Installation Help

[loulou-99]

Hi there,

Looking for some help with this installation. Please see output. Thank you! pnlNipype installation output.txt

[tashrifbillah]

pynrrd folks upgraded from Python 3.6. This is the error you ran into:

ERROR: Package 'pynrrd' requires a different Python: 3.6.15 not in '>=3.7'
                                                                              failed
CondaEnvException: Pip failed

Remove all = version string from https://github.com/pnlbwh/pnlpipe/blob/7f5128c0070a96b413fd3fa8686f67e953909f57/python_env/environment36.yml#L7 and try again.

[loulou-99]

I seemed to have the same issue after a few days of running. Wondering if I should remove = from other rows?

This is my environment36.yml file:

name: pnlpipe3

channels:

• conda-forge

dependencies:

• python
• ipython
• pytest
• plumbum
• future
• numpy
• pandas
• vtk<=8.2.0
• cmake
• nibabel
• nilearn
• dipy<1.3.0
• pyyaml
• psutil
• csvkit
• gcc_linux-64<=7.3.0
• gxx_linux-64<=7.3.0
• joblib
• matplotlib
• conda-build
• luigi
• sqlalchemy
• dash
• statsmodels
• tensorflow==1.12.0
• keras==2.2.4
• scikit-image
• h5py<3
• git
• pip
• pip:
  • git+https://github.com/SlicerDMRI/whitematteranalysis.git
  • git+https://github.com/dstrohl/Python_log_indenter.git
  • git+https://github.com/mhe/pynrrd.git
  • git+https://github.com/pnlbwh/conversion.git

[tashrifbillah]

Sure, remove them all and see if the environment builds for you.

[loulou-99]

Thanks - this fixed the issue. Could you advise how to fix this issue for installing the rest of the software? Thank you.

(pnlpipe3) jennifer@dart:~/pnlNipype> cmd/install.py UKFTractography
Cloning into 'ukftractography'...
fatal: unable to connect to github.com:
github.com[0: 140.82.112.4]: errno=Connection timed out

Traceback (most recent call last):
  File "/home/jennifer/pnlNipype/cmd/install.py", line 31, in <module>
    SoftwareCommand()
  File "/home/jennifer/miniconda3/envs/pnlpipe3/lib/python3.10/site-packages/plumbum/cli/application.py", line 177, in __new__
    return cls.run()
  File "/home/jennifer/miniconda3/envs/pnlpipe3/lib/python3.10/site-packages/plumbum/cli/application.py", line 634, in run
    retcode = inst.main(*tailargs)
  File "/home/jennifer/pnlNipype/cmd/install.py", line 28, in main
    softwareModule.make()
  File "/home/jennifer/pnlNipype/pnlpipe_software/UKFTractography.py", line 20, in make
    repo = downloadGithubRepo('pnlbwh/ukftractography', commit)
  File "/home/jennifer/pnlNipype/pnlpipe_software/__init__.py", line 102, in downloadGithubRepo
    git['clone', url] & FG
  File "/home/jennifer/miniconda3/envs/pnlpipe3/lib/python3.10/site-packages/plumbum/commands/modifiers.py", line 145, in __rand__
    cmd(
  File "/home/jennifer/miniconda3/envs/pnlpipe3/lib/python3.10/site-packages/plumbum/commands/base.py", line 113, in __call__
    return self.run(args, **kwargs)[1]
  File "/home/jennifer/miniconda3/envs/pnlpipe3/lib/python3.10/site-packages/plumbum/commands/base.py", line 252, in run
    return p.run()
  File "/home/jennifer/miniconda3/envs/pnlpipe3/lib/python3.10/site-packages/plumbum/commands/base.py", line 215, in runner
    return run_proc(p, retcode, timeout)
  File "/home/jennifer/miniconda3/envs/pnlpipe3/lib/python3.10/site-packages/plumbum/commands/processes.py", line 304, in run_proc
    return _check_process(proc, retcode, timeout, stdout, stderr)
  File "/home/jennifer/miniconda3/envs/pnlpipe3/lib/python3.10/site-packages/plumbum/commands/processes.py", line 17, in _check_process
    proc.verify(retcode, timeout, stdout, stderr)
  File "/home/jennifer/miniconda3/envs/pnlpipe3/lib/python3.10/site-packages/plumbum/machines/base.py", line 27, in verify
    raise ProcessExecutionError(
plumbum.commands.processes.ProcessExecutionError: Unexpected exit code: 128
Command line: | /home/jennifer/miniconda3/envs/pnlpipe3/bin/git clone git://github.com/pnlbwh/ukftractography.git

[tashrifbillah]

/home/jennifer/miniconda3/envs/pnlpipe3/bin/git clone git://github.com/pnlbwh/ukftractography.git

Does this raise the same error directly on your terminal?

[loulou-99]

Yes.

Output:

(pnlpipe3) jennifer@dart:~> /home/jennifer/miniconda3/envs/pnlpipe3/bin/git clone git://github.com/pnlbwh/ukftractography.git
Cloning into 'ukftractography'...
fatal: unable to connect to github.com:
github.com[0: 140.82.113.4]: errno=Connection timed out

[tashrifbillah]

The problem is that your shell is using git protocol as opposed to intended https protocol to clone GitHub and I do not understand why it is doing so. It did not happen for other users.

[loulou-99]

Thanks, I will see if our developers can assist in a work around.

[tashrifbillah]

Hi, I have been able to reproduce your issue at our end. It appears that something has changed with GitHub. Will follow up with a fix.

[tashrifbillah]

Jennifer:

I want you to do two things:

cd ~/pnlNipype/
git pull origin master
git submodule update

Now my fix will be available in your computer. Then you can resume installation:

cd ~/pnlNipype/
cmd/install.py UKFTractography

[loulou-99]

Thanks.

I was successful with dcm2niix and tract_querier, but did throw errors with UKFTractography and ANTs (outputs attached).

UKF - dec30.txt ANTs - dec30.txt

[tashrifbillah]

Jennifer, consider using our pre-built docker or singularity containers. The errors you are running into are user-specific and require good programming knowledge on part of the user to solve.

[loulou-99]

Hi there, I was able to reproduce these errors on a separate machine/OS. Please confirm that this error is user-specific.