Homebrew-core: Attempting to upgrade/install python(2) is failing with “Bad interpreter: operation not permitted”

[dljessup]

I tried repeatedly to upgrade python using the command brew upgrade python, and it failed, with the first five failure lines being:

./configure: /usr/local/Homebrew/Library/Homebrew/shims/super/sed: /bin/bash: bad interpreter: Operation not permitted

I attempted to uninstall and reinstall python to no effect except that now I have to run brew install python instead of brew upgrade python, and I had to uninstall vim and macvim. The first five lines of failure are still the above.

I have recorded a gist log to https://gist.github.com/dljessup/2bb32a77ce8183cde96b7feb0ca01d7d

I have attached the output from when I run the command brew install python as brew-upgrade-python.LOG.

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[shoeffner]

Try updating XCode via the App Store, start it and install the additional components, as explained here: https://github.com/macvim-dev/macvim/issues/546#issuecomment-330986310.

[dljessup]

Thank you @shoeffner. Unfortunately, that doesn't appear to be the problem; I am getting exactly the same failures now as before I updated XCode.

[ionescu77]

Same here, unfortunatelly!

I tried all sugestions. I opened xcode. It downloaded the extra components. I restarted my MacMini. Brew doctor. Double update.

I get the same error.

Mac Sierra softwareupdate -l tells me I am up to date.

[fxcoudert]

Another possibility for getting these errors would be that one of the files involved (or directories, or drive) is marked as quarantined. Do you have a particular filesystem setup?

[theemathas]

Note that I also ran into this problem while trying to install macvim with the options --with-override-system-vim.

[dljessup]

@fxcoudert: I don't know what you're asking when you ask if I have a particular filesystem setup. I have the single SSD that came standard with my Macbook. If I run df, I have the following:

Filesystem    512-blocks      Used Available Capacity iused      ifree %iused  Mounted on
/dev/disk1     487830528 122805768 364512760    26% 1555298 4293411981    0%   /
devfs                370       370         0   100%     643          0  100%   /dev
map -hosts             0         0         0   100%       0          0  100%   /net
map auto_home          0         0         0   100%       0          0  100%   /home
map -fstab             0         0         0   100%       0          0  100%   /Network/Servers

Regarding quarantined files, I have looked to see if any of the involved files have the com.apple.quarantine extended attribute, and so far as I can tell, they do not.

[ilovezfs]

What's the output of

git -C $(brew --repo) status

[dljessup]

@ilovezfs:

On branch master
nothing to commit, working tree clean

[ilovezfs]

And how about

HOMEBREW_ENV_FILTERING=1 brew install python

[dljessup]

brew.log

[jrasanen]

Hm, I get this

```--- ~ » brew upgrade 1 ↵
==> Upgrading 1 outdated package, with result:
macvim 8.0-138
==> Upgrading macvim --with-override-system-vim --with-lua --with-luajit
==> Downloading https://github.com/macvim-dev/macvim/archive/snapshot-138.tar.gz
Already downloaded: /Users/jrasanen/Library/Caches/Homebrew/macvim-8.0-138.tar.gz
==> ./configure --with-features=huge --enable-multibyte --with-macarchs=x86_64 --enable-perlinterp --enable-rubyinterp --enable-tclinterp --enable-terminal --with-tlib=ncurses --with-compiledby=Homebrew --with-local-dir=/usr/local --enabl
==> make
Last 15 lines from /Users/jrasanen/Library/Logs/Homebrew/macvim/02.make:
cd /tmp/macvim-20171005-88188-9fewzn/macvim-snapshot-138/src/MacVim
builtin-copy -exclude .DS_Store -exclude CVS -exclude .svn -exclude .git -exclude .hg -strip-debug-symbols -strip-tool /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/strip -resolve-src-symlinks /tmp/macvim-20171005-88188-9fewzn/macvim-snapshot-138/src/MacVim/icons/MacVim.icns /tmp/macvim-20171005-88188-9fewzn/macvim-snapshot-138/src/MacVim/build/Release/MacVim.app/Contents/Resources

CopyPlistFile build/Release/MacVim.app/Contents/Resources/KeyBinding.plist KeyBinding.plist
cd /tmp/macvim-20171005-88188-9fewzn/macvim-snapshot-138/src/MacVim
builtin-copyPlist --outdir /tmp/macvim-20171005-88188-9fewzn/macvim-snapshot-138/src/MacVim/build/Release/MacVim.app/Contents/Resources -- KeyBinding.plist

* BUILD FAILED *

The following build commands failed:
StripNIB English.lproj/FindAndReplace.nib
(1 failure)
make[1]: * [macvim] Error 65
make: * [first] Error 2

READ THIS: https://docs.brew.sh/Troubleshooting.html

These open issues may also help:
Attempting to upgrade/install python(2) is failing with “Bad interpreter: operation not permitted” https://github.com/Homebrew/homebrew-core/issues/18816```

[dljessup]

A little bit of further research:

/usr/local/Homebrew/Library/Homebrew/shims/super/sed is a shellscript which finagles with some environment variables and calls /usr/bin/sed. The first line was a shebang:
#!/bin/bash
By changing this to /bin/sh, I verified that it was this shebang line that was being rejected with “operation not permitted”.

However, when I tried to do some more testing this morning, I stopped getting the “Operation not permitted” errors and instead getting

configure: error: in `/private/tmp/python-20171006-21003-18wm7zp/Python-2.7.14':
configure: error: C compiler cannot create executables

[dljessup]

I'm going to go ahead and close this issue because the install, while still not working, is now breaking at a different, later place.

[theemathas]

For those who are still trying to figure this out, this might be related to #19191. In my case, I fixed it by opening XCode and clicking "Install additional components" when prompted.