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)
Hello,
Running
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:
pept.txt