Homebrew: brew doctor throwing up a lot of errors, how can I fix them? [closed]

Question

I installed homebrew a long time ago and I don't use it that much, but I was thinking of starting to get back into it as it's a very useful and easy to use package installer. Anyway, I ran the brew doctor and got a whole host of warnings which I'm not sure how to fix! I'm especially scared of deleting .dylib, .la and .pc files, in case my packages that weren't installed via homebrew needed them. Any help on the issue would be greatly appreciated, if it matters I'm running Mac OS X Mountain Lion (10.8.3), my list of warnings is as follows:

UOS-12044:~ as34g12$ brew doctor
Warning: /usr/local/include 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 header file to this directory, the install will
fail during the link step.

You should probably `chown` /usr/local/include
Warning: /usr/local/share 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 file to this directory, the install will
fail during the link step.

You should probably `chown` /usr/local/share
Warning: Some directories in /usr/local/share/locale aren't writable.
This can happen if you "sudo make install" software that isn't managed
by Homebrew. If a brew tries to add locale information to one of these
directories, then the install will fail during the link step.
You should probably `chown` them:

    /usr/local/share/locale
    /usr/local/share/locale/be
    /usr/local/share/locale/be/LC_MESSAGES
    /usr/local/share/locale/ca
    /usr/local/share/locale/ca/LC_MESSAGES
    /usr/local/share/locale/da
    /usr/local/share/locale/da/LC_MESSAGES
    /usr/local/share/locale/de
    /usr/local/share/locale/de/LC_MESSAGES
    /usr/local/share/locale/el
    /usr/local/share/locale/el/LC_MESSAGES
    /usr/local/share/locale/es
    /usr/local/share/locale/es/LC_MESSAGES
    /usr/local/share/locale/fr
    /usr/local/share/locale/fr/LC_MESSAGES
    /usr/local/share/locale/ja
    /usr/local/share/locale/ja/LC_MESSAGES
    /usr/local/share/locale/nl
    /usr/local/share/locale/nl/LC_MESSAGES
    /usr/local/share/locale/sv
    /usr/local/share/locale/sv/LC_MESSAGES
    /usr/local/share/locale/tr
    /usr/local/share/locale/tr/LC_MESSAGES
Warning: Some directories in /usr/local/share/man aren't writable.
This can happen if you "sudo make install" software that isn't managed
by Homebrew. If a brew tries to add locale information to one of these
directories, then the install will fail during the link step.
You should probably `chown` them:

    /usr/local/share/man/de
    /usr/local/share/man/de/man1
Warning: The /usr/local directory is not writable.
Even if this directory was writable when you installed Homebrew, other
software may change permissions on this directory. Some versions of the
"InstantOn" component of Airfoil are known to do this.

You should probably change the ownership and permissions of /usr/local
back to your user account.
Warning: Setting DYLD_LIBRARY_PATH can break dynamic linking.
You should probably unset it.
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:

    /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
    /soft/star-hikianalia/bin/gsl-config
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/libatomic.1.dylib
    /usr/local/lib/libg2c.0.0.0.dylib
    /usr/local/lib/libgcc_ext.10.4.dylib
    /usr/local/lib/libgcc_ext.10.5.dylib
    /usr/local/lib/libgcc_s.1.dylib
    /usr/local/lib/libgfortran.3.dylib
    /usr/local/lib/libgomp.1.dylib
    /usr/local/lib/libitm.1.dylib
    /usr/local/lib/libmacfuse_i32.2.dylib
    /usr/local/lib/libmacfuse_i64.2.dylib
    /usr/local/lib/libntfs-3g.80.dylib
    /usr/local/lib/libntfs.9.0.0.dylib
    /usr/local/lib/libosxfuse_i32.2.dylib
    /usr/local/lib/libosxfuse_i64.2.dylib
    /usr/local/lib/libquadmath.0.dylib
    /usr/local/lib/libssp.0.dylib
    /usr/local/lib/libstdc++.6.dylib
    /usr/local/lib/libublio.1.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/libatomic.la
    /usr/local/lib/libfftw3.la
    /usr/local/lib/libfftw3_threads.la
    /usr/local/lib/libfftw3f.la
    /usr/local/lib/libfftw3f_threads.la
    /usr/local/lib/libg2c.la
    /usr/local/lib/libgfortran.la
    /usr/local/lib/libgmp.la
    /usr/local/lib/libgomp.la
    /usr/local/lib/libitm.la
    /usr/local/lib/libmpc.la
    /usr/local/lib/libmpfr.la
    /usr/local/lib/libntfs-3g.la
    /usr/local/lib/libntfs.la
    /usr/local/lib/libosxfuse_i32.la
    /usr/local/lib/libosxfuse_i64.la
    /usr/local/lib/libquadmath.la
    /usr/local/lib/libssp.la
    /usr/local/lib/libssp_nonshared.la
    /usr/local/lib/libstdc++.la
    /usr/local/lib/libsupc++.la
    /usr/local/lib/libublio.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/cfitsio.pc
    /usr/local/lib/pkgconfig/fftw3.pc
    /usr/local/lib/pkgconfig/fftw3f.pc
    /usr/local/lib/pkgconfig/libntfs-3g.pc
    /usr/local/lib/pkgconfig/libublio.pc
    /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/libatlas.a
    /usr/local/lib/libatomic.a
    /usr/local/lib/libcblas.a
    /usr/local/lib/libcfitsio.a
    /usr/local/lib/libf77blas.a
    /usr/local/lib/libfftw3.a
    /usr/local/lib/libfftw3_threads.a
    /usr/local/lib/libfftw3f.a
    /usr/local/lib/libfftw3f_threads.a
    /usr/local/lib/libfrtbegin.a
    /usr/local/lib/libg2c.a
    /usr/local/lib/libgfortran.a
    /usr/local/lib/libgmp.a
    /usr/local/lib/libgomp.a
    /usr/local/lib/libiberty.a
    /usr/local/lib/libitm.a
    /usr/local/lib/liblapack.a
    /usr/local/lib/libmpc.a
    /usr/local/lib/libmpfr.a
    /usr/local/lib/libntfs-3g.a
    /usr/local/lib/libntfs.a
    /usr/local/lib/libptcblas.a
    /usr/local/lib/libptf77blas.a
    /usr/local/lib/libquadmath.a
    /usr/local/lib/libssp.a
    /usr/local/lib/libssp_nonshared.a
    /usr/local/lib/libstdc++.a
    /usr/local/lib/libsupc++.a
    /usr/local/lib/libublio.a
Warning: You have unlinked kegs in your Cellar
Leaving kegs unlinked can lead to build-trouble and cause brews that depend on
those kegs to fail to run properly once built. Run `brew link` on these:

    fftw
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
Warning: Some installed formula are missing dependencies.
You should `brew install` the missing dependencies:

    brew install gmp harfbuzz icu4c libmpc mpfr

Run `brew missing` for more details.

Thanks in advance for the help!

Answer 1

It states in the error message what the problem is;

Warning: /usr/local/include isn't writable
You should probably change the ownership and permissions of /usr/local

back to your user account.

If you run ls -l /usr/local/ you should have an output like this:

total 4
-rw-r--r--    1 user  admin    493 23 Apr 15:14 CONTRIBUTING.md
drwxr-xr-x   17 user  admin    578  5 May 14:54 Cellar
drwxr-xr-x    3 user  admin    102 23 Apr 16:33 Frameworks
drwxr-xr-x   10 user  admin    340 24 Apr 08:50 Library

Where user is your username and admin is your group. If you see something more like:

drwxr-xr-x   17 root  wheel    578  5 May 14:54 Cellar

you will have to run chown -R user:admin /usr/local which will change the ownership back to your user.

This should solve the first part. However, be warned, this could stop other software working if you have previously run "sudo make install" software that isn't managed by Homebrew.

There is also a great answer on How do i fix brew doctor errors that addresses your DYLD_LIBRARY_PATH issues.