Missing objcopy on Miniforge3 Docker

[mfansler]

• I read the conda-forge documentation and could not find the solution for my problem there.

Issue

Running PyInstaller on condaforge/miniforge3:4.10.3-1 image fails to generate functional binaries. This is due to the assumption that linux-64 platform includes the objcopy command supplied by binutils. This could be remedied by adding binutils as a dependency.

Recreate Steps

## launch docker
docker run --rm -it condaforge/miniforge3:4.10.3-1

## within docker BASH session
conda create -yn pi python=3.9 pyinstaller

## activate 'pi' env
conda activate pi

## create dummy script
echo "import sys; print(sys.path)" > script.py

## test
pyinstaller -F script.py

Result

Throws error message:

FileNotFoundError: [Errno 2] No such file or directory: 'objcopy'

Full Output

172 INFO: PyInstaller: 4.3
172 INFO: Python: 3.9.6 (conda)
175 INFO: Platform: Linux-5.10.25-linuxkit-x86_64-with-glibc2.31
176 INFO: wrote /script.spec
178 INFO: UPX is not available.
180 INFO: Extending PYTHONPATH with paths
['/', '/']
183 INFO: checking Analysis
183 INFO: Building Analysis because Analysis-00.toc is non existent
183 INFO: Initializing module dependency graph...
184 INFO: Caching module graph hooks...
190 INFO: Analyzing base_library.zip ...
2091 INFO: Processing pre-find module path hook distutils from '/opt/conda/envs/pi/lib/python3.9/site-packages/PyInstaller/hooks/pre_find_module_path/hook-distutils.py'.
2092 INFO: distutils: retargeting to non-venv dir '/opt/conda/envs/pi/lib/python3.9'
4405 INFO: Caching module dependency graph...
4560 INFO: running Analysis Analysis-00.toc
4570 INFO: Analyzing /script.py
4571 INFO: Processing module hooks...
4572 INFO: Loading module hook 'hook-pickle.py' from '/opt/conda/envs/pi/lib/python3.9/site-packages/PyInstaller/hooks'...
4574 INFO: Loading module hook 'hook-multiprocessing.util.py' from '/opt/conda/envs/pi/lib/python3.9/site-packages/PyInstaller/hooks'...
4575 INFO: Loading module hook 'hook-difflib.py' from '/opt/conda/envs/pi/lib/python3.9/site-packages/PyInstaller/hooks'...
4577 INFO: Loading module hook 'hook-sysconfig.py' from '/opt/conda/envs/pi/lib/python3.9/site-packages/PyInstaller/hooks'...
4583 INFO: Loading module hook 'hook-lib2to3.py' from '/opt/conda/envs/pi/lib/python3.9/site-packages/PyInstaller/hooks'...
4599 INFO: Loading module hook 'hook-_tkinter.py' from '/opt/conda/envs/pi/lib/python3.9/site-packages/PyInstaller/hooks'...
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/opt/conda/envs/pi/lib/python3.9/tkinter/__init__.py", line 37, in <module>
    import _tkinter # If this fails your Python may not be configured for Tk
ImportError: libX11.so.6: cannot open shared object file: No such file or directory
Traceback (most recent call last):
  File "<string>", line 1, in <module>
ImportError: libX11.so.6: cannot open shared object file: No such file or directory
4643 ERROR: Tcl/Tk improperly installed on this system.
4644 INFO: Loading module hook 'hook-distutils.py' from '/opt/conda/envs/pi/lib/python3.9/site-packages/PyInstaller/hooks'...
4644 INFO: Loading module hook 'hook-xml.etree.cElementTree.py' from '/opt/conda/envs/pi/lib/python3.9/site-packages/PyInstaller/hooks'...
4645 INFO: Loading module hook 'hook-xml.py' from '/opt/conda/envs/pi/lib/python3.9/site-packages/PyInstaller/hooks'...
4683 INFO: Loading module hook 'hook-heapq.py' from '/opt/conda/envs/pi/lib/python3.9/site-packages/PyInstaller/hooks'...
4685 INFO: Loading module hook 'hook-encodings.py' from '/opt/conda/envs/pi/lib/python3.9/site-packages/PyInstaller/hooks'...
4725 INFO: Loading module hook 'hook-distutils.util.py' from '/opt/conda/envs/pi/lib/python3.9/site-packages/PyInstaller/hooks'...
4739 INFO: Looking for ctypes DLLs
4770 INFO: Analyzing run-time hooks ...
4774 INFO: Including run-time hook '/opt/conda/envs/pi/lib/python3.9/site-packages/PyInstaller/hooks/rthooks/pyi_rth_multiprocessing.py'
4782 INFO: Looking for dynamic libraries
5205 INFO: Looking for eggs
5205 INFO: Python library not in binary dependencies. Doing additional searching...
5214 INFO: Using Python library /opt/conda/envs/pi/lib/libpython3.9.so.1.0
5219 INFO: Warnings written to /build/script/warn-script.txt
5244 INFO: Graph cross-reference written to /build/script/xref-script.html
5255 INFO: checking PYZ
5255 INFO: Building PYZ because PYZ-00.toc is non existent
5255 INFO: Building PYZ (ZlibArchive) /build/script/PYZ-00.pyz
5592 INFO: Building PYZ (ZlibArchive) /build/script/PYZ-00.pyz completed successfully.
5596 INFO: checking PKG
5597 INFO: Building PKG because PKG-00.toc is non existent
5597 INFO: Building PKG (CArchive) PKG-00.pkg
13615 INFO: Building PKG (CArchive) PKG-00.pkg completed successfully.
13617 INFO: Bootloader /opt/conda/envs/pi/lib/python3.9/site-packages/PyInstaller/bootloader/Linux-64bit/run
13618 INFO: checking EXE
13618 INFO: Building EXE because EXE-00.toc is non existent
13618 INFO: Building EXE from EXE-00.toc
13618 INFO: Appending archive to ELF section in EXE /dist/script
Traceback (most recent call last):
  File "/opt/conda/envs/pi/bin/pyinstaller", line 11, in <module>
    sys.exit(run())
  File "/opt/conda/envs/pi/lib/python3.9/site-packages/PyInstaller/__main__.py", line 114, in run
    run_build(pyi_config, spec_file, **vars(args))
  File "/opt/conda/envs/pi/lib/python3.9/site-packages/PyInstaller/__main__.py", line 65, in run_build
    PyInstaller.building.build_main.main(pyi_config, spec_file, **kwargs)
  File "/opt/conda/envs/pi/lib/python3.9/site-packages/PyInstaller/building/build_main.py", line 737, in main
    build(specfile, kw.get('distpath'), kw.get('workpath'), kw.get('clean_build'))
  File "/opt/conda/envs/pi/lib/python3.9/site-packages/PyInstaller/building/build_main.py", line 684, in build
    exec(code, spec_namespace)
  File "/script.spec", line 21, in <module>
    exe = EXE(pyz,
  File "/opt/conda/envs/pi/lib/python3.9/site-packages/PyInstaller/building/api.py", line 450, in __init__
    self.__postinit__()
  File "/opt/conda/envs/pi/lib/python3.9/site-packages/PyInstaller/building/datastruct.py", line 160, in __postinit__
    self.assemble()
  File "/opt/conda/envs/pi/lib/python3.9/site-packages/PyInstaller/building/api.py", line 616, in assemble
    retcode, stdout, stderr = exec_command_all(
  File "/opt/conda/envs/pi/lib/python3.9/site-packages/PyInstaller/compat.py", line 461, in exec_command_all
    proc = subprocess.Popen(cmdargs, bufsize=-1,  # Default OS buffer size.
  File "/opt/conda/envs/pi/lib/python3.9/subprocess.py", line 951, in __init__
    self._execute_child(args, executable, preexec_fn, close_fds,
  File "/opt/conda/envs/pi/lib/python3.9/subprocess.py", line 1821, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'objcopy'

Expected Result

It should successfully build the binary.

Workaround

The error can be overcome by installing binutils. That is, running the above recreate steps, but with

conda create -yn pi python=3.9 pyinstaller binutils

enables error-free running of the last step.

Recommended Solution

The feedstock maintainers should consider including binutils as a runtime dependency, at least for linux-64 builds. The recipe should include a end-to-end test that would catch this failure in future builds.

[jakirkham]

I'm hesitant to do this as it would likely cause issues for packages building in conda-forge relying on pyinstaller. This is because they normally would be getting build utilities (like the compiler and binutils) from the build environment. Including this in pyinstaller would pull this in the host environment. This would then likely lead to clashes between these two environments.

Given this, is there a reason one can't install this themselves or grab it from the system?

[mfansler]

@jakirkham thanks for the reply. Yes, one can simply install the binutils to get things working. I created this issue partially to document that workaround for others, partially to spark a discussion as to adding it as an explicit dependency.

If there are non-trivial consequences to the latter, then it sounds better to leave it as is.

[nehaljwani]

Other ways to consider: either vendor a copy of objcopy and patch pyinstaller to use that or urge the developers of pyinstaller to switch to a solution that doesn't require dependency on objcopy (using some ELF library like py-lief or pyelftools). All objcopy is used for is this.

[nehaljwani]

Turns there is already a fallback in place, the path just doesn't get hit. Let's see what upstream devs have to say about pyinstaller/pyinstaller#5991