brew audit fails to run because of gem installation failure

[equal-l2]

I'm posting here because I'm not sure this would occur with the other box, though this is reproducible with my box.

Bug report

Please note we will close your issue without comment if you delete, do not read or do not fill out the issue checklist below and provide ALL the requested information. If you repeatedly fail to use the issue template, we will block you from ever submitting issues to Homebrew again.

• ran brew update and can still reproduce the problem?
• ran brew doctor, fixed all issues and can still reproduce the problem?
• ran brew config and brew doctor and included their output with your issue?

What you were trying to do (and why)

brew audit --strict appstream-glib

What happened (include command output)

It failed to run because of gem installation failure.

Command output

Fetching gem metadata from https://rubygems.org/.........
Using concurrent-ruby 1.1.7
Using minitest 5.14.2
Using thread_safe 0.3.6
Using zeitwerk 2.4.0
Using ast 2.4.1
Using bindata 2.4.8
Using bundler 1.17.2
Using docile 1.3.2
Fetching byebug 11.1.3
Fetching json 2.3.1
Using simplecov-html 0.12.2
Using coderay 1.1.3
Using colorize 0.8.1
Using highline 2.0.3
Using connection_pool 2.2.3
Using diff-lcs 1.4.4
Fetching unf_ext 0.0.7.7
Installing byebug 11.1.3 with native extensions
Installing json 2.3.1 with native extensions
Installing unf_ext 0.0.7.7 with native extensions
Fetching hpricot 0.8.6
Installing hpricot 0.8.6 with native extensions
Using mime-types-data 3.2020.0512
Using net-http-digest_auth 1.4.1
Using mini_portile2 2.4.0
Using ntlm-http 0.1.1
Using webrobots 0.1.2
Using method_source 1.0.0
Using mustache 1.1.1
Using parallel 1.19.2
Using rainbow 3.0.0
Using sorbet-runtime 0.5.5891
Using plist 3.5.0
Fetching rdiscount 2.2.0.2
Installing rdiscount 2.2.0.2 with native extensions
Using regexp_parser 1.7.1
Using rexml 3.2.4
Using rspec-support 3.9.3
Using ruby-progressbar 1.10.1
Using unicode-display_width 1.7.0
Using ruby-macho 2.2.0
Using sorbet-static 0.5.5891 (universal-darwin-19)
Using thor 1.0.1
Using i18n 1.8.5
Using tzinfo 1.2.7
Using elftools 1.1.3
Using parser 2.7.1.4
Using simplecov 0.19.0
Using commander 4.5.2
Using net-http-persistent 4.0.0
Using mime-types 3.3.1
Fetching nokogiri 1.10.10
Installing nokogiri 1.10.10 with native extensions
Using pry 0.13.1
Using parallel_tests 3.2.0
Using rspec-core 3.9.2
Using rspec-expectations 3.9.2
Using rspec-mocks 3.9.1
Using sorbet 0.5.5891
Using activesupport 6.0.3.2
Using patchelf 1.3.0
Using rubocop-ast 0.3.0
Using parlour 4.0.1
Using rspec-retry 0.6.2
Using rspec-its 1.3.0
Using rspec 3.9.0
Using spoom 1.0.4
Gem::Ext::BuildError: ERROR: Failed to build gem native extension.
current directory: /usr/local/Homebrew/Library/Homebrew/vendor/bundle/ruby/2.6.0/gems/byebug-11.1.3/ext/byebug

/System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/bin/ruby -I

/System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib/ruby/2.6.0 -r ./siteconf20200909-47076-1th4zn.rb

extconf.rb

creating Makefile
current directory: /usr/local/Homebrew/Library/Homebrew/vendor/bundle/ruby/2.6.0/gems/byebug-11.1.3/ext/byebug

make "DESTDIR=" clean
current directory: /usr/local/Homebrew/Library/Homebrew/vendor/bundle/ruby/2.6.0/gems/byebug-11.1.3/ext/byebug

make "DESTDIR="

make: *** No rule to make target

/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/include/ruby-2.6.0/universal-darwin19/ruby/config.h', needed by breakpoint.o'.  Stop.
make failed, exit code 2
Gem files will remain installed in /usr/local/Homebrew/Library/Homebrew/vendor/bundle/ruby/2.6.0/gems/byebug-11.1.3 for

inspection.

Results logged to

/usr/local/Homebrew/Library/Homebrew/vendor/bundle/ruby/2.6.0/extensions/universal-darwin-19/2.6.0/byebug-11.1.3/gem_make.out
An error occurred while installing byebug (11.1.3), and Bundler cannot continue.

Make sure that gem install byebug -v '11.1.3' --source 'https://rubygems.org/' succeeds before bundling.
In Gemfile:

byebug
Gem::Ext::BuildError: ERROR: Failed to build gem native extension.
current directory:

/usr/local/Homebrew/Library/Homebrew/vendor/bundle/ruby/2.6.0/gems/json-2.3.1/ext/json/ext/generator

/System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/bin/ruby -I

/System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib/ruby/2.6.0 -r ./siteconf20200909-47076-1pzhd1t.rb

extconf.rb

creating Makefile
current directory: /usr/local/Homebrew/Library/Homebrew/vendor/bundle/ruby/2.6.0/gems/json-2.3.1/ext/json/ext/generator

make "DESTDIR=" clean
current directory: /usr/local/Homebrew/Library/Homebrew/vendor/bundle/ruby/2.6.0/gems/json-2.3.1/ext/json/ext/generator

make "DESTDIR="

compiling generator.c

In file included from generator.c:1:

In file included from ./../fbuffer/fbuffer.h:5:

In file included from

/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/include/ruby-2.6.0/ruby.h:33:

/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/include/ruby-2.6.0/ruby/ruby.h:24:10:

fatal error: 'ruby/config.h' file not found

#include "ruby/config.h"

^~~~~~~~~~~~~~~

/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/include/ruby-2.6.0/ruby/ruby.h:24:10:

note: did not find header 'config.h' in framework 'ruby' (loaded from

'/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/System/Library/Frameworks')

1 error generated.

make: *** [generator.o] Error 1
make failed, exit code 2
Gem files will remain installed in /usr/local/Homebrew/Library/Homebrew/vendor/bundle/ruby/2.6.0/gems/json-2.3.1 for

inspection.

Results logged to

/usr/local/Homebrew/Library/Homebrew/vendor/bundle/ruby/2.6.0/extensions/universal-darwin-19/2.6.0/json-2.3.1/gem_make.out
An error occurred while installing json (2.3.1), and Bundler cannot continue.

Make sure that gem install json -v '2.3.1' --source 'https://rubygems.org/' succeeds before bundling.
In Gemfile:

codecov was resolved to 0.2.11, which depends on

json
Gem::Ext::BuildError: ERROR: Failed to build gem native extension.
current directory: /usr/local/Homebrew/Library/Homebrew/vendor/bundle/ruby/2.6.0/gems/unf_ext-0.0.7.7/ext/unf_ext

/System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/bin/ruby -I

/System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib/ruby/2.6.0 -r ./siteconf20200909-47076-ln5ym8.rb

extconf.rb

checking for -lstdc++... *** extconf.rb failed ***

Could not create Makefile due to some reason, probably lack of necessary

libraries and/or headers.  Check the mkmf.log file for more details.  You may

need configuration options.
Provided configuration options:

--with-opt-dir

--without-opt-dir

--with-opt-include

--without-opt-include=${opt-dir}/include

--with-opt-lib

--without-opt-lib=${opt-dir}/lib

--with-make-prog

--without-make-prog

--srcdir=.

--curdir

--ruby=/System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/bin/$(RUBY_BASE_NAME)

--with-static-libstdc++

--without-static-libstdc++

--with-stdc++lib

--without-stdc++lib

/System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib/ruby/2.6.0/mkmf.rb:467:in try_do': The compiler failed to generate an executable file. (RuntimeError) You have to install development tools first. from /System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib/ruby/2.6.0/mkmf.rb:546:in block in try_link0'

from /System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib/ruby/2.6.0/tmpdir.rb:93:in mktmpdir' from /System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib/ruby/2.6.0/mkmf.rb:543:in try_link0'

from /System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib/ruby/2.6.0/mkmf.rb:570:in try_link' from /System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib/ruby/2.6.0/mkmf.rb:789:in try_func'

from /System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib/ruby/2.6.0/mkmf.rb:1016:in block in have_library' from /System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib/ruby/2.6.0/mkmf.rb:959:in block in checking_for'

from /System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib/ruby/2.6.0/mkmf.rb:361:in block (2 levels) in postpone' from /System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib/ruby/2.6.0/mkmf.rb:331:in open'

from /System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib/ruby/2.6.0/mkmf.rb:361:in block in postpone' from /System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib/ruby/2.6.0/mkmf.rb:331:in open'

from /System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib/ruby/2.6.0/mkmf.rb:357:in postpone' from /System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib/ruby/2.6.0/mkmf.rb:958:in checking_for'

from /System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib/ruby/2.6.0/mkmf.rb:1011:in have_library' from extconf.rb:6:in 
'

To see why this extension failed to compile, please check the mkmf.log which can be found here:
/usr/local/Homebrew/Library/Homebrew/vendor/bundle/ruby/2.6.0/extensions/universal-darwin-19/2.6.0/unf_ext-0.0.7.7/mkmf.log
extconf failed, exit code 1
Gem files will remain installed in /usr/local/Homebrew/Library/Homebrew/vendor/bundle/ruby/2.6.0/gems/unf_ext-0.0.7.7 for

inspection.

Results logged to

/usr/local/Homebrew/Library/Homebrew/vendor/bundle/ruby/2.6.0/extensions/universal-darwin-19/2.6.0/unf_ext-0.0.7.7/gem_make.out
An error occurred while installing unf_ext (0.0.7.7), and Bundler cannot continue.

Make sure that gem install unf_ext -v '0.0.7.7' --source 'https://rubygems.org/' succeeds before bundling.
In Gemfile:

mechanize was resolved to 2.7.6, which depends on

http-cookie was resolved to 1.0.3, which depends on

domain_name was resolved to 0.5.20190701, which depends on

unf was resolved to 0.1.4, which depends on

unf_ext
Gem::Ext::BuildError: ERROR: Failed to build gem native extension.
current directory: /usr/local/Homebrew/Library/Homebrew/vendor/bundle/ruby/2.6.0/gems/hpricot-0.8.6/ext/fast_xs

/System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/bin/ruby -I

/System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib/ruby/2.6.0 -r ./siteconf20200909-47076-1ue0hg0.rb

extconf.rb

checking for stdio.h... *** extconf.rb failed ***

Could not create Makefile due to some reason, probably lack of necessary

libraries and/or headers.  Check the mkmf.log file for more details.  You may

need configuration options.
Provided configuration options:

--with-opt-dir

--without-opt-dir

--with-opt-include

--without-opt-include=${opt-dir}/include

--with-opt-lib

--without-opt-lib=${opt-dir}/lib

--with-make-prog

--without-make-prog

--srcdir=.

--curdir

--ruby=/System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/bin/$(RUBY_BASE_NAME)

/System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib/ruby/2.6.0/mkmf.rb:467:in try_do': The compiler failed to generate an executable file. (RuntimeError) You have to install development tools first. from /System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib/ruby/2.6.0/mkmf.rb:585:in block in try_compile'

from /System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib/ruby/2.6.0/mkmf.rb:534:in with_werror' from /System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib/ruby/2.6.0/mkmf.rb:585:in try_compile'

from /System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib/ruby/2.6.0/mkmf.rb:1109:in block in have_header' from /System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib/ruby/2.6.0/mkmf.rb:959:in block in checking_for'

from /System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib/ruby/2.6.0/mkmf.rb:361:in block (2 levels) in postpone' from /System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib/ruby/2.6.0/mkmf.rb:331:in open'

from /System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib/ruby/2.6.0/mkmf.rb:361:in block in postpone' from /System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib/ruby/2.6.0/mkmf.rb:331:in open'

from /System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib/ruby/2.6.0/mkmf.rb:357:in postpone' from /System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib/ruby/2.6.0/mkmf.rb:958:in checking_for'

from /System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib/ruby/2.6.0/mkmf.rb:1108:in have_header' from extconf.rb:2:in 
'

To see why this extension failed to compile, please check the mkmf.log which can be found here:
/usr/local/Homebrew/Library/Homebrew/vendor/bundle/ruby/2.6.0/extensions/universal-darwin-19/2.6.0/hpricot-0.8.6/mkmf.log
extconf failed, exit code 1
Gem files will remain installed in /usr/local/Homebrew/Library/Homebrew/vendor/bundle/ruby/2.6.0/gems/hpricot-0.8.6 for

inspection.

Results logged to

/usr/local/Homebrew/Library/Homebrew/vendor/bundle/ruby/2.6.0/extensions/universal-darwin-19/2.6.0/hpricot-0.8.6/gem_make.out
An error occurred while installing hpricot (0.8.6), and Bundler cannot continue.

Make sure that gem install hpricot -v '0.8.6' --source 'https://rubygems.org/' succeeds before bundling.
In Gemfile:

ronn was resolved to 0.7.3, which depends on

hpricot

Error: failed to run /System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/bin/bundle install!
  

What you expected to happen

Successfully run brew audit

Step-by-step reproduction instructions (by running brew commands)

brew audit --strict appstream-glib

Output of brew config and brew doctor commands

brew config

HOMEBREW_VERSION: 2.5.0-22-gb94f9dc
ORIGIN: https://github.com/Homebrew/brew
HEAD: b94f9dccd71f43397eb028eecccd147375e9fd00
Last commit: 2 hours ago
Core tap ORIGIN: https://github.com/Homebrew/homebrew-core
Core tap HEAD: d0fe2d712e49c561e2b04071638813d7d10f6c11
Core tap last commit: 4 hours ago
Core tap branch: master
HOMEBREW_PREFIX: /usr/local
HOMEBREW_CASK_OPTS: []
HOMEBREW_EDITOR: nvim
HOMEBREW_MAKE_JOBS: 8
Homebrew Ruby: 2.6.3 => /System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/bin/ruby
CPU: octa-core 64-bit kabylake
Clang: 11.0 build 1103
Git: 2.28.0 => /usr/local/bin/git
Curl: 7.64.1 => /usr/bin/curl
Java: 14.0.2
macOS: 10.15.6-x86_64
CLT: 12.0.0.0.1.1597368733
Xcode: 11.7

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:
  /Users/equall2/.cargo/bin/cargo-install-update-config

Warning: Unbrewed header files were found in /usr/local/include.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.

Unexpected header files:
  /usr/local/include/python3.8/greenlet/greenlet.h

[jonchang]

Yea, this is a pretty common error with system Ruby on the newer macOS versions, related to your Xcode, CLT installs, or mixing system and brewed Ruby. Stack Overflow has a few things that you could try, check out this link: https://stackoverflow.com/questions/53135863/macos-mojave-ruby-config-h-file-not-found

[equal-l2]

Thank you for your advice, CLT was the culprit in my case.
With the following, the problem has fixed.

$ sudo rm -rf /Library/Developer/CommandLineTools
$ xcode-select --install

I wish there's an FAQ or troubleshooting documentation for this kind of problem, as beginner contributors occasionally come across this.