Installation issue: grep recursive search

bryceg · February 17, 2023, 8:00pm

Hi all,

I’m helping a new student install Mrtrix on their system, and we’re running into an issue during installation. We are following the application package installer process, and running into an issue early in installation. See below for an image of the output we’re seeing:

The process then hangs on this grep stage indefinitely.

So far, we’ve updated our python installation which had no effect. Is this a permissions issue, or something to do with the computer’s file system? I’m not clear on what type of process is happening during the ‘Fixing python shebang’ step, so it’s hard to troubleshoot why grep is hanging. I am happy to provide any additional information for clarification as needed.

Thank you for your time!

bjeurissen · February 18, 2023, 12:06am

I have not encountered this problem before. What version of macOS are you running?

The issue is unrelated to your python version but happens during the installation script (which is a bash script) at this line:

github.com

MRtrix3/macos-installer/blob/01e510ea8a4b3773d3dd784d504fd92d25892da3/install#L89


      
              fi
            fi
          done
          
          
echo "Unpacking "${tarball}" to /usr/local/mrtrix3 ..."
          tar oxf "${tarball}" -C /usr/local
          rm "${tarball}"
          
          
echo "Fixing python shebang ..."
          cd /usr/local/mrtrix3/bin
          for f in $(grep -lr '^#!/usr/bin/env python'); do
            sed -i '' 's|^#!/usr/bin/env python$|#!/usr/bin/python3|' ${f}
          done
          
          
echo "Applying patch to show correct version numbers in scripts ..."
          cd /usr/local/mrtrix3
          curl -s https://github.com/MRtrix3/mrtrix3/commit/4a293d30e1c0686037ae637f67932d497eb71ee6.patch | patch -s -p1
          
          
echo "Creating symlinks in /usr/local/bin ..."
          cd /usr/local/bin
          touch /usr/local/mrtrix3/symlinks

bjeurissen · February 18, 2023, 12:11am

The installation script indeed used a grep syntax not supported in older macos installations. I have just pushed a fix, please rerun the installation.

bryceg · March 6, 2023, 5:50pm

Thank you very much for looking into this! Our student re-ran the installation and encountered no further issues.