License error on install

[NicLeMaitre]

Hi there

I'm hoping that you can help me. On trying to install the JCVI package in python, I get the following error:

Collecting jcvi==1.5.3
Using cached jcvi-1.5.3.tar.gz (782 kB)
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'done'
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status 'error'

error: subprocess-exited-with-error

Preparing metadata (pyproject.toml) did not run successfully.
exit code: 1

[67 lines of output]
C:\Users\nicho\AppData\Local\Temp\pip-build-env-pptg_v6n\overlay\Lib\site-packages\setuptools\config_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: project.license as a TOML table is deprecated
!!

      ********************************************************************************
      Please use a simple string containing a SPDX expression for `project.license`. You can also use `project.license-files`.

      By 2026-Feb-18, you need to update your project and remove deprecated calls
      or your builds will no longer be supported.

      See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
      ********************************************************************************

!!
corresp(dist, value, root_dir)
C:\Users\nicho\AppData\Local\Temp\pip-build-env-pptg_v6n\overlay\Lib\site-packages\setuptools\config_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated.
!!

      ********************************************************************************
      Please consider removing the following classifiers in favor of a SPDX license expression:

      License :: OSI Approved :: BSD License

      See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
      ********************************************************************************

!!
dist._finalize_license_expression()
C:\Users\nicho\AppData\Local\Temp\pip-build-env-pptg_v6n\overlay\Lib\site-packages\setuptools\dist.py:760: SetuptoolsDeprecationWarning: License classifiers are deprecated.
!!

      ********************************************************************************
      Please consider removing the following classifiers in favor of a SPDX license expression:

      License :: OSI Approved :: BSD License

      See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
      ********************************************************************************

!!
self._finalize_license_expression()
running build_ext
Compiling src/jcvi/assembly/chic.pyx because it changed.
[1/1] Cythonizing src/jcvi/assembly/chic.pyx
building 'jcvi.assembly.chic' extension
error: Microsoft Visual C++ 14.0 or greater is required. Get it with "Microsoft C++ Build Tools": https://visualstudio.microsoft.com/visual-cpp-build-tools/
Using custom wheel tag: cp313-cp313-win_amd64
Traceback (most recent call last):
File "C:\Users\nicho\PycharmProjects\T.distchum_genome.venv\Lib\site-packages\pip_vendor\pyproject_hooks_in_process_in_process.py", line 353, in
main()
~~~~^^
File "C:\Users\nicho\PycharmProjects\T.distchum_genome.venv\Lib\site-packages\pip_vendor\pyproject_hooks_in_process_in_process.py", line 335, in main
json_out['return_val'] = hook(**hook_input['kwargs'])
~~~~^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\nicho\PycharmProjects\T.distchum_genome.venv\Lib\site-packages\pip_vendor\pyproject_hooks_in_process_in_process.py", line 152, in prepare_metadata_for_build_wheel
whl_basename = backend.build_wheel(metadata_directory, config_settings)
File "C:\Users\nicho\AppData\Local\Temp\pip-build-env-pptg_v6n\overlay\Lib\site-packages\hatchling\build.py", line 58, in build_wheel
return os.path.basename(next(builder.build(directory=wheel_directory, versions=['standard'])))
~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\nicho\AppData\Local\Temp\pip-build-env-pptg_v6n\overlay\Lib\site-packages\hatchling\builders\plugin\interface.py", line 147, in build
build_hook.initialize(version, build_data)
~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\nicho\AppData\Local\Temp\pip-install-8yp_cnuf\jcvi_c870867a368d435bb7f9974d96e58ec0\build.py", line 13, in initialize
subprocess.check_call(["python", "setup.py", "build_ext", "--inplace"])
~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\nicho\AppData\Local\Programs\Python\Python313\Lib\subprocess.py", line 421, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['python', 'setup.py', 'build_ext', '--inplace']' returned non-zero exit status 1.
[end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

[Adamtaranto]

You are missing a C++ compiler for windows, please install "Microsoft C++ Build Tools": https://visualstudio.microsoft.com/visual-cpp-build-tools/ and try again.

Let me know if that works.

[NicLeMaitre]

Installed the V C++, and it got further but then a new error came up:

Collecting jcvi==1.5.3
Using cached jcvi-1.5.3.tar.gz (782 kB)
Installing build dependencies: started
Installing build dependencies: still running...
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'done'
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status 'done'
Collecting biopython (from jcvi==1.5.3)
Downloading biopython-1.85-cp313-cp313-win_amd64.whl.metadata (13 kB)
Collecting boto3 (from jcvi==1.5.3)
Downloading boto3-1.37.18-py3-none-any.whl.metadata (6.7 kB)
Collecting brewer2mpl (from jcvi==1.5.3)
Downloading brewer2mpl-1.4.1-py2.py3-none-any.whl.metadata (3.7 kB)
Collecting crossmap (from jcvi==1.5.3)
Downloading CrossMap-0.7.3-py3-none-any.whl.metadata (4.5 kB)
Collecting cython (from jcvi==1.5.3)
Using cached Cython-3.0.12-cp313-cp313-win_amd64.whl.metadata (3.6 kB)
Collecting deap (from jcvi==1.5.3)
Downloading deap-1.4.2-cp313-cp313-win_amd64.whl.metadata (13 kB)
Collecting ete3 (from jcvi==1.5.3)
Downloading ete3-3.1.3.tar.gz (4.8 MB)
---------------------------------------- 4.8/4.8 MB 9.5 MB/s eta 0:00:00
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'done'
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status 'done'
Collecting ftpretty (from jcvi==1.5.3)
Downloading ftpretty-0.4.0-py2.py3-none-any.whl.metadata (6.6 kB)
Collecting genomepy (from jcvi==1.5.3)
Downloading genomepy-0.16.1-py3-none-any.whl.metadata (26 kB)
Collecting gffutils (from jcvi==1.5.3)
Downloading gffutils-0.13-py3-none-any.whl.metadata (1.5 kB)
Collecting goatools (from jcvi==1.5.3)
Downloading goatools-1.4.12-py3-none-any.whl.metadata (14 kB)
Collecting graphviz (from jcvi==1.5.3)
Downloading graphviz-0.20.3-py3-none-any.whl.metadata (12 kB)
Collecting jinja2 (from jcvi==1.5.3)
Downloading jinja2-3.1.6-py3-none-any.whl.metadata (2.9 kB)
Collecting matplotlib (from jcvi==1.5.3)
Downloading matplotlib-3.10.1-cp313-cp313-win_amd64.whl.metadata (11 kB)
Collecting more-itertools (from jcvi==1.5.3)
Downloading more_itertools-10.6.0-py3-none-any.whl.metadata (37 kB)
Collecting natsort (from jcvi==1.5.3)
Downloading natsort-8.4.0-py3-none-any.whl.metadata (21 kB)
Collecting networkx (from jcvi==1.5.3)
Downloading networkx-3.4.2-py3-none-any.whl.metadata (6.3 kB)
Collecting numpy<2 (from jcvi==1.5.3)
Downloading numpy-1.26.4.tar.gz (15.8 MB)
---------------------------------------- 15.8/15.8 MB 7.9 MB/s eta 0:00:00
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'done'
Installing backend dependencies: started
Installing backend dependencies: finished with status 'done'
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): still running...
Preparing metadata (pyproject.toml): still running...
Preparing metadata (pyproject.toml): still running...
Preparing metadata (pyproject.toml): finished with status 'done'
Collecting ortools (from jcvi==1.5.3)
Downloading ortools-9.12.4544-cp313-cp313-win_amd64.whl.metadata (3.4 kB)
Collecting pybedtools (from jcvi==1.5.3)
Downloading pybedtools-0.12.0.tar.gz (12.6 MB)
---------------------------------------- 12.6/12.6 MB 2.9 MB/s eta 0:00:00
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'done'
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status 'done'
Collecting pyefd (from jcvi==1.5.3)
Downloading pyefd-1.6.0-py2.py3-none-any.whl.metadata (7.4 kB)
Collecting pypdf (from jcvi==1.5.3)
Downloading pypdf-5.4.0-py3-none-any.whl.metadata (7.3 kB)
Collecting pytesseract (from jcvi==1.5.3)
Downloading pytesseract-0.3.13-py3-none-any.whl.metadata (11 kB)
Collecting rich (from jcvi==1.5.3)
Downloading rich-13.9.4-py3-none-any.whl.metadata (18 kB)
Collecting scikit-image (from jcvi==1.5.3)
Downloading scikit_image-0.25.2-cp313-cp313-win_amd64.whl.metadata (14 kB)
Collecting scipy (from jcvi==1.5.3)
Downloading scipy-1.15.2-cp313-cp313-win_amd64.whl.metadata (60 kB)
Collecting seaborn (from jcvi==1.5.3)
Downloading seaborn-0.13.2-py3-none-any.whl.metadata (5.4 kB)
Collecting wand (from jcvi==1.5.3)
Downloading Wand-0.6.13-py2.py3-none-any.whl.metadata (4.0 kB)
Collecting webcolors (from jcvi==1.5.3)
Downloading webcolors-24.11.1-py3-none-any.whl.metadata (2.2 kB)
Collecting botocore<1.38.0,>=1.37.18 (from boto3->jcvi==1.5.3)
Downloading botocore-1.37.18-py3-none-any.whl.metadata (5.7 kB)
Collecting jmespath<2.0.0,>=0.7.1 (from boto3->jcvi==1.5.3)
Downloading jmespath-1.0.1-py3-none-any.whl.metadata (7.6 kB)
Collecting s3transfer<0.12.0,>=0.11.0 (from boto3->jcvi==1.5.3)
Downloading s3transfer-0.11.4-py3-none-any.whl.metadata (1.7 kB)
Collecting pysam (from crossmap->jcvi==1.5.3)
Downloading pysam-0.23.0.tar.gz (4.8 MB)
---------------------------------------- 4.8/4.8 MB 2.6 MB/s eta 0:00:00
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'error'

error: subprocess-exited-with-error

Getting requirements to build wheel did not run successfully.
exit code: 1

[60 lines of output]

pysam: cython is available - using cythonize if necessary

pysam: htslib mode is shared

pysam: HTSLIB_CONFIGURE_OPTIONS=None

'.' is not recognized as an internal or external command,
operable program or batch file.
'.' is not recognized as an internal or external command,
operable program or batch file.

pysam: htslib configure options: None

Traceback (most recent call last):
File "C:\Users\nicho\PycharmProjects\T.distchum_genome.venv\Lib\site-packages\pip_vendor\pyproject_hooks_in_process_in_process.py", line 389, in
main()
~~~~^^
File "C:\Users\nicho\PycharmProjects\T.distchum_genome.venv\Lib\site-packages\pip_vendor\pyproject_hooks_in_process_in_process.py", line 373, in main
json_out["return_val"] = hook(**hook_input["kwargs"])
~~~~^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\nicho\PycharmProjects\T.distchum_genome.venv\Lib\site-packages\pip_vendor\pyproject_hooks_in_process_in_process.py", line 143, in get_requires_for_build_wheel
return hook(config_settings)
File "C:\Users\nicho\AppData\Local\Temp\pip-build-env-ed3yx30_\overlay\Lib\site-packages\setuptools\build_meta.py", line 334, in get_requires_for_build_wheel
return self.get_build_requires(config_settings, requirements=[])
~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\nicho\AppData\Local\Temp\pip-build-env-ed3yx30\overlay\Lib\site-packages\setuptools\build_meta.py", line 304, in get_build_requires
self.run_setup()
~~~~~~~~~~~~~~^^
File "C:\Users\nicho\AppData\Local\Temp\pip-build-env-ed3yx30\overlay\Lib\site-packages\setuptools\build_meta.py", line 522, in run_setup
super().run_setup(setup_script=setup_script)
~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\nicho\AppData\Local\Temp\pip-build-env-ed3yx30_\overlay\Lib\site-packages\setuptools\build_meta.py", line 320, in run_setup
exec(code, locals())
~~~~^^^^^^^^^^^^^^^^
File "", line 441, in
File "", line 81, in run_make_print_config
File "C:\Users\nicho\AppData\Local\Programs\Python\Python313\Lib\subprocess.py", line 474, in check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
**kwargs).stdout
^^^^^^^^^
File "C:\Users\nicho\AppData\Local\Programs\Python\Python313\Lib\subprocess.py", line 556, in run
with Popen(*popenargs, **kwargs) as process:
~~~~~^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\nicho\AppData\Local\Programs\Python\Python313\Lib\subprocess.py", line 1038, in init
self._execute_child(args, executable, preexec_fn, close_fds,
~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
pass_fds, cwd, env,
^^^^^^^^^^^^^^^^^^^
...<5 lines>...
gid, gids, uid, umask,
^^^^^^^^^^^^^^^^^^^^^^
start_new_session, process_group)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\nicho\AppData\Local\Programs\Python\Python313\Lib\subprocess.py", line 1550, in _execute_child
hp, ht, pid, tid = _winapi.CreateProcess(executable, args,
~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^
# no special security
^^^^^^^^^^^^^^^^^^^^^
...<4 lines>...
cwd,
^^^^
startupinfo)
^^^^^^^^^^^^
FileNotFoundError: [WinError 2] The system cannot find the file specified
[end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error

Getting requirements to build wheel did not run successfully.
exit code: 1

See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.

[Adamtaranto]

Please try to conda install pysam separately.

[NicLeMaitre]

Unfortunately there is no pysam build for winx64 :(

So I guess that's it unless I install linux. Not an option on a locked work pc unfortunately. Thanks for the help.

[Adamtaranto]

WSL2 should work if you have permission to install that.

Alternatively, click the green "code" tab on the JCVI homepage and open a github codespace for this repo - that will be in a linux machine. Might work if your dataset is not very large.

[NicLeMaitre]

I'm trying to map a genome to a reference, small dataset this is not. Thanks for all your help!