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MannLabs / alphapept

A modular, python-based framework for mass spectrometry. Powered by nbdev.
https://mannlabs.github.io/alphapept/
Apache License 2.0
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cannot install pythonnet 2.5.2 in linux #545

Closed grandrea closed 1 year ago

grandrea commented 1 year ago

Hello,

Running 

pip install pythonnet==2.5.2

results in TrustFailure/Authentication Failure.

I am within a conda environment in linux Centos 8 64 bit. I have successfully installed alphapept and it "runs" except it does not find results for thermo .raw. I have installed mono via conda-forge (i am not admin) and added it to the path. mono version is 6.12.0.90 . I attach my conda environment.

Installation of pythonnet 3.1 is successful, but that does not help alphapept process thermo files, it seems?

Error trace:

bash-4.4$ pip install pythonnet==2.5.2
WARNING: Ignoring invalid distribution -umba (/home/andrea.graziadei/miniconda3/envs/pept/lib/python3.8/site-packages)
WARNING: Ignoring invalid distribution -umba (/home/andrea.graziadei/miniconda3/envs/pept/lib/python3.8/site-packages)
Collecting pythonnet==2.5.2
  Downloading pythonnet-2.5.2.tar.gz (1.9 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.9/1.9 MB 14.1 MB/s eta 0:00:00
  Preparing metadata (setup.py) ... done
Requirement already satisfied: pycparser in ./miniconda3/envs/pept/lib/python3.8/site-packages (from pythonnet==2.5.2) (2.21)
Building wheels for collected packages: pythonnet
  Building wheel for pythonnet (setup.py) ... error
  error: subprocess-exited-with-error

  × python setup.py bdist_wheel did not run successfully.
  │ exit code: 1
  ╰─> [56 lines of output]
      running bdist_wheel
      running build
      running build_ext
      Checking for updates from https://www.nuget.org/api/v2/.
      Error: TrustFailure (Authentication failed, see inner exception.)
        Authentication failed, see inner exception.
        Ssl error:1000007d:SSL routines:OPENSSL_internal:CERTIFICATE_VERIFY_FAILED
          at /home/conda/feedstock_root/build_artifacts/mono_1614918204952/work/external/boringssl/ssl/handshake_client.c:1132
      Traceback (most recent call last):
        File "<string>", line 2, in <module>
        File "<pip-setuptools-caller>", line 34, in <module>
        File "/tmp/pip-install-jksfkkte/pythonnet_2649fa1ce8614f9c9f2ebee59b50e1de/setup.py", line 630, in <module>
          setup(
        File "/home/andrea.graziadei/miniconda3/envs/pept/lib/python3.8/site-packages/setuptools/__init__.py", line 87, in setup
          return distutils.core.setup(**attrs)
        File "/home/andrea.graziadei/miniconda3/envs/pept/lib/python3.8/site-packages/setuptools/_distutils/core.py", line 185, in setup
          return run_commands(dist)
        File "/home/andrea.graziadei/miniconda3/envs/pept/lib/python3.8/site-packages/setuptools/_distutils/core.py", line 201, in run_commands
          dist.run_commands()
        File "/home/andrea.graziadei/miniconda3/envs/pept/lib/python3.8/site-packages/setuptools/_distutils/dist.py", line 969, in run_commands
          self.run_command(cmd)
        File "/home/andrea.graziadei/miniconda3/envs/pept/lib/python3.8/site-packages/setuptools/dist.py", line 1208, in run_command
          super().run_command(command)
        File "/home/andrea.graziadei/miniconda3/envs/pept/lib/python3.8/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
          cmd_obj.run()
        File "/tmp/pip-install-jksfkkte/pythonnet_2649fa1ce8614f9c9f2ebee59b50e1de/setup.py", line 612, in run
          return bdist_wheel.bdist_wheel.run(self)
        File "/home/andrea.graziadei/miniconda3/envs/pept/lib/python3.8/site-packages/wheel/bdist_wheel.py", line 325, in run
          self.run_command("build")
        File "/home/andrea.graziadei/miniconda3/envs/pept/lib/python3.8/site-packages/setuptools/_distutils/cmd.py", line 318, in run_command
          self.distribution.run_command(command)
        File "/home/andrea.graziadei/miniconda3/envs/pept/lib/python3.8/site-packages/setuptools/dist.py", line 1208, in run_command
          super().run_command(command)
        File "/home/andrea.graziadei/miniconda3/envs/pept/lib/python3.8/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
          cmd_obj.run()
        File "/home/andrea.graziadei/miniconda3/envs/pept/lib/python3.8/site-packages/setuptools/_distutils/command/build.py", line 132, in run
          self.run_command(cmd_name)
        File "/home/andrea.graziadei/miniconda3/envs/pept/lib/python3.8/site-packages/setuptools/_distutils/cmd.py", line 318, in run_command
          self.distribution.run_command(command)
        File "/home/andrea.graziadei/miniconda3/envs/pept/lib/python3.8/site-packages/setuptools/dist.py", line 1208, in run_command
          super().run_command(command)
        File "/home/andrea.graziadei/miniconda3/envs/pept/lib/python3.8/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
          cmd_obj.run()
        File "/home/andrea.graziadei/miniconda3/envs/pept/lib/python3.8/site-packages/setuptools/_distutils/command/build_ext.py", line 346, in run
          self.build_extensions()
        File "/home/andrea.graziadei/miniconda3/envs/pept/lib/python3.8/site-packages/setuptools/_distutils/command/build_ext.py", line 468, in build_extensions
          self._build_extensions_serial()
        File "/home/andrea.graziadei/miniconda3/envs/pept/lib/python3.8/site-packages/setuptools/_distutils/command/build_ext.py", line 494, in _build_extensions_serial
          self.build_extension(ext)
        File "/tmp/pip-install-jksfkkte/pythonnet_2649fa1ce8614f9c9f2ebee59b50e1de/setup.py", line 249, in build_extension
          self._install_packages()
        File "/tmp/pip-install-jksfkkte/pythonnet_2649fa1ce8614f9c9f2ebee59b50e1de/setup.py", line 438, in _install_packages
          subprocess.check_call(cmd, shell=use_shell)
        File "/home/andrea.graziadei/miniconda3/envs/pept/lib/python3.8/subprocess.py", line 364, in check_call
          raise CalledProcessError(retcode, cmd)
      subprocess.CalledProcessError: Command 'mono tools/nuget/nuget.exe update -self' 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: Failed building wheel for pythonnet
  Running setup.py clean for pythonnet
Failed to build pythonnet
WARNING: Ignoring invalid distribution -umba (/home/andrea.graziadei/miniconda3/envs/pept/lib/python3.8/site-packages)
Installing collected packages: pythonnet
  Running setup.py install for pythonnet ... error
  error: subprocess-exited-with-error

  × Running setup.py install for pythonnet did not run successfully.
  │ exit code: 1
  ╰─> [6 lines of output]
      usage: setup.py [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...]
         or: setup.py --help [cmd1 cmd2 ...]
         or: setup.py --help-commands
         or: setup.py cmd --help

      error: option --single-version-externally-managed not recognized
      [end of output]

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

× Encountered error while trying to install package.
╰─> pythonnet

note: This is an issue with the package mentioned above, not pip.
hint: See above for output from the failure.
WARNING: Ignoring invalid distribution -umba (/home/andrea.graziadei/miniconda3/envs/pept/lib/python3.8/site-packages)
WARNING: Ignoring invalid distribution -umba (/home/andrea.graziadei/miniconda3/envs/pept/lib/python3.8/site-packages)
WARNING: Ignoring invalid distribution -umba (/home/andrea.graziadei/miniconda3/envs/pept/lib/python3.8/site-packages)

pept.txt

grandrea commented 1 year ago

For anyone else running into this issue.

I have managed to solve the problem by installing pythonnet via conda and alphapept now runs fine from thermo .raw

conda install -c conda-forge pythonnet==2.5.2