Brew: Since upgrading to OSX Mojave, am receiving warnings about commonmarker-0.17.9/0.17.7.1

Created on 22 Oct 2018  路  16Comments  路  Source: Homebrew/brew

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

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Since upgrading to OSX Mojave this morning, I get the following warnings whenever I run any brew command:

Ignoring commonmarker-0.17.9 because its extensions are not built.  Try: gem pristine commonmarker --version 0.17.9
Ignoring commonmarker-0.17.7.1 because its extensions are not built.  Try: gem pristine commonmarker --version 0.17.7.1

As requested:

$ brew config
Ignoring commonmarker-0.17.9 because its extensions are not built.  Try: gem pristine commonmarker --version 0.17.9
Ignoring commonmarker-0.17.7.1 because its extensions are not built.  Try: gem pristine commonmarker --version 0.17.7.1
HOMEBREW_VERSION: 1.7.7
ORIGIN: https://github.com/Homebrew/brew
HEAD: c54a657cd5987cba2718f7012a55101324fde8b1
Last commit: 2 weeks ago
Core tap ORIGIN: https://github.com/Homebrew/homebrew-core
Core tap HEAD: d2e1518558c1b08a8c98f1837e714b923b656849
Core tap last commit: 4 hours ago
HOMEBREW_PREFIX: /usr/local
CPU: quad-core 64-bit haswell
Homebrew Ruby: 2.3.7 => /System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/bin/ruby
Clang: 10.0 build 1000
Git: 2.19.1 => /usr/local/bin/git
Curl: 7.54.0 => /usr/bin/curl
Java: 10.0.2
macOS: 10.14-x86_64
CLT: 10.0.0.0.1.1535735448
Xcode: N/A
$ brew doctor
Ignoring commonmarker-0.17.9 because its extensions are not built.  Try: gem pristine commonmarker --version 0.17.9
Ignoring commonmarker-0.17.7.1 because its extensions are not built.  Try: gem pristine commonmarker --version 0.17.7.1
Your system is ready to brew.

I have run gem install commonmarker:

$ gem list | grep commonmarker
commonmarker (0.18.1)

I've also attempted to follow the instructions in the warning:

$ gem pristine commonmarker --version 0.17.9
ERROR:  While executing gem ... (Gem::Exception)
    Failed to find gems ["commonmarker"] = 0.17.9
outdated

Most helpful comment

I did, don't get me wrong, but also had to add /usr/local/lib/ruby/gems/2.5.0/bin to my PATH and still I was experiencing some weird behaviours from the previous existing gem binaries in /usr/local/bin.

I understand the risks of linking a keg-only formula, but I guess I fancy the 'think twice' rationale behind the --force option in the link command that allows the user to keep control of her own environment while still leveraging the awesome capabilities of the brew tool.

All 16 comments

Where is that gem installed? Does brew cleanup help at all?

That gem appears to be installed at /usr/local/lib/ruby/gems/2.5.0/gems/commonmarker-0.18.1.

Full gem env output:

$ gem env
RubyGems Environment:
  - RUBYGEMS VERSION: 2.7.7
  - RUBY VERSION: 2.5.3 (2018-10-18 patchlevel 105) [x86_64-darwin18]
  - INSTALLATION DIRECTORY: /usr/local/lib/ruby/gems/2.5.0
  - USER INSTALLATION DIRECTORY: /Users/tom/.gem/ruby/2.5.0
  - RUBY EXECUTABLE: /usr/local/opt/ruby/bin/ruby
  - EXECUTABLE DIRECTORY: /usr/local/bin
  - SPEC CACHE DIRECTORY: /Users/tom/.gem/specs
  - SYSTEM CONFIGURATION DIRECTORY: /usr/local/Cellar/ruby/2.5.3/etc
  - RUBYGEMS PLATFORMS:
    - ruby
    - x86_64-darwin-18
  - GEM PATHS:
     - /usr/local/lib/ruby/gems/2.5.0
     - /Users/tom/.gem/ruby/2.5.0
     - /usr/local/Cellar/ruby/2.5.3/lib/ruby/gems/2.5.0
  - GEM CONFIGURATION:
     - :update_sources => true
     - :verbose => true
     - :backtrace => false
     - :bulk_threshold => 1000
  - REMOTE SOURCES:
     - https://rubygems.org/
  - SHELL PATH:
     - /usr/local/opt/icu4c/sbin
     - /usr/local/opt/icu4c/bin
     - /Users/tom/.cabal/bin
     - /Users/tom/Library/Haskell/bin
     - /opt/local/bin
     - /opt/local/sbin
     - /.composer/vendor/bin
     - /Users/tom/.go/bin
     - /usr/local/bin
     - /usr/local/sbin
     - /usr/local/bin
     - /usr/bin
     - /bin
     - /usr/sbin
     - /sbin
     - /usr/local/MacGPG2/bin

brew cleanup did not fix the issue:

$ brew cleanup
Ignoring commonmarker-0.17.9 because its extensions are not built.  Try: gem pristine commonmarker --version 0.17.9
Ignoring commonmarker-0.17.7.1 because its extensions are not built.  Try: gem pristine commonmarker --version 0.17.7.1
Removing: /usr/local/Cellar/apr/1.6.3... (60 files, 1.3MB)
Removing: /usr/local/Cellar/cairo/1.14.12... (118 files, 5.8MB)
Removing: /Users/tom/Library/Caches/Homebrew/cairo--1.14.12.high_sierra.bottle.tar.gz... (1.6MB)
Removing: /usr/local/Cellar/composer/1.6.5... (3 files, 1.8MB)
Removing: /usr/local/Cellar/composer/1.7.0... (3 files, 1.8MB)
Removing: /usr/local/Cellar/composer/1.7.1... (3 files, 1.8MB)
Removing: /usr/local/Cellar/freetds/1.00.92... (2,094 files, 11.9MB)
Removing: /usr/local/Cellar/freetds/1.00.94... (2,094 files, 11.9MB)
Removing: /usr/local/Cellar/freetds/1.00.97... (2,094 files, 11.9MB)
Removing: /usr/local/Cellar/freetds/1.00.98... (2,094 files, 11.9MB)
Removing: /Users/tom/Library/Caches/Homebrew/freetds--1.00.97.high_sierra.bottle.tar.gz... (2.3MB)
Removing: /Users/tom/Library/Caches/Homebrew/freetds--1.00.98.high_sierra.bottle.tar.gz... (2.3MB)
Removing: /usr/local/Cellar/gdbm/1.16... (19 files, 578.5KB)
Removing: /usr/local/Cellar/gdbm/1.17... (20 files, 581.4KB)
Removing: /usr/local/Cellar/git/2.18.0... (1,488 files, 35.2MB)
Removing: /usr/local/Cellar/git/2.19.0... (1,499 files, 309MB)
Removing: /usr/local/Cellar/git/2.19.0_1... (1,512 files, 318.2MB)
Removing: /usr/local/Cellar/git/2.19.0_2... (1,512 files, 40.1MB)
Removing: /Users/tom/Library/Caches/Homebrew/git--2.19.0_2.high_sierra.bottle.tar.gz... (14.7MB)
Removing: /Users/tom/Library/Caches/Homebrew/git--2.19.0.high_sierra.bottle.tar.gz... (13MB)
Removing: /Users/tom/Library/Caches/Homebrew/git--2.19.0_1.high_sierra.bottle.tar.gz... (14.7MB)
Removing: /usr/local/Cellar/glib/2.56.1... (430 files, 23.7MB)
Removing: /usr/local/Cellar/glib/2.56.2... (430 files, 23.7MB)
Removing: /usr/local/Cellar/glib/2.58.0_1... (435 files, 18.4MB)
Removing: /Users/tom/Library/Caches/Homebrew/glib--2.56.2.high_sierra.bottle.tar.gz... (7MB)
Removing: /Users/tom/Library/Caches/Homebrew/glib--2.58.0_1.high_sierra.bottle.tar.gz... (5.6MB)
Removing: /usr/local/Cellar/gnuplot/5.2.4... (45 files, 2.5MB)
Removing: /Users/tom/Library/Caches/Homebrew/gnuplot--5.2.4.high_sierra.bottle.tar.gz... (1MB)
Removing: /usr/local/Cellar/imagemagick/7.0.8-12... (1,515 files, 23.2MB)
Removing: /usr/local/Cellar/libpng/1.6.34... (26 files, 1.2MB)
Removing: /usr/local/Cellar/libpq/10.4... (2,430 files, 26.9MB)
Removing: /usr/local/Cellar/libpq/10.5... (2,436 files, 27.0MB)
Removing: /usr/local/Cellar/mono/5.12.0.226_1... (3,548 files, 395.7MB)
Removing: /usr/local/Cellar/node/10.10.0... (3,940 files, 49.3MB)
Removing: /usr/local/Cellar/node/10.11.0... (3,940 files, 46.3MB)
Removing: /usr/local/Cellar/node/10.9.0... (4,022 files, 49.0MB)
Removing: /Users/tom/Library/Caches/Homebrew/node--10.11.0.high_sierra.bottle.tar.gz... (12.6MB)
Removing: /Users/tom/Library/Caches/Homebrew/node--10.10.0.high_sierra.bottle.tar.gz... (13MB)
Removing: /usr/local/Cellar/openssl/1.0.2o_2... (1,792 files, 12.3MB)
Removing: /usr/local/Cellar/php/7.2.10... (515 files, 74.9MB)
Removing: /usr/local/Cellar/php/7.2.8... (516 files, 79.1MB)
Removing: /usr/local/Cellar/php/7.2.9... (516 files, 79.1MB)
Removing: /usr/local/Cellar/php/7.2.9_2... (515 files, 74.9MB)
Removing: /Users/tom/Library/Caches/Homebrew/php--7.2.10.high_sierra.bottle.tar.gz... (19.5MB)
Removing: /Users/tom/Library/Caches/Homebrew/php--7.2.9_2.high_sierra.bottle.tar.gz... (19.5MB)
Removing: /usr/local/Cellar/ruby/2.5.1... (16,227 files, 27.5MB)
Removing: /usr/local/Cellar/ruby/2.5.2... (16,221 files, 27.2MB)
Removing: /Users/tom/Library/Caches/Homebrew/ruby--2.5.2.high_sierra.bottle.tar.gz... (7.7MB)
Removing: /Users/tom/Library/Caches/Homebrew/ruby--2.5.1.high_sierra.bottle.tar.gz... (8MB)
Removing: /usr/local/Cellar/sqlite/3.24.0... (11 files, 3.5MB)
Removing: /usr/local/Cellar/sqlite/3.25.1... (11 files, 3.7MB)
Removing: /Users/tom/Library/Caches/Homebrew/sqlite--3.25.1.high_sierra.bottle.tar.gz... (1.8MB)
Removing: /usr/local/Cellar/telnet/54.50.1... (4 files, 246KB)
Removing: /usr/local/Cellar/unixodbc/2.3.6... (46 files, 1.8MB)
Removing: /Users/tom/Library/Caches/Homebrew/mono-5.12.0.226_1.high_sierra.bottle.tar.gz... (132.3MB)
Removing: /Users/tom/Library/Caches/Homebrew/node-10.9.0.high_sierra.bottle.tar.gz... (13MB)
Removing: /Users/tom/Library/Caches/Homebrew/libpq-10.5.high_sierra.bottle.tar.gz... (6.1MB)
Removing: /Users/tom/Library/Caches/Homebrew/apr-1.6.3.high_sierra.bottle.tar.gz... (390.7KB)
Removing: /Users/tom/Library/Caches/Homebrew/php-7.2.8.high_sierra.bottle.tar.gz... (21.7MB)
Removing: /Users/tom/Library/Caches/Homebrew/gdbm-1.16.high_sierra.bottle.tar.gz... (189.7KB)
Removing: /Users/tom/Library/Caches/Homebrew/freetds-1.00.94.high_sierra.bottle.tar.gz... (2.3MB)
Removing: /Users/tom/Library/Caches/Homebrew/libpng-1.6.34.high_sierra.bottle.tar.gz... (444.4KB)
Removing: /Users/tom/Library/Caches/Homebrew/openssl-1.0.2o_2.high_sierra.bottle.tar.gz... (3.7MB)
Removing: /Users/tom/Library/Caches/Homebrew/cabal-install-2.2.0.0.high_sierra.bottle.tar.gz... (6.1MB)
Removing: /Users/tom/Library/Caches/Homebrew/git-2.18.0.high_sierra.bottle.tar.gz... (13.3MB)
Removing: /Users/tom/Library/Caches/Homebrew/gdbm-1.17.high_sierra.bottle.tar.gz... (190.7KB)
Removing: /Users/tom/Library/Caches/Homebrew/freetds-1.00.92.high_sierra.bottle.tar.gz... (2.3MB)
Removing: /Users/tom/Library/Caches/Homebrew/php-7.2.9.high_sierra.bottle.tar.gz... (21.7MB)
Removing: /Users/tom/Library/Caches/Homebrew/unixodbc-2.3.6.high_sierra.bottle.tar.gz... (562.8KB)
Removing: /Users/tom/Library/Caches/Homebrew/composer-1.7.1.phar... (1.8MB)
Removing: /Users/tom/Library/Caches/Homebrew/composer-1.6.5.phar... (1.8MB)
Removing: /Users/tom/Library/Caches/Homebrew/libpq-10.4.high_sierra.bottle.tar.gz... (6MB)
Removing: /Users/tom/Library/Caches/Homebrew/sqlite-3.24.0.high_sierra.bottle.tar.gz... (1.7MB)
Removing: /Users/tom/Library/Caches/Homebrew/glib-2.56.1.high_sierra.bottle.tar.gz... (7MB)
Removing: /Users/tom/Library/Caches/Homebrew/telnet-54.50.1.high_sierra.bottle.1.tar.gz... (94.2KB)
Removing: /Users/tom/Library/Caches/Homebrew/composer-1.7.0.phar... (1.8MB)
Removing: /Users/tom/Library/Logs/Homebrew/libtool... (64B)
Removing: /Users/tom/Library/Logs/Homebrew/gmp... (64B)
Removing: /Users/tom/Library/Logs/Homebrew/wget... (64B)
Removing: /Users/tom/Library/Logs/Homebrew/darcs... (64B)
Removing: /Users/tom/Library/Logs/Homebrew/libidn2... (64B)
Removing: /Users/tom/Library/Logs/Homebrew/libxml2... (64B)
Removing: /Users/tom/Library/Logs/Homebrew/python@2... (3 files, 123.7KB)
Removing: /Users/tom/Library/Logs/Homebrew/libpng... (64B)
Removing: /Users/tom/Library/Logs/Homebrew/gdbm... (64B)
Removing: /Users/tom/Library/Logs/Homebrew/freetype... (64B)
Removing: /Users/tom/Library/Logs/Homebrew/argon2... (64B)
Removing: /Users/tom/Library/Logs/Homebrew/python... (3 files, 127.8KB)
Removing: /Users/tom/Library/Logs/Homebrew/libunistring... (64B)
Removing: /Users/tom/Library/Logs/Homebrew/libyaml... (64B)
Removing: /Users/tom/Library/Logs/Homebrew/apr-util... (64B)
Removing: /Users/tom/Library/Logs/Homebrew/icu4c... (64B)
Removing: /Users/tom/Library/Logs/Homebrew/composer... (104B)
Removing: /Users/tom/Library/Logs/Homebrew/glib... (64B)
Removing: /Users/tom/Library/Logs/Homebrew/readline... (64B)
Removing: /Users/tom/Library/Logs/Homebrew/webp... (64B)
Removing: /Users/tom/Library/Logs/Homebrew/sqlite... (64B)
Removing: /Users/tom/Library/Logs/Homebrew/php... (12 files, 2.2KB)
Removing: /Users/tom/Library/Logs/Homebrew/xz... (64B)
Removing: /Users/tom/Library/Logs/Homebrew/unixodbc... (64B)
Removing: /Users/tom/Library/Logs/Homebrew/ntfs-3g... (64B)
Removing: /Users/tom/Library/Logs/Homebrew/ghc... (230B)
Removing: /Users/tom/Library/Logs/Homebrew/freetds... (64B)
Removing: /Users/tom/Library/Logs/Homebrew/gettext... (64B)
Removing: /Users/tom/Library/Logs/Homebrew/libsodium... (64B)
Removing: /Users/tom/Library/Logs/Homebrew/apr... (64B)
Removing: /Users/tom/Library/Logs/Homebrew/autoconf... (64B)
Removing: /Users/tom/Library/Logs/Homebrew/mono... (64B)
Removing: /Users/tom/Library/Logs/Homebrew/libpq... (64B)
Removing: /Users/tom/Library/Logs/Homebrew/aspell... (64B)
Removing: /Users/tom/Library/Logs/Homebrew/pcre2... (64B)
Removing: /Users/tom/Library/Logs/Homebrew/pcre... (64B)
Removing: /Users/tom/Library/Logs/Homebrew/cabal-install... (64B)
Removing: /Users/tom/Library/Logs/Homebrew/node... (64B)
Removing: /Users/tom/Library/Logs/Homebrew/jpeg... (64B)
Removing: /Users/tom/Library/Logs/Homebrew/libzip... (64B)
Removing: /Users/tom/Library/Logs/Homebrew/openssl... (64B)
Removing: /Users/tom/Library/Logs/Homebrew/bash-completion... (64B)
Removing: /Users/tom/Library/Logs/Homebrew/ruby... (64B)
Removing: /Users/tom/Library/Logs/Homebrew/git... (64B)
Removing: /Users/tom/Library/Logs/Homebrew/libffi... (64B)
Removing: /Users/tom/Library/Logs/Homebrew/telnet... (64B)
==> This operation has freed approximately 2.2GB of disk space.

$ brew cleanup
Ignoring commonmarker-0.17.9 because its extensions are not built.  Try: gem pristine commonmarker --version 0.17.9
Ignoring commonmarker-0.17.7.1 because its extensions are not built.  Try: gem pristine commonmarker --version 0.17.7.1

What does /usr/bin/gem env output?

Ah-ha, interesting:

$ /usr/bin/gem env
Ignoring commonmarker-0.17.9 because its extensions are not built.  Try: gem pristine commonmarker --version 0.17.9
Ignoring commonmarker-0.17.7.1 because its extensions are not built.  Try: gem pristine commonmarker --version 0.17.7.1
RubyGems Environment:
  - RUBYGEMS VERSION: 2.5.2.3
  - RUBY VERSION: 2.3.7 (2018-03-28 patchlevel 456) [universal.x86_64-darwin18]
  - INSTALLATION DIRECTORY: /Library/Ruby/Gems/2.3.0
  - USER INSTALLATION DIRECTORY: /Users/tom/.gem/ruby/2.3.0
  - RUBY EXECUTABLE: /System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/bin/ruby
  - EXECUTABLE DIRECTORY: /usr/local/bin
  - SPEC CACHE DIRECTORY: /Users/tom/.gem/specs
  - SYSTEM CONFIGURATION DIRECTORY: /Library/Ruby/Site
  - RUBYGEMS PLATFORMS:
    - ruby
    - universal-darwin-18
  - GEM PATHS:
     - /Library/Ruby/Gems/2.3.0
     - /Users/tom/.gem/ruby/2.3.0
     - /System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/lib/ruby/gems/2.3.0
  - GEM CONFIGURATION:
     - :update_sources => true
     - :verbose => true
     - :backtrace => false
     - :bulk_threshold => 1000
  - REMOTE SOURCES:
     - https://rubygems.org/
  - SHELL PATH:
     - /usr/local/opt/icu4c/sbin
     - /usr/local/opt/icu4c/bin
     - /Users/tom/.cabal/bin
     - /Users/tom/Library/Haskell/bin
     - /opt/local/bin
     - /opt/local/sbin
     - /.composer/vendor/bin
     - /Users/tom/.go/bin
     - /usr/local/bin
     - /usr/local/sbin
     - /usr/local/bin
     - /usr/bin
     - /bin
     - /usr/sbin
     - /sbin
     - /usr/local/MacGPG2/bin

I have ruby installed via homebrew so, as you suspected, it seems to be shadowing the native ruby install, which is what's having issues. I followed the instructions using the full gem path:

$ sudo /usr/bin/gem pristine commonmarker --version 0.17.9
Ignoring commonmarker-0.17.9 because its extensions are not built.  Try: gem pristine commonmarker --version 0.17.9
Ignoring commonmarker-0.17.7.1 because its extensions are not built.  Try: gem pristine commonmarker --version 0.17.7.1
Restoring gems to pristine condition...
Building native extensions.  This could take a while...
Restored commonmarker-0.17.9

$ sudo /usr/bin/gem pristine commonmarker --version 0.17.7.1
Ignoring commonmarker-0.17.7.1 because its extensions are not built.  Try: gem pristine commonmarker --version 0.17.7.1
Restoring gems to pristine condition...
Building native extensions.  This could take a while...
Restored commonmarker-0.17.7.1

$ brew doctor
Your system is ready to brew.

No more warnings.

Many thanks for the assistance here. Very much appreciated.

No more warnings.

Glad you got it sorted 馃憤.

@Homebrew/core Stuff like this makes me debate whether Ruby should be keg-only; I've stopped using it personally because of how much it messes around with stuff systemwide like this and I'm lucky it's not used as a dependency for anything I use. Thoughts?

I hate running sudo gem install blah when using system ruby (it just feels wrong after using homebrew for so long) but I'm inclined to agree with you @MikeMcQuaid. I've run into many issues over the years where my ruby environment gets borked, and leaves me super confused. (I'm no Ruby expert...)

So put me down as a vote in favor of making it keg only, I guess, but, I defer to the ruby experts out there, so maybe only count it if there's a tie. :trollface: 馃槅

I defer to the ruby experts out there

FWIW in the context of the Homebrew project I may be a Ruby "expert"; it's been my main go-to language for my hobby projects and day job for the last ~6 years.

Seeing as I've ended up inadvertently being included in this discussion, I have a question from curiosity:

What is the point, in general, of having the ruby package be "keg only".

From my understanding, it being keg only means that it's installed but not symlinked or set up in a way that it ends up on the path for the user. Correct?

In what circumstances would a person want to install the ruby package but still continue to use the system default install?

And perhaps I can be of assistance in that explaining the pros and cons to me of either choice may crystallise in your minds what the right choice is.

whether Ruby should be keg-only

馃憤

From my understanding, it being keg only means that it's installed but not symlinked or set up in a way that it ends up on the path for the user. Correct?

Not symlinked _by default_, yes.

In what circumstances would a person want to install the ruby package but still continue to use the system default install?

Not just the system default install but any other Ruby you may have installed e.g. with rbenv etc.

Hi @MikeMcQuaid, I know I'm late to the discussion, but making Ruby keg-only has broken a few things at least in my case; nothing irremediable but definitively inconvenient. It sorts of remind me the situation with the python formula last year.

I don't want to reopen the debate, you have an undeniable edge on anything brew related and sure know best, but I've noticed that I'm unable to brew link --force ruby to make my environment happy again:

$ brew link --force ruby
Warning: Refusing to link macOS-provided software: ruby
If you need to have ruby first in your PATH run:
  echo 'export PATH="/usr/local/opt/ruby/bin:$PATH"' >> ~/.zshrc

For compilers to find ruby you may need to set:
  export LDFLAGS="-L/usr/local/opt/ruby/lib"
  export CPPFLAGS="-I/usr/local/opt/ruby/include"

Is that by design or should I report a bug?

That is by design. Did you try to follow those instructions?

I did, don't get me wrong, but also had to add /usr/local/lib/ruby/gems/2.5.0/bin to my PATH and still I was experiencing some weird behaviours from the previous existing gem binaries in /usr/local/bin.

I understand the risks of linking a keg-only formula, but I guess I fancy the 'think twice' rationale behind the --force option in the link command that allows the user to keep control of her own environment while still leveraging the awesome capabilities of the brew tool.

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