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This is probably bad form for this board, and feel free to delete it if it is, but running brew doctor reveals the following:

Warning: /usr/local/lib/pkgconfig isn't writable.
This can happen if you "sudo make install" software that isn't managed
by Homebrew.

If a brew tries to write a .pc file to this directory, the install will
fail during the link step.

You should probably `chown` /usr/local/lib/pkgconfig
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 what 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:

/opt/local/bin/freetype-config
/opt/local/bin/libpng-config
/opt/local/bin/libpng15-config
/opt/local/bin/Magick++-config
/opt/local/bin/Magick-config
/opt/local/bin/MagickCore-config
/opt/local/bin/MagickWand-config
/opt/local/bin/ncurses5-config
/opt/local/bin/ncursesw5-config
/opt/local/bin/pkg-config
/opt/local/bin/python2-config
/opt/local/bin/python2.7-config
/opt/local/bin/Wand-config
/opt/local/bin/xml2-config
/Users/Paul/.rvm/gems/ruby-1.9.3-p194/bin/passenger-config
/Library/Frameworks/Python.framework/Versions/2.7/bin/python-config
/Library/Frameworks/Python.framework/Versions/2.7/bin/python2-config
/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7-config

Warning: /Library/Frameworks/Mono.framework detected
This can be picked up by CMake's build system and likely cause the build to
fail. You may need to move this file out of the way to compile CMake.
Warning: You have Macports or Fink installed.
This can cause trouble. You don't have to uninstall them, but you may like to
try temporarily moving them away, eg.

  sudo mv /opt/local ~/macports

Warning: Your Homebrew is outdated
You haven't updated for at least 24 hours, this is a long time in brewland!
Warning: You have leftover files from an older version of Xcode.
You should delete them using:
  Developer/Library/uninstall-developer-folder

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


    Unexpected dylibs:
    /usr/local/lib/libFLAC++.2.1.2.dylib    /usr/local/lib/libFLAC++.2.dylib                          /usr/local/lib/libFLAC++.dylib    /usr/local/lib/libFLAC.4.1.2.dylib    /usr/local/lib/libFLAC.4.dylib    /usr/local/lib/libFLAC.dylib    /usr/local/lib/libguide.dylib    /usr/local/lib/libmacfuse_i32.2.dylib    /usr/local/lib/libmacfuse_i64.2.dylib    /usr/local/lib/libosxfuse_i32.2.dylib    /usr/local/lib/libosxfuse_i64.2.dylib    /usr/local/lib/libusb-1.0.0.dylib
Warning: Unbrewed .la files were found in /usr/local/lib.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.

Unexpected .la files:
    /usr/local/lib/libFLAC++.la    /usr/local/lib/libFLAC.la    /usr/local/lib/libosxfuse_i32.la    /usr/local/lib/libosxfuse_i64.la
Warning: Unbrewed .pc files were found in /usr/local/lib/pkgconfig.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.

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

Unexpected static libraries:
    /usr/local/lib/libFLAC++.a    /usr/local/lib/libFLAC.a
Warning: Suspicious Git newline settings found.

The detected Git newline settings can cause checkout problems:
  core.autocrlf = input
  core.safecrlf = true

If you are not routinely dealing with Windows-based projects,
consider removing these settings.
Warning: You have uncommitted modifications to Homebrew
If this a surprise to you, then you should stash these modifications.
Stashing returns Homebrew to a pristine state but can be undone
should you later need to do so for some reason.
    cd /usr/local/Library && git stash && git clean -f
Error: Homebrew doesn't know what compiler versions ship with your version of
Xcode. Please file an issue with the output of `brew --config`:
  https://github.com/mxcl/homebrew/issues

Thanks!
Warning: /usr/bin occurs before /usr/local/bin
This means that system-provided programs will be used instead of those
provided by Homebrew. The following tools exist at both paths:

    2to3
    2to3-2.7
    idle
    idle2.7
    pydoc
    pydoc2.7
    python
    python-config
    python2.7
    python2.7-config
    pythonw
    pythonw2.7
    smtpd.py
    smtpd2.7.py

Consider amending your PATH so that /usr/local/bin
occurs before /usr/bin in your PATH.
Warning: You have a non-Homebrew 'pkg-config' in your PATH:
  /usr/bin/pkg-config => /Library/Frameworks/Mono.framework/Versions/2.10.8/bin/pkg-config

This was most likely created by the Mono installer. `./configure` may
have problems finding brew-installed packages using this other pkg-config.

I don't even know where to start here. I know enough about this sort of thing to run brew doctor and maybe fix a permissions error, but this is just overwhelming.

Any help as to which of these errors are important, which I can ignore, issues I might have with other programs if I "fix" these, would be appreciated.

I only used MacPorts to install Image Magick and probably have no use for it otherwise, and I have no idea why I have the Mono Framework. I have no plans to be an iOS developer anytime soon.

share|improve this question
    
Did you try to reinstall homebrew? –  Festus Tamakloe Jan 16 '13 at 16:16
    
It looks like your /usr/local contains Homebrew stuff and also other software you might have installed with administrator permissions. I would suggest un-installing Homebrew and reinstalling it in a location where you have full permissions (e.g., ~/homebrew). I would also suggest getting rid of Macports stuff. A Homebrew developer would surely give you the best advice, though. I suggest you post the output above on the Homebrew website: github.com/mxcl/homebrew/issues?sort=created&state=open –  Dominique Jan 16 '13 at 22:55
    
You need to really remove all the compiled stuff and mono and then decide on which pakageing solution you want to use macports or homebrew and then stick to that one - unless you understand the issues of how they conflict. –  Mark Feb 26 '13 at 16:10
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