Installation error of apbspdb2pqr

[jongseo-park]

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• Confirmed this is a problem with brew installing one, specific formula and not every time you run brew? If it's a general brew problem please file this issue at https://github.com/Homebrew/brew/issues/new.
• Ran brew update and retried your prior step?
• Ran brew doctor, fixed all issues and retried your prior step?
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To help us debug your issue please explain:

• What you were trying to do (and why)

brew install brewsci/bio/apbspdb2pqr

• What happened (include command output)

==> Cloning https://github.com/Electrostatics/apbs-pdb2pqr.git
Updating /Users/jongseo/Library/Caches/Homebrew/apbspdb2pqr--git
==> Checking out tag vAPBS-1.5.0
HEAD is now at aa353941 adding juans changes to rexpcalc
HEAD is now at aa353941 adding juans changes to rexpcalc
Entering 'apbs/externals/bem'
Entering 'apbs/externals/fetk'
Entering 'apbs/externals/geoflow_c'
Entering 'apbs/externals/mesh_routines'
Entering 'apbs/externals/pb_s_am'
/Users/jongseo/Library/Caches/Homebrew/apbspdb2pqr--git/apbs/externals/bem
/Users/jongseo/Library/Caches/Homebrew/apbspdb2pqr--git/apbs/externals/fetk
/Users/jongseo/Library/Caches/Homebrew/apbspdb2pqr--git/apbs/externals/geoflow_c
/Users/jongseo/Library/Caches/Homebrew/apbspdb2pqr--git/apbs/externals/mesh_routines
/Users/jongseo/Library/Caches/Homebrew/apbspdb2pqr--git/apbs/externals/pb_s_am
==> Installing apbspdb2pqr from brewsci/bio
==> cmake .. -DCMAKE_POLICY_DEFAULT_CMP0046=OLD -DCMAKE_POLICY_DEFAULT_CMP0078=O
==> make install
==> python scons/scons.py PREFIX=/opt/homebrew/Cellar/apbspdb2pqr/1.5.0/pdb2pqr 
Last 15 lines from /Users/jongseo/Library/Logs/Homebrew/apbspdb2pqr/03.python:
2022-03-19 15:07:21 +0000

python
scons/scons.py
PREFIX=/opt/homebrew/Cellar/apbspdb2pqr/1.5.0/pdb2pqr
APBS=/opt/homebrew/Cellar/apbspdb2pqr/1.5.0/bin/apbs
BUILD_PDB2PKA=False


If reporting this issue please do so at (not Homebrew/brew or Homebrew/core):
  https://github.com/brewsci/homebrew-bio/issues

These open issues may also help:
apbspdb2pqr 3.0.0 https://github.com/brewsci/homebrew-bio/pull/1481

• What you expected to happen
  Successful installation of the abps & pdb2pqr

• Step-by-step reproduction instructions (by running brew install commands)
  brew install brewsci/bio/apbspdb2pqr

Recently, I have updated the macOS version to 12.3.

And I think that this error was occurred due to the deprecation of python2 in macOS 12.3.

When I checked the file in ~/Library/Logs/Homebrew/apbspdb2pqr/03.python,

there is a path list as below

PATH: /opt/homebrew/Library/Homebrew/shims/mac/super:
/opt/homebrew/opt/cmake/bin:/opt/homebrew/opt/icu4c/bin:
/opt/homebrew/opt/gdbm/bin:/opt/homebrew/opt/[email protected]/bin:
/opt/homebrew/opt/sqlite/bin:/opt/homebrew/opt/xz/bin:
/opt/homebrew/opt/[email protected]/bin:/opt/homebrew/opt/pcre/bin:
/opt/homebrew/opt/swig/bin:/usr/bin:/bin:/usr/sbin:/sbin

Since the python2 is deprecated in the macOS 12.3, I installed pyenv and create a environment with python2.7.18, and created a symbolic link of .../.pyenv/versions/2.7.18/bin/python2.7 to /opt/homebrew/bin/python.

And the symbolic link /opt/homebrew/bin/python was not on the path list.

So, I re-created the symbolic link to /opt/homebrew/opt/[email protected]/bin/python that is on the path list.

Finally, the installation was success using brew install brewsci/bio/apbspdb2pqr.

Unfortunately, I don't know the Ruby, so I couldn't modify the apbspdb2pqr.rb file.

I hope it will be updated soon.

[YoshitakaMo]

I created apbspdb2pqr.rb a long time ago, but for now, I recommend you install it without Homebrew because the installation from source on macOS (both Intel Mac and M1) requires some tricks. See also Electrostatics/FETK#62 and my formula. I recommend their official binaries instead.

But it is possible to create a patch and release a new Formula without waiting for the developer to fix it. I'll try to update when I have time.

[YoshitakaMo]

@jongseo-park I renewed apbs 3.4.0 #1541 . Now that apbs and pdb2pqr packages are independently developed, the formulae should be divided.

$ brew uninstall apbs2pdb2pqr
$ brew install brewsci/bio/apbs

pdb2pqr is currently recommended to be installed with pip.