scripts/exePythonTest2.py"` Trying to run the file created I got the error `ModuleNotFoundError: No module named 'pkg_resources.py2_warn'` The error changed! Then I changed the Current Command to `pyinstaller --noconfirm --onedir --console --hidden-import "_libsbml" --hidden-import "pkg_resources.py2_warn" "C:/phd/Eric/SBMLComp-master/Scripts/exePythonTest2.py"` And got the error `ModuleNotFoundError: No module named '_libsbml'` which is the same error I got when I did not include "_libsbml" on the hidden-import field. Maybe it could not handle two hidden-import parameters simultaneously?
Author
Owner

@brentvollebregt commented on GitHub (Jun 11, 2020):

No need to be sorry; I'm just making sure that auto-py-to-exe is generating the correct command - using PyInstaller manually can help verify this.

From what I see above:

  • You adding --hidden-import "_libsbml" gave you the error ModuleNotFoundError: No module named 'pkg_resources.py2_warn'
  • But then when adding --hidden-import "_libsbml" --hidden-import "pkg_resources.py2_warn" you got the error ModuleNotFoundError: No module named '_libsbml'.

This seems like a PyInstaller issue. If you select all by --debug in the advanced tab (or use --debug all), are these modules mentioned in the output when bundling the script?

<!-- gh-comment-id:642547065 --> @brentvollebregt commented on GitHub (Jun 11, 2020): No need to be sorry; I'm just making sure that auto-py-to-exe is generating the correct command - using PyInstaller manually can help verify this. From what I see above: - You adding `--hidden-import "_libsbml"` gave you the error `ModuleNotFoundError: No module named 'pkg_resources.py2_warn'` - But then when adding `--hidden-import "_libsbml" --hidden-import "pkg_resources.py2_warn"` you got the error `ModuleNotFoundError: No module named '_libsbml'`. This seems like a PyInstaller issue. If you select `all` by `--debug` in the advanced tab (or use `--debug all`), are these modules mentioned in the output when bundling the script?
Author
Owner

@rcolpo commented on GitHub (Jun 11, 2020):

When I use --debug "all" the Current Command becomes
pyinstaller --noconfirm --onedir --console --debug "all" --hidden-import "_libsbml" --hidden-import "pkg_resources.py2_warn" "C:/phd/Eric/SBMLComp-master/Scripts/exePythonTest2.py"
and any executable file is generated.
The modules included on the --hidden-import field ("_libsbml" and "pkg_resources.py2_warn") don't have any particular highlight on the output section, which is shown below:

Running auto-py-to-exe v2.7.4
Building directory: C:\Users\colpoama\AppData\Local\Temp\tmp1v4nfdz2
Provided command: pyinstaller --noconfirm --onedir --console --debug "all" --hidden-import "_libsbml" --hidden-import "pkg_resources.py2_warn"  "C:/phd/Eric/SBMLComp-master/Scripts/exePythonTest2.py"
Recursion Limit is set to 5000
Executing: pyinstaller --noconfirm --onedir --console --debug all --hidden-import _libsbml --hidden-import pkg_resources.py2_warn C:/phd/Eric/SBMLComp-master/Scripts/exePythonTest2.py --distpath C:\Users\colpoama\AppData\Local\Temp\tmp1v4nfdz2\application --workpath C:\Users\colpoama\AppData\Local\Temp\tmp1v4nfdz2\build --specpath C:\Users\colpoama\AppData\Local\Temp\tmp1v4nfdz2

596438 INFO: PyInstaller: 3.6
596444 INFO: Python: 3.7.6
596446 INFO: Platform: Windows-10-10.0.18362-SP0
596450 INFO: wrote C:\Users\colpoama\AppData\Local\Temp\tmp1v4nfdz2\exePythonTest2.spec
596457 INFO: UPX is not available.
596464 INFO: Extending PYTHONPATH with paths
['C:\\phd\\Eric\\SBMLComp-master\\Scripts',
 'C:\\Users\\colpoama\\AppData\\Local\\Temp\\tmp1v4nfdz2']
596467 INFO: checking Analysis
596473 INFO: Building Analysis because Analysis-02.toc is non existent
596479 INFO: Reusing cached module dependency graph...
596665 INFO: Caching module graph hooks...
596800 INFO: running Analysis Analysis-02.toc
596807 INFO: Adding Microsoft.Windows.Common-Controls to dependent assemblies of final executable
  required by c:\users\colpoama\appdata\local\programs\python\python37\python.exe
596935 INFO: Analyzing C:\phd\Eric\SBMLComp-master\Scripts\exePythonTest2.py
601556 INFO: Processing pre-find module path hook   distutils
601562 INFO: distutils: retargeting to non-venv dir 'c:\\users\\colpoama\\appdata\\local\\programs\\python\\python37\\lib'
603990 INFO: Processing pre-safe import module hook   setuptools.extern.six.moves
605025 INFO: Processing pre-find module path hook   site
605031 INFO: site: retargeting to fake-dir 'c:\\users\\colpoama\\appdata\\local\\programs\\python\\python37\\lib\\site-packages\\PyInstaller\\fake-modules'
613220 INFO: Processing pre-safe import module hook   six.moves
621065 INFO: Processing pre-safe import module hook   urllib3.packages.six.moves
666556 INFO: Processing pre-safe import module hook   win32com
677247 INFO: Analyzing hidden import 'pkg_resources.py2_warn'
677252 INFO: Processing module hooks...
677256 INFO: Loading module hook "hook-certifi.py"...
677266 INFO: Loading module hook "hook-distutils.py"...
677272 INFO: Loading module hook "hook-encodings.py"...
677492 INFO: Loading module hook "hook-importlib_metadata.py"...
677498 INFO: Loading module hook "hook-IPython.py"...
677538 INFO: Excluding import 'tkinter'
677551 INFO:   Removing import of tkinter from module IPython.lib.clipboard
677559 INFO: Excluding import 'PyQt5'
677572 INFO:   Removing import of PyQt5 from module IPython.external.qt_loaders
677578 INFO: Excluding import 'PyQt4'
677593 INFO:   Removing import of PyQt4 from module IPython.external.qt_loaders
677598 INFO: Excluding import 'gtk'
677617 INFO: Excluding import 'PySide'
677633 INFO:   Removing import of PySide from module IPython.external.qt_loaders
677641 INFO: Excluding import 'matplotlib'
677662 INFO:   Removing import of matplotlib.pyplot from module IPython.core.pylabtools
677670 INFO:   Removing import of matplotlib._pylab_helpers from module IPython.core.pylabtools
677677 INFO:   Removing import of matplotlib.figure from module IPython.core.pylabtools
677684 INFO:   Removing import of matplotlib from module IPython.core.pylabtools
677696 INFO:   Removing import of matplotlib.mathtext from module IPython.lib.latextools
677701 INFO:   Removing import of matplotlib from module IPython.lib.latextools
677710 INFO: Loading module hook "hook-jedi.py"...
677962 INFO: Loading module hook "hook-jinja2.py"...
678003 INFO: Loading module hook "hook-jsonschema.py"...
678016 INFO: Loading module hook "hook-lib2to3.py"...
678036 INFO: Loading module hook "hook-matplotlib.backends.py"...
679283 INFO:   Matplotlib backend "GTK3Agg": ignored
    cairo backend requires that pycairo>=1.11.0 or cairocffiis installed
679910 INFO:   Matplotlib backend "GTK3Cairo": ignored
    cairo backend requires that pycairo>=1.11.0 or cairocffiis installed
680736 INFO:   Matplotlib backend "MacOSX": ignored
    cannot import name '_macosx' from 'matplotlib.backends' (C:\Users\colpoama\AppData\Roaming\Python\Python37\site-packages\matplotlib\backends\__init__.py)
682257 INFO:   Matplotlib backend "nbAgg": added
682944 INFO:   Matplotlib backend "Qt4Agg": ignored
    Failed to import any qt binding
683460 INFO:   Matplotlib backend "Qt4Cairo": ignored
    cairo backend requires that pycairo>=1.11.0 or cairocffiis installed
684001 INFO:   Matplotlib backend "Qt5Agg": ignored
    Failed to import any qt binding
684557 INFO:   Matplotlib backend "Qt5Cairo": ignored
    cairo backend requires that pycairo>=1.11.0 or cairocffiis installed
685284 INFO:   Matplotlib backend "TkAgg": added
686141 INFO:   Matplotlib backend "TkCairo": ignored
    cairo backend requires that pycairo>=1.11.0 or cairocffiis installed
686996 INFO:   Matplotlib backend "WebAgg": added
687816 INFO:   Matplotlib backend "WX": ignored
    No module named 'wx'
688463 INFO:   Matplotlib backend "WXAgg": ignored
    No module named 'wx'
689056 INFO:   Matplotlib backend "WXCairo": ignored
    No module named 'wx'
689602 INFO:   Matplotlib backend "agg": added
690097 INFO:   Matplotlib backend "cairo": ignored
    cairo backend requires that pycairo>=1.11.0 or cairocffiis installed
690840 INFO:   Matplotlib backend "pdf": added
691657 INFO:   Matplotlib backend "pgf": added
692255 INFO:   Matplotlib backend "ps": added
692911 INFO:   Matplotlib backend "svg": added
693672 INFO:   Matplotlib backend "template": added
694214 INFO: Loading module hook "hook-matplotlib.py"...
694699 INFO: Loading module hook "hook-nbconvert.py"...
694734 INFO: Loading module hook "hook-nbformat.py"...
694752 INFO: Loading module hook "hook-notebook.py"...
696592 INFO: Loading module hook "hook-numpy.core.py"...
696601 INFO: Loading module hook "hook-numpy.py"...
696609 INFO: Loading module hook "hook-pandas.py"...
697555 INFO: Loading module hook "hook-pkg_resources.py"...
698847 INFO: Excluding import '__main__'
698864 INFO:   Removing import of __main__ from module pkg_resources
698875 INFO: Loading module hook "hook-pycparser.py"...
698901 INFO: Loading module hook "hook-pydoc.py"...
698912 INFO: Loading module hook "hook-pygments.py"...
701943 INFO: Loading module hook "hook-pytest.py"...
703238 INFO: Loading module hook "hook-pythoncom.py"...
703883 INFO: Loading module hook "hook-pytz.py"...
703986 INFO: Loading module hook "hook-pywintypes.py"...
704579 INFO: Loading module hook "hook-scipy.io.matlab.py"...
704587 INFO: Loading module hook "hook-scipy.linalg.py"...
704597 INFO: Loading module hook "hook-scipy.py"...
704617 INFO: Loading module hook "hook-scipy.sparse.csgraph.py"...
704631 INFO: Loading module hook "hook-scipy.special._ellip_harm_2.py"...
704643 INFO: Loading module hook "hook-scipy.special._ufuncs.py"...
704652 INFO: Loading module hook "hook-setuptools.py"...
705708 INFO: Loading module hook "hook-sqlite3.py"...
705937 INFO: Loading module hook "hook-sysconfig.py"...
705945 INFO: Loading module hook "hook-win32com.py"...
706576 INFO: Loading module hook "hook-xml.dom.domreg.py"...
706586 INFO: Loading module hook "hook-xml.etree.cElementTree.py"...
706598 INFO: Loading module hook "hook-xml.py"...
706615 INFO: Loading module hook "hook-zmq.py"...
709165 INFO: Loading module hook "hook-_tkinter.py"...
709540 INFO: checking Tree
709546 INFO: Building Tree because Tree-04.toc is non existent
709559 INFO: Building Tree Tree-04.toc
709658 INFO: checking Tree
709667 INFO: Building Tree because Tree-05.toc is non existent
709678 INFO: Building Tree Tree-05.toc
709709 INFO: Loading module hook "hook-gevent.py"...
710227 WARNING: Unable to find package for requirement zope.interface from package gevent.
710234 WARNING: Unable to find package for requirement greenlet from package gevent.
710245 WARNING: Unable to find package for requirement zope.event from package gevent.
710258 INFO: Packages required by gevent:
['cffi', 'setuptools']
712304 INFO: Looking for ctypes DLLs
712561 INFO: Analyzing run-time hooks ...
712604 INFO: Including run-time hook 'pyi_rth_pkgres.py'
712622 INFO: Including run-time hook 'pyi_rth_win32comgenpy.py'
712632 INFO: Including run-time hook 'pyi_rth_multiprocessing.py'
712644 INFO: Including run-time hook 'pyi_rth__tkinter.py'
712656 INFO: Including run-time hook 'pyi_rth_traitlets.py'
712668 INFO: Including run-time hook 'pyi_rth_certifi.py'
712683 INFO: Including run-time hook 'pyi_rth_mplconfig.py'
712699 INFO: Including run-time hook 'pyi_rth_mpldata.py'
712800 INFO: Looking for dynamic libraries
715039 WARNING: lib not found: libzmq.cp37-win_amd64.pyd dependency of C:\Users\colpoama\AppData\Roaming\Python\Python37\site-packages\zmq\backend\cython\utils.cp37-win_amd64.pyd
715061 WARNING: lib not found: libzmq.cp37-win_amd64.pyd dependency of C:\Users\colpoama\AppData\Roaming\Python\Python37\site-packages\zmq\backend\cython\message.cp37-win_amd64.pyd
715089 WARNING: lib not found: libzmq.cp37-win_amd64.pyd dependency of C:\Users\colpoama\AppData\Roaming\Python\Python37\site-packages\zmq\backend\cython\context.cp37-win_amd64.pyd
715111 WARNING: lib not found: libzmq.cp37-win_amd64.pyd dependency of C:\Users\colpoama\AppData\Roaming\Python\Python37\site-packages\zmq\backend\cython\_device.cp37-win_amd64.pyd
715132 WARNING: lib not found: libzmq.cp37-win_amd64.pyd dependency of C:\Users\colpoama\AppData\Roaming\Python\Python37\site-packages\zmq\backend\cython\socket.cp37-win_amd64.pyd
715157 WARNING: lib not found: libzmq.cp37-win_amd64.pyd dependency of C:\Users\colpoama\AppData\Roaming\Python\Python37\site-packages\zmq\backend\cython\_proxy_steerable.cp37-win_amd64.pyd
715178 WARNING: lib not found: libzmq.cp37-win_amd64.pyd dependency of C:\Users\colpoama\AppData\Roaming\Python\Python37\site-packages\zmq\backend\cython\_poll.cp37-win_amd64.pyd
715204 WARNING: lib not found: libzmq.cp37-win_amd64.pyd dependency of C:\Users\colpoama\AppData\Roaming\Python\Python37\site-packages\zmq\backend\cython\error.cp37-win_amd64.pyd
715225 WARNING: lib not found: libzmq.cp37-win_amd64.pyd dependency of C:\Users\colpoama\AppData\Roaming\Python\Python37\site-packages\zmq\backend\cython\_version.cp37-win_amd64.pyd
716655 INFO: Looking for eggs
716663 INFO: Using Python library c:\users\colpoama\appdata\local\programs\python\python37\python37.dll
716679 INFO: Found binding redirects: 
[]
An error occurred while packaging
Traceback (most recent call last):
  File "c:\users\colpoama\appdata\local\programs\python\python37\lib\site-packages\auto_py_to_exe\packaging.py", line 131, in package
    run_pyinstaller()
  File "c:\users\colpoama\appdata\local\programs\python\python37\lib\site-packages\PyInstaller\__main__.py", line 114, in run
    run_build(pyi_config, spec_file, **vars(args))
  File "c:\users\colpoama\appdata\local\programs\python\python37\lib\site-packages\PyInstaller\__main__.py", line 65, in run_build
    PyInstaller.building.build_main.main(pyi_config, spec_file, **kwargs)
  File "c:\users\colpoama\appdata\local\programs\python\python37\lib\site-packages\PyInstaller\building\build_main.py", line 734, in main
    build(specfile, kw.get('distpath'), kw.get('workpath'), kw.get('clean_build'))
  File "c:\users\colpoama\appdata\local\programs\python\python37\lib\site-packages\PyInstaller\building\build_main.py", line 681, in build
    exec(code, spec_namespace)
  File "C:\Users\colpoama\AppData\Local\Temp\tmp1v4nfdz2\exePythonTest2.spec", line 17, in <module>
    noarchive=True)
  File "c:\users\colpoama\appdata\local\programs\python\python37\lib\site-packages\PyInstaller\building\build_main.py", line 244, in __init__
    self.__postinit__()
  File "c:\users\colpoama\appdata\local\programs\python\python37\lib\site-packages\PyInstaller\building\datastruct.py", line 160, in __postinit__
    self.assemble()
  File "c:\users\colpoama\appdata\local\programs\python\python37\lib\site-packages\PyInstaller\building\build_main.py", line 500, in assemble
    for name, path, typecode in compile_py_files(new_toc, CONF['workpath']):
  File "c:\users\colpoama\appdata\local\programs\python\python37\lib\site-packages\PyInstaller\utils\misc.py", line 152, in compile_py_files
    with open(obj_fnm, 'rb') as fh:
FileNotFoundError: [Errno 2] No such file or directory: '-'

Project output will not be moved to output folder
Complete.

If I have no modules on the --hidden-import field, I still have the same error.
When I don't include --debug "all", the executable file is generated but I have the error mentioned before.
When I remove the line import cobra, making my code is simply print(1), I have a working executable file.

<!-- gh-comment-id:642757398 --> @rcolpo commented on GitHub (Jun 11, 2020): When I use `--debug "all"` the Current Command becomes `pyinstaller --noconfirm --onedir --console --debug "all" --hidden-import "_libsbml" --hidden-import "pkg_resources.py2_warn" "C:/phd/Eric/SBMLComp-master/Scripts/exePythonTest2.py"` and any executable file is generated. The modules included on the --hidden-import field ("_libsbml" and "pkg_resources.py2_warn") don't have any particular highlight on the output section, which is shown below: ``` Running auto-py-to-exe v2.7.4 Building directory: C:\Users\colpoama\AppData\Local\Temp\tmp1v4nfdz2 Provided command: pyinstaller --noconfirm --onedir --console --debug "all" --hidden-import "_libsbml" --hidden-import "pkg_resources.py2_warn" "C:/phd/Eric/SBMLComp-master/Scripts/exePythonTest2.py" Recursion Limit is set to 5000 Executing: pyinstaller --noconfirm --onedir --console --debug all --hidden-import _libsbml --hidden-import pkg_resources.py2_warn C:/phd/Eric/SBMLComp-master/Scripts/exePythonTest2.py --distpath C:\Users\colpoama\AppData\Local\Temp\tmp1v4nfdz2\application --workpath C:\Users\colpoama\AppData\Local\Temp\tmp1v4nfdz2\build --specpath C:\Users\colpoama\AppData\Local\Temp\tmp1v4nfdz2 596438 INFO: PyInstaller: 3.6 596444 INFO: Python: 3.7.6 596446 INFO: Platform: Windows-10-10.0.18362-SP0 596450 INFO: wrote C:\Users\colpoama\AppData\Local\Temp\tmp1v4nfdz2\exePythonTest2.spec 596457 INFO: UPX is not available. 596464 INFO: Extending PYTHONPATH with paths ['C:\\phd\\Eric\\SBMLComp-master\\Scripts', 'C:\\Users\\colpoama\\AppData\\Local\\Temp\\tmp1v4nfdz2'] 596467 INFO: checking Analysis 596473 INFO: Building Analysis because Analysis-02.toc is non existent 596479 INFO: Reusing cached module dependency graph... 596665 INFO: Caching module graph hooks... 596800 INFO: running Analysis Analysis-02.toc 596807 INFO: Adding Microsoft.Windows.Common-Controls to dependent assemblies of final executable required by c:\users\colpoama\appdata\local\programs\python\python37\python.exe 596935 INFO: Analyzing C:\phd\Eric\SBMLComp-master\Scripts\exePythonTest2.py 601556 INFO: Processing pre-find module path hook distutils 601562 INFO: distutils: retargeting to non-venv dir 'c:\\users\\colpoama\\appdata\\local\\programs\\python\\python37\\lib' 603990 INFO: Processing pre-safe import module hook setuptools.extern.six.moves 605025 INFO: Processing pre-find module path hook site 605031 INFO: site: retargeting to fake-dir 'c:\\users\\colpoama\\appdata\\local\\programs\\python\\python37\\lib\\site-packages\\PyInstaller\\fake-modules' 613220 INFO: Processing pre-safe import module hook six.moves 621065 INFO: Processing pre-safe import module hook urllib3.packages.six.moves 666556 INFO: Processing pre-safe import module hook win32com 677247 INFO: Analyzing hidden import 'pkg_resources.py2_warn' 677252 INFO: Processing module hooks... 677256 INFO: Loading module hook "hook-certifi.py"... 677266 INFO: Loading module hook "hook-distutils.py"... 677272 INFO: Loading module hook "hook-encodings.py"... 677492 INFO: Loading module hook "hook-importlib_metadata.py"... 677498 INFO: Loading module hook "hook-IPython.py"... 677538 INFO: Excluding import 'tkinter' 677551 INFO: Removing import of tkinter from module IPython.lib.clipboard 677559 INFO: Excluding import 'PyQt5' 677572 INFO: Removing import of PyQt5 from module IPython.external.qt_loaders 677578 INFO: Excluding import 'PyQt4' 677593 INFO: Removing import of PyQt4 from module IPython.external.qt_loaders 677598 INFO: Excluding import 'gtk' 677617 INFO: Excluding import 'PySide' 677633 INFO: Removing import of PySide from module IPython.external.qt_loaders 677641 INFO: Excluding import 'matplotlib' 677662 INFO: Removing import of matplotlib.pyplot from module IPython.core.pylabtools 677670 INFO: Removing import of matplotlib._pylab_helpers from module IPython.core.pylabtools 677677 INFO: Removing import of matplotlib.figure from module IPython.core.pylabtools 677684 INFO: Removing import of matplotlib from module IPython.core.pylabtools 677696 INFO: Removing import of matplotlib.mathtext from module IPython.lib.latextools 677701 INFO: Removing import of matplotlib from module IPython.lib.latextools 677710 INFO: Loading module hook "hook-jedi.py"... 677962 INFO: Loading module hook "hook-jinja2.py"... 678003 INFO: Loading module hook "hook-jsonschema.py"... 678016 INFO: Loading module hook "hook-lib2to3.py"... 678036 INFO: Loading module hook "hook-matplotlib.backends.py"... 679283 INFO: Matplotlib backend "GTK3Agg": ignored cairo backend requires that pycairo>=1.11.0 or cairocffiis installed 679910 INFO: Matplotlib backend "GTK3Cairo": ignored cairo backend requires that pycairo>=1.11.0 or cairocffiis installed 680736 INFO: Matplotlib backend "MacOSX": ignored cannot import name '_macosx' from 'matplotlib.backends' (C:\Users\colpoama\AppData\Roaming\Python\Python37\site-packages\matplotlib\backends\__init__.py) 682257 INFO: Matplotlib backend "nbAgg": added 682944 INFO: Matplotlib backend "Qt4Agg": ignored Failed to import any qt binding 683460 INFO: Matplotlib backend "Qt4Cairo": ignored cairo backend requires that pycairo>=1.11.0 or cairocffiis installed 684001 INFO: Matplotlib backend "Qt5Agg": ignored Failed to import any qt binding 684557 INFO: Matplotlib backend "Qt5Cairo": ignored cairo backend requires that pycairo>=1.11.0 or cairocffiis installed 685284 INFO: Matplotlib backend "TkAgg": added 686141 INFO: Matplotlib backend "TkCairo": ignored cairo backend requires that pycairo>=1.11.0 or cairocffiis installed 686996 INFO: Matplotlib backend "WebAgg": added 687816 INFO: Matplotlib backend "WX": ignored No module named 'wx' 688463 INFO: Matplotlib backend "WXAgg": ignored No module named 'wx' 689056 INFO: Matplotlib backend "WXCairo": ignored No module named 'wx' 689602 INFO: Matplotlib backend "agg": added 690097 INFO: Matplotlib backend "cairo": ignored cairo backend requires that pycairo>=1.11.0 or cairocffiis installed 690840 INFO: Matplotlib backend "pdf": added 691657 INFO: Matplotlib backend "pgf": added 692255 INFO: Matplotlib backend "ps": added 692911 INFO: Matplotlib backend "svg": added 693672 INFO: Matplotlib backend "template": added 694214 INFO: Loading module hook "hook-matplotlib.py"... 694699 INFO: Loading module hook "hook-nbconvert.py"... 694734 INFO: Loading module hook "hook-nbformat.py"... 694752 INFO: Loading module hook "hook-notebook.py"... 696592 INFO: Loading module hook "hook-numpy.core.py"... 696601 INFO: Loading module hook "hook-numpy.py"... 696609 INFO: Loading module hook "hook-pandas.py"... 697555 INFO: Loading module hook "hook-pkg_resources.py"... 698847 INFO: Excluding import '__main__' 698864 INFO: Removing import of __main__ from module pkg_resources 698875 INFO: Loading module hook "hook-pycparser.py"... 698901 INFO: Loading module hook "hook-pydoc.py"... 698912 INFO: Loading module hook "hook-pygments.py"... 701943 INFO: Loading module hook "hook-pytest.py"... 703238 INFO: Loading module hook "hook-pythoncom.py"... 703883 INFO: Loading module hook "hook-pytz.py"... 703986 INFO: Loading module hook "hook-pywintypes.py"... 704579 INFO: Loading module hook "hook-scipy.io.matlab.py"... 704587 INFO: Loading module hook "hook-scipy.linalg.py"... 704597 INFO: Loading module hook "hook-scipy.py"... 704617 INFO: Loading module hook "hook-scipy.sparse.csgraph.py"... 704631 INFO: Loading module hook "hook-scipy.special._ellip_harm_2.py"... 704643 INFO: Loading module hook "hook-scipy.special._ufuncs.py"... 704652 INFO: Loading module hook "hook-setuptools.py"... 705708 INFO: Loading module hook "hook-sqlite3.py"... 705937 INFO: Loading module hook "hook-sysconfig.py"... 705945 INFO: Loading module hook "hook-win32com.py"... 706576 INFO: Loading module hook "hook-xml.dom.domreg.py"... 706586 INFO: Loading module hook "hook-xml.etree.cElementTree.py"... 706598 INFO: Loading module hook "hook-xml.py"... 706615 INFO: Loading module hook "hook-zmq.py"... 709165 INFO: Loading module hook "hook-_tkinter.py"... 709540 INFO: checking Tree 709546 INFO: Building Tree because Tree-04.toc is non existent 709559 INFO: Building Tree Tree-04.toc 709658 INFO: checking Tree 709667 INFO: Building Tree because Tree-05.toc is non existent 709678 INFO: Building Tree Tree-05.toc 709709 INFO: Loading module hook "hook-gevent.py"... 710227 WARNING: Unable to find package for requirement zope.interface from package gevent. 710234 WARNING: Unable to find package for requirement greenlet from package gevent. 710245 WARNING: Unable to find package for requirement zope.event from package gevent. 710258 INFO: Packages required by gevent: ['cffi', 'setuptools'] 712304 INFO: Looking for ctypes DLLs 712561 INFO: Analyzing run-time hooks ... 712604 INFO: Including run-time hook 'pyi_rth_pkgres.py' 712622 INFO: Including run-time hook 'pyi_rth_win32comgenpy.py' 712632 INFO: Including run-time hook 'pyi_rth_multiprocessing.py' 712644 INFO: Including run-time hook 'pyi_rth__tkinter.py' 712656 INFO: Including run-time hook 'pyi_rth_traitlets.py' 712668 INFO: Including run-time hook 'pyi_rth_certifi.py' 712683 INFO: Including run-time hook 'pyi_rth_mplconfig.py' 712699 INFO: Including run-time hook 'pyi_rth_mpldata.py' 712800 INFO: Looking for dynamic libraries 715039 WARNING: lib not found: libzmq.cp37-win_amd64.pyd dependency of C:\Users\colpoama\AppData\Roaming\Python\Python37\site-packages\zmq\backend\cython\utils.cp37-win_amd64.pyd 715061 WARNING: lib not found: libzmq.cp37-win_amd64.pyd dependency of C:\Users\colpoama\AppData\Roaming\Python\Python37\site-packages\zmq\backend\cython\message.cp37-win_amd64.pyd 715089 WARNING: lib not found: libzmq.cp37-win_amd64.pyd dependency of C:\Users\colpoama\AppData\Roaming\Python\Python37\site-packages\zmq\backend\cython\context.cp37-win_amd64.pyd 715111 WARNING: lib not found: libzmq.cp37-win_amd64.pyd dependency of C:\Users\colpoama\AppData\Roaming\Python\Python37\site-packages\zmq\backend\cython\_device.cp37-win_amd64.pyd 715132 WARNING: lib not found: libzmq.cp37-win_amd64.pyd dependency of C:\Users\colpoama\AppData\Roaming\Python\Python37\site-packages\zmq\backend\cython\socket.cp37-win_amd64.pyd 715157 WARNING: lib not found: libzmq.cp37-win_amd64.pyd dependency of C:\Users\colpoama\AppData\Roaming\Python\Python37\site-packages\zmq\backend\cython\_proxy_steerable.cp37-win_amd64.pyd 715178 WARNING: lib not found: libzmq.cp37-win_amd64.pyd dependency of C:\Users\colpoama\AppData\Roaming\Python\Python37\site-packages\zmq\backend\cython\_poll.cp37-win_amd64.pyd 715204 WARNING: lib not found: libzmq.cp37-win_amd64.pyd dependency of C:\Users\colpoama\AppData\Roaming\Python\Python37\site-packages\zmq\backend\cython\error.cp37-win_amd64.pyd 715225 WARNING: lib not found: libzmq.cp37-win_amd64.pyd dependency of C:\Users\colpoama\AppData\Roaming\Python\Python37\site-packages\zmq\backend\cython\_version.cp37-win_amd64.pyd 716655 INFO: Looking for eggs 716663 INFO: Using Python library c:\users\colpoama\appdata\local\programs\python\python37\python37.dll 716679 INFO: Found binding redirects: [] An error occurred while packaging Traceback (most recent call last): File "c:\users\colpoama\appdata\local\programs\python\python37\lib\site-packages\auto_py_to_exe\packaging.py", line 131, in package run_pyinstaller() File "c:\users\colpoama\appdata\local\programs\python\python37\lib\site-packages\PyInstaller\__main__.py", line 114, in run run_build(pyi_config, spec_file, **vars(args)) File "c:\users\colpoama\appdata\local\programs\python\python37\lib\site-packages\PyInstaller\__main__.py", line 65, in run_build PyInstaller.building.build_main.main(pyi_config, spec_file, **kwargs) File "c:\users\colpoama\appdata\local\programs\python\python37\lib\site-packages\PyInstaller\building\build_main.py", line 734, in main build(specfile, kw.get('distpath'), kw.get('workpath'), kw.get('clean_build')) File "c:\users\colpoama\appdata\local\programs\python\python37\lib\site-packages\PyInstaller\building\build_main.py", line 681, in build exec(code, spec_namespace) File "C:\Users\colpoama\AppData\Local\Temp\tmp1v4nfdz2\exePythonTest2.spec", line 17, in <module> noarchive=True) File "c:\users\colpoama\appdata\local\programs\python\python37\lib\site-packages\PyInstaller\building\build_main.py", line 244, in __init__ self.__postinit__() File "c:\users\colpoama\appdata\local\programs\python\python37\lib\site-packages\PyInstaller\building\datastruct.py", line 160, in __postinit__ self.assemble() File "c:\users\colpoama\appdata\local\programs\python\python37\lib\site-packages\PyInstaller\building\build_main.py", line 500, in assemble for name, path, typecode in compile_py_files(new_toc, CONF['workpath']): File "c:\users\colpoama\appdata\local\programs\python\python37\lib\site-packages\PyInstaller\utils\misc.py", line 152, in compile_py_files with open(obj_fnm, 'rb') as fh: FileNotFoundError: [Errno 2] No such file or directory: '-' Project output will not be moved to output folder Complete. ``` If I have no modules on the `--hidden-import` field, I still have the same error. When I don't include `--debug "all"`, the executable file is generated but I have the error mentioned before. When I remove the line `import cobra`, making my code is simply `print(1)`, I have a working executable file.
Author
Owner

@brentvollebregt commented on GitHub (Jun 12, 2020):

So adding --debug all to your command make this error occur when packaging the script? That's odd.

Typically you need to use --hidden-import when not using the import keyword, but looking back at your original script, you were using it, so using --hidden-import probably won't help - PyInstaller just can't find the import.

Maybe if you can locate where the .py associated with the import is, you could add it's location to --paths to tell PyInstaller to look there.

<!-- gh-comment-id:643087134 --> @brentvollebregt commented on GitHub (Jun 12, 2020): So adding `--debug all` to your command make this error occur when packaging the script? That's odd. Typically you need to use `--hidden-import` when not using the `import` keyword, but looking back at your original script, you were using it, so using `--hidden-import` probably won't help - PyInstaller just can't find the import. Maybe if you can locate where the .py associated with the import is, you could add it's location to `--paths` to tell PyInstaller to look there.
Author
Owner

@rcolpo commented on GitHub (Jun 12, 2020):

Thank you. Adding the module location to --paths solved the problem. Thank you very much.

<!-- gh-comment-id:643389707 --> @rcolpo commented on GitHub (Jun 12, 2020): Thank you. Adding the module location to `--paths` solved the problem. Thank you very much.
Sign in to join this conversation.
No milestone
No project
No assignees
1 participant
Notifications
Due date
The due date is invalid or out of range. Please use the format "yyyy-mm-dd".

No due date set.

Dependencies

No dependencies set.

Reference
starred/auto-py-to-exe#98
No description provided.