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compneuro-ncu / fmridenoise

Tool for automatic denoising, denoising strategies comparison, and functional connectivity data quality control.
Apache License 2.0
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problems installing fmridenoise #87

Open atkinsonap opened 3 years ago

atkinsonap commented 3 years ago

Hello,

I'm unable to install fmridenoise on my Mac (OS Mojave, with the preinstalled Python 2 and the latest installation of Python 3.9). I've tried several ways:

  1. Via Terminal (bash), with commands (a) pip install fmridenoise (b) python3 -m pip install fmridenoise

  2. Downloaded the latest version of fmridenoise from github, unzipped it, cd in Terminal to the downloaded location, and enter following command in Terminal: python setup.py install.

The respective error messages are below. I'd be grateful for your help.

Both 1(a) and 1(b) give the following error message:

ERROR: Command errored out with exit status 1:
 command: /Library/Frameworks/Python.framework/Versions/3.9/bin/python3 -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/fw/l5xdrbkd7m93pk1_r2hkzfx40000gn/T/pip-install-ojcjdsoo/fmridenoise_d93b800b0d4641e396e6a1d99445df6d/setup.py'"'"'; __file__='"'"'/private/var/folders/fw/l5xdrbkd7m93pk1_r2hkzfx40000gn/T/pip-install-ojcjdsoo/fmridenoise_d93b800b0d4641e396e6a1d99445df6d/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/fw/l5xdrbkd7m93pk1_r2hkzfx40000gn/T/pip-pip-egg-info-3xw5zobi
     cwd: /private/var/folders/fw/l5xdrbkd7m93pk1_r2hkzfx40000gn/T/pip-install-ojcjdsoo/fmridenoise_d93b800b0d4641e396e6a1d99445df6d/
Complete output (5 lines):
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/private/var/folders/fw/l5xdrbkd7m93pk1_r2hkzfx40000gn/T/pip-install-ojcjdsoo/fmridenoise_d93b800b0d4641e396e6a1d99445df6d/setup.py", line 8, in <module>
    with open(join(__dir_path, "requirements.txt"), 'r') as fh:
FileNotFoundError: [Errno 2] No such file or directory: '/private/var/folders/fw/l5xdrbkd7m93pk1_r2hkzfx40000gn/T/pip-install-ojcjdsoo/fmridenoise_d93b800b0d4641e396e6a1d99445df6d/requirements.txt'
----------------------------------------

ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.

Option 2 gave me the following error:

Traceback (most recent call last): File "setup.py", line 3, in import versioneer File "/Users/Atkinson/fmridenoise-0.2.0/versioneer.py", line 1739 file=sys.stderr) ^ SyntaxError: invalid syntax

SiegfriedWagner commented 3 years ago

I will address it tomorrow. For now it looks like I haven't put requirements.txt in MANIFEST.in.

atkinsonap commented 3 years ago

Hello,

Thanks very much.

Another thing I noticed: one of the requirements is numpy<1.16.5,>=1.11. But the latest version of numpy, which I have installed, is v1.19.0. Can fmridenoise run with this more recent version of numpy or do I need to install an older version?

Regards,

Anthony

On 21 Jan 2021, at 18:58, Siegfried Wagner notifications@github.com wrote:

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I will address it tomorrow. For now it looks like I haven't put requirements.txt in MANIFEST.in.

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SiegfriedWagner commented 3 years ago

I acknowledged both you suggestions and included them in version 0.2.1. Please check if everything is working now, if everything is fine we can close this issue. Btw. I wonder how is our software running on Mac - we had no access to any, so some platform dependent bugs may occur.

atkinsonap commented 3 years ago

That’s great, thanks very much.

The installation seems to have worked — I got the 'Successfully installed fmridenoise-0.2.1' at the end of the installation.

But I can’t seem to run it. I just get the following error:

-bash: /Library/Frameworks/Python.framework/Versions/3.9/bin/fmridenoise: /usr/bin/sh: bad interpreter: No such file or directory

I’ve done a quick google search and I think the problem is that my system's sh interpreter is at /bin/sh rather than at /usr/bin/sh

If there’s a solution I can make at my end, then I’m happy to try what you recommend.

Thanks,

Anthony

On 22 Jan 2021, at 17:42, Siegfried Wagner notifications@github.com wrote:

[EXTERNAL EMAIL]

I acknowledged both you suggestions and included them in version 0.2.1. Please check if everything is working now, if everything is fine we can close this issue. Btw. I wonder how is our software running on Mac - we had no access to any, so some platform dependent bugs may occur.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/compneuro-ncu/fmridenoise/issues/87#issuecomment-765577502, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKIYPIEDTMSTWUDO3P7A6KLS3G2HDANCNFSM4WNF5I6Q.

SiegfriedWagner commented 3 years ago

fmridenoise console command is just calling this file https://github.com/compneuro-ncu/fmridenoise/blob/master/fmridenoise/scripts/fmridenoise - shebang is not suitable for mac (and for windows too) for now you can just get access to fmridenoise by calling python -O -m fmridenoise - it should work as calling the script. I will change it in next minor release from /usr/bin/sh to /bin/sh.

atkinsonap commented 3 years ago

Thanks Siegfried. I got it running OK with that command (after changing python to python3). 'fmridenoise compare' ran through all the subjects I specified, but there were some errors along the way and the group report was not produced. Attached are the 4 crash report files. I haven't managed to work out whether the problem is in the code and/or at my end. Could you please look into this when you get the chance?

Thanks,

Anthony

From: Siegfried Wagner notifications@github.com Sent: 22 January 2021 19:48 To: compneuro-ncu/fmridenoise fmridenoise@noreply.github.com Cc: ATKINSON, ANTHONY P. a.p.atkinson@durham.ac.uk; Author author@noreply.github.com Subject: Re: [compneuro-ncu/fmridenoise] problems installing fmridenoise (#87)

[EXTERNAL EMAIL]

fmridenoise console command is just calling this file https://github.com/compneuro-ncu/fmridenoise/blob/master/fmridenoise/scripts/fmridenoise - shebang is not suitable for mac (and for windows too) for now you can just get access to fmridenoise by calling python -O -m fmridenoise - it should work as calling the script. I will change it in next minor release from /usr/bin/sh to /bin/sh.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/compneuro-ncu/fmridenoise/issues/87#issuecomment-765645763, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AKIYPICHFLE5IQYHQZKVG7LS3HJBFANCNFSM4WNF5I6Q.