Installation problem with BREW on Mac OsX

1

Hi,

I had a running mrtrix version. After uninstalling it, and trying to reinstall:

I receive the following error using during installation:

Treanus-MBP:~ stefan$ brew tap MRtrix3/mrtrix3
==> Tapping mrtrix3/mrtrix3
Cloning into ‘/usr/local/Homebrew/Library/Taps/mrtrix3/homebrew-mrtrix3’…
remote: Counting objects: 5, done.
remote: Compressing objects: 100% (5/5), done.
remote: Total 5 (delta 0), reused 4 (delta 0), pack-reused 0
Unpacking objects: 100% (5/5), done.
Error: Invalid formula: /usr/local/Homebrew/Library/Taps/mrtrix3/homebrew-mrtrix3/mrtrix3.rb
mrtrix3: /usr/local/Homebrew/Library/Taps/mrtrix3/homebrew-mrtrix3/mrtrix3.rb:40: syntax error, unexpected tIDENTIFIER, expecting keyword_end
revision 0 option “stable”, "Install latest ta…
^
Error: Cannot tap mrtrix3/mrtrix3: invalid syntax in tap!

Any help?

2

Hi Stefan,

Thanks for reporting. Should be fixed now.

Cheers,
Max

3

Hi Max, I have this when I try to install, please help:

uqhvo1$ brew tap MRtrix3/mrtrix3
Updating Homebrew…
==> Tapping mrtrix3/mrtrix3
Cloning into ‘/usr/local/Homebrew/Library/Taps/mrtrix3/homebrew-mrtrix3’…
remote: Counting objects: 5, done.
remote: Compressing objects: 100% (5/5), done.
remote: Total 5 (delta 0), reused 3 (delta 0), pack-reused 0
Unpacking objects: 100% (5/5), done.
Error: Invalid formula: /usr/local/Homebrew/Library/Taps/mrtrix3/homebrew-mrtrix3/mrtrix3.rb
mrtrix3: /usr/local/Homebrew/Library/Taps/mrtrix3/homebrew-mrtrix3/mrtrix3.rb:40: syntax error, unexpected tIDENTIFIER, expecting keyword_end
revision 0 option “test”, “Run tests after installation.”
^
Error: Cannot tap mrtrix3/mrtrix3: invalid syntax in tap!

4

Hi,

I forgot to update the update script on the computer that updates the formula. Should work now.

5

Currently, the master branch does not compile on macOS. You might want to wait until this pull request is merged.

6

Hi Max,
any idea how long this will take?
Thanks in advance,
Stefan.

7

Hi @Stefan_Sunaert,

The above pull request has just been merged, so it should be fixed after updating your install!

Cheers,
Thijs

8

Hi, thank you. The mrtrix tap works now. However, installing was an issue. I got this:

uqhvo1$ brew install mrtrix3
Updating Homebrew…
==> Installing mrtrix3 from mrtrix3/mrtrix3
==> Installing dependencies for mrtrix3/mrtrix3/mrtrix3: readline, sqlite, gdbm, python
==> Installing mrtrix3/mrtrix3/mrtrix3 dependency: readline
==> Downloading https://homebrew.bintray.com/bottles/readline-7.0.3_1.sierra.bot
######################################################################## 100.0%
==> Pouring readline-7.0.3_1.sierra.bottle.tar.gz
==> Using the sandbox
Warning: The post-install step did not complete successfully
You can try again using brew postinstall readline
==> Caveats
This formula is keg-only, which means it was not symlinked into /usr/local,
because macOS provides the BSD libedit library, which shadows libreadline.
In order to prevent conflicts when programs look for libreadline we are
defaulting this GNU Readline installation to keg-only…

For compilers to find this software you may need to set:
LDFLAGS: -L/usr/local/opt/readline/lib
CPPFLAGS: -I/usr/local/opt/readline/include

==> Summary
:beer: /usr/local/Cellar/readline/7.0.3_1: 46 files, 1.5MB
==> Installing mrtrix3/mrtrix3/mrtrix3 dependency: sqlite
==> Downloading https://homebrew.bintray.com/bottles/sqlite-3.19.2.sierra.bottle
######################################################################## 100.0%
==> Pouring sqlite-3.19.2.sierra.bottle.tar.gz
Warning: The post-install step did not complete successfully
You can try again using brew postinstall sqlite
==> Caveats
This formula is keg-only, which means it was not symlinked into /usr/local,
because macOS provides an older sqlite3.

If you need to have this software first in your PATH run:
echo ‘export PATH="/usr/local/opt/sqlite/bin:$PATH"’ >> ~/.bash_profile

For compilers to find this software you may need to set:
LDFLAGS: -L/usr/local/opt/sqlite/lib
CPPFLAGS: -I/usr/local/opt/sqlite/include
For pkg-config to find this software you may need to set:
PKG_CONFIG_PATH: /usr/local/opt/sqlite/lib/pkgconfig

==> Summary
:beer: /usr/local/Cellar/sqlite/3.19.2: 12 files, 2.9MB
==> Installing mrtrix3/mrtrix3/mrtrix3 dependency: gdbm
==> Downloading https://homebrew.bintray.com/bottles/gdbm-1.13.sierra.bottle.tar
######################################################################## 100.0%
==> Pouring gdbm-1.13.sierra.bottle.tar.gz
Warning: The post-install step did not complete successfully
You can try again using brew postinstall gdbm
==> Summary
:beer: /usr/local/Cellar/gdbm/1.13: 19 files, 554.4KB
==> Installing mrtrix3/mrtrix3/mrtrix3 dependency: python
Warning: Building python from source:
The bottle needs the Apple Command Line Tools to be installed.
You can install them, if desired, with:
xcode-select --install

==> Downloading https://www.python.org/ftp/python/2.7.13/Python-2.7.13.tar.xz
######################################################################## 100.0%
==> ./configure --prefix=/usr/local/Cellar/python/2.7.13 --enable-ipv6 --dataroo
==> make
==> make install PYTHONAPPSDIR=/usr/local/Cellar/python/2.7.13
==> make frameworkinstallextras PYTHONAPPSDIR=/usr/local/Cellar/python/2.7.13/sh
==> Downloading https://files.pythonhosted.org/packages/26/d1/dc7fe14ce4a3ff3fae
######################################################################## 100.0%
==> Downloading https://files.pythonhosted.org/packages/11/b6/abcb525026a4be042b
######################################################################## 100.0%
==> Downloading https://files.pythonhosted.org/packages/c9/1d/bd19e691fd4cfe908c
######################################################################## 100.0%
Error: parent directory is world writable but not sticky
Please report this bug:
http://docs.brew.sh/Troubleshooting.html
/System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/lib/ruby/2.0.0/tmpdir.rb:92:in mktmpdir' /usr/local/Homebrew/Library/Homebrew/utils/fork.rb:6:insafe_fork’
/usr/local/Homebrew/Library/Homebrew/formula_installer.rb:658:in build' /usr/local/Homebrew/Library/Homebrew/formula_installer.rb:312:ininstall’
/usr/local/Homebrew/Library/Homebrew/formula_installer.rb:529:in install_dependency' /usr/local/Homebrew/Library/Homebrew/formula_installer.rb:496:inblock in install_dependencies’
/usr/local/Homebrew/Library/Homebrew/formula_installer.rb:496:in each' /usr/local/Homebrew/Library/Homebrew/formula_installer.rb:496:ininstall_dependencies’
/usr/local/Homebrew/Library/Homebrew/formula_installer.rb:245:in install' /usr/local/Homebrew/Library/Homebrew/cmd/install.rb:322:ininstall_formula’
/usr/local/Homebrew/Library/Homebrew/cmd/install.rb:207:in block in install' /usr/local/Homebrew/Library/Homebrew/cmd/install.rb:205:ineach’
/usr/local/Homebrew/Library/Homebrew/cmd/install.rb:205:in install' /usr/local/Homebrew/Library/Homebrew/brew.rb:92:in’

9

I think you have an issue with your homebrew: You might want to fix that first. For instance: https://github.com/Homebrew/legacy-homebrew/issues/29212

Have a look at this:

Cheers,
Max

10

Some problems installing here. I’ve updated & upgraded brew, but it seems to another issue:

I’m on High Sierra 10.13.2

brew install mrtrix3
Warning: Calling 'depends_on :python' is deprecated!
Use 'depends_on "python"' instead.
/usr/local/Homebrew/Library/Taps/mrtrix3/homebrew-mrtrix3/mrtrix3.rb:56:in `<class:Mrtrix3>'
Please report this to the mrtrix3/mrtrix3 tap!

==> Installing mrtrix3 from mrtrix3/mrtrix3
Warning: Calling 'depends_on :python' is deprecated!
Use 'depends_on "python"' instead.
/usr/local/Homebrew/Library/Taps/mrtrix3/homebrew-mrtrix3/mrtrix3.rb:56:in `<class:Mrtrix3>'
Please report this to the mrtrix3/mrtrix3 tap!

Error: undefined method `parent' for nil:NilClass
Please report this bug:
  https://docs.brew.sh/Troubleshooting.html
/usr/local/Homebrew/Library/Taps/mrtrix3/homebrew-mrtrix3/mrtrix3.rb:14:in `block in <class:Qt5Requirement>'
/usr/local/Homebrew/Library/Homebrew/requirement.rb:80:in `instance_eval'
/usr/local/Homebrew/Library/Homebrew/requirement.rb:80:in `modify_build_environment'
/System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/lib/ruby/2.3.0/set.rb:306:in `each_key'
/System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/lib/ruby/2.3.0/set.rb:306:in `each'
/System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/lib/ruby/2.3.0/delegate.rb:341:in `block in delegating_block'
/usr/local/Homebrew/Library/Homebrew/build.rb:84:in `install'
/usr/local/Homebrew/Library/Homebrew/build.rb:189:in `<main>'
11

Thank you for reporting this! I have fixed the deprecation warnings but not the part of the code that caused the exception. I was able to reproduce the error up to an hour ago but now I can’t anymore. Would you mind trying it again?

brew update
brew install mrtrix3

For reference:
My current version of homebrew is 1.5.1-9-gea0af7d. The changes in homebrew a few hours ago seem unrelated. In any case, I went back to yesterday’s homebrew version 6b8502d1e1c03a0d2eeb106f8480c542dc7f7d16 and the version of the MRtrix3 formula that failed to install (19edd7f94e2090e225776f29989b74f902691831) but also that seems to work now. When I got the error, installing mrtrix3 with --debug and --verbose flags should have triggered homebrew’s debugger but it also failed to do that and bailed out as in the error message above. I suspect something must have changed in how homebrew handles exceptions but I am a bit at a loss why it is working now… :confused: