Sorry, I just realized there are a few more things my friend recommended I install, are these all okay to install? brew install gcc brew install Caskroom/cask/xquartz brew install tcl-tk brew install python
brew tap salilab/salilab
brew install modeller
On Fri, May 29, 2020 at 12:03 PM Xiao Ran Luo xrluo00@berkeley.edu wrote:
> Thank you! I reinstalled my OS yesterday -does that mean that whatever I > broke in my operating system is fixed now? I just installed Homebrew > (technically for the first time, since my Mac reverted to an April backup) > and typed "brew doctor" and "which python3", which gave: > > > Luos-Air:~ luoxiaoran$ brew doctor > > *Please note that these warnings are just used to help the Homebrew > maintainers* > > *with debugging if you file an issue. If everything you use Homebrew for > is* > > *working fine: please don't worry or file an issue; just ignore this. > Thanks!* > > > Warning: "config" scripts exist outside your system or Homebrew > directories. > > `./configure` scripts often look for *-config scripts to determine if > > software packages are installed, and which additional flags to use when > > compiling and linking. > > > Having additional scripts in your path can confuse software installed via > > Homebrew if the config script overrides a system or Homebrew-provided > > script of the same name. We found the following "config" scripts: > > /Library/Frameworks/Python.framework/Versions/3.8/bin/python3-config > > /Library/Frameworks/Python.framework/Versions/3.8/bin/python3.8-config > > Luos-Air:~ luoxiaoran$ which python3 > > /Library/Frameworks/Python.framework/Versions/3.8/bin/python3 > > Luos-Air:~ luoxiaoran$ > > > So I guess I am still not using Homebrew's Python -how do I switch to > using Homebrew's Python? And what is broken in my Homebrew installation? I > don't remember installing multiple versions of Python before April, but it > is a possibility -how do I uninstall those versions if it is needed to > switch to using Homebrew's Python? Thanks! > > > Best, > > Luna > > On Fri, May 29, 2020 at 9:53 AM Modeller Caretaker < > modeller-care@salilab.org> wrote: > >> On 5/28/20 10:58 PM, Xiao Ran Luo wrote: >> > is there a way to prevent the mismatch between >> > the Homebrew Python and Apple's Python? >> >> The Homebrew Modeller package is designed to work with Homebrew's >> Python, i.e. /usr/local/bin/python3 (it will also work with Homebrew's >> python@3.8 package, but by default that's not in your path). So if >> "import modeller" fails there are are really only 3 possibilities: >> >> 1. You are not using Homebrew's Python, i.e. "which python3" does not >> print "/usr/local/bin/python3" >> or "/usr/local/opt/python@3.8/bin/python3". >> >> 2. Something is broken in your Homebrew installation, i.e. "brew doctor" >> does not print "Your system is ready to brew." >> >> 3. Something is broken elsewhere in your operating system because of you >> deleting the Python framework and/or installing multiple versions of >> Python. >> >> Ben Webb, Modeller Caretaker >> -- >> modeller-care@salilab.org https://salilab.org/modeller/ >> Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage >> >