How can I set up Homebrew without destroying my system?

Question

Succumbing to pressure, I've installed Homebrew and given it a whirl. But I'm surprised at the experience so far. My impression of Homebrew is that it serves as an easy to use, safe, and self-contained package manager for OS X. But this has not been my experience.

(1) The first thing it does is change a bunch of permissions on a number of scary looking directories:

    ==> The following directories will be made group writable:
    /usr/local/.
    /usr/local/bin
    /usr/local/include
    /usr/local/lib
    /usr/local/lib/pkgconfig
    /usr/local/share
    /usr/local/share/man
    /usr/local/share/man/man1
    /usr/local/share/man/man3
    /usr/local/share/man/man7
    /usr/local/share/info
    /usr/local/share/doc
    ==> The following directories will have their group set to admin:
    /usr/local/.
    /usr/local/bin
    /usr/local/include
    /usr/local/lib
    /usr/local/lib/pkgconfig
    /usr/local/share
    /usr/local/share/man
    /usr/local/share/man/man1
    /usr/local/share/man/man3
    /usr/local/share/man/man7
    /usr/local/share/info
    /usr/local/share/doc

(2) The next thing it does (following the recommended procedure to run brew doctor) is ask me to delete a whole bunch of scary looking files:

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
    /usr/local/share/man/mann

Warning: Broken symlinks were found. Remove them with `brew prune`:
  /usr/local/share/ghostscript/9.05/Resource/Font/blex.pfb
  [hundreds...]

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/libasan.1.dylib
    /usr/local/lib/libasan.2.dylib
    /usr/local/lib/libatomic.1.dylib
    /usr/local/lib/libcdt.5.dylib
    /usr/local/lib/libcgraph.6.dylib
    /usr/local/lib/libcilkrts.5.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/libgcc_s.10.4.dylib
    /usr/local/lib/libgcc_s.10.5.dylib
    /usr/local/lib/libgfortran.2.0.0.dylib
    /usr/local/lib/libgfortran.3.dylib
    /usr/local/lib/libgmp.10.dylib
    /usr/local/lib/libgmpxx.4.dylib
    /usr/local/lib/libgomp.1.dylib
    /usr/local/lib/libgvc.6.dylib
    /usr/local/lib/libgvpr.2.dylib
    /usr/local/lib/libitm.1.dylib
    /usr/local/lib/liblkdynam.dylib
    /usr/local/lib/liblkrealt.dylib
    /usr/local/lib/liblksec.dylib
    /usr/local/lib/liblksock.dylib
    /usr/local/lib/libmpc.3.dylib
    /usr/local/lib/libmpfr.4.dylib
    /usr/local/lib/libpathplan.4.dylib
    /usr/local/lib/libquadmath.0.dylib
    /usr/local/lib/libssp.0.dylib
    /usr/local/lib/libstdc++.6.dylib
    /usr/local/lib/libtcl8.6.dylib
    /usr/local/lib/libtk8.6.dylib
    /usr/local/lib/libubsan.0.dylib
    /usr/local/lib/libxdot.4.dylib

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/c++/5.0.0/backward/auto_ptr.h
    [hundreds...]

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/libasan.la
    /usr/local/lib/libatomic.la
    /usr/local/lib/libcilkrts.la
    /usr/local/lib/libgfortran.la
    /usr/local/lib/libgmp.la
    /usr/local/lib/libgmpxx.la
    /usr/local/lib/libgomp.la
    /usr/local/lib/libitm.la
    /usr/local/lib/libmpc.la
    /usr/local/lib/libmpfr.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/libubsan.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/libcdt.pc
    /usr/local/lib/pkgconfig/libcgraph.pc
    /usr/local/lib/pkgconfig/libgvc.pc
    /usr/local/lib/pkgconfig/libgvpr.pc
    /usr/local/lib/pkgconfig/libpathplan.pc
    /usr/local/lib/pkgconfig/libxdot.pc
    /usr/local/lib/pkgconfig/tcl.pc
    /usr/local/lib/pkgconfig/tk.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/libatomic.a
    /usr/local/lib/libcilkrts.a
    /usr/local/lib/libgfortran.a
    /usr/local/lib/libgmp.a
    /usr/local/lib/libgmpxx.a
    /usr/local/lib/libgomp.a
    /usr/local/lib/libitm.a
    /usr/local/lib/libmpc.a
    /usr/local/lib/libmpfr.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/libtclstub8.6.a
    /usr/local/lib/libtkstub8.6.a

(3) It fails to install, for example, attempting to install matplotlib-basemap gives me

==> Installing matplotlib-basemap from homebrew/homebrew-python
==> Installing dependencies for matplotlib-basemap: numpy, pkg-config, libpng, freetype, matplotlib, jpeg, libtiff, little-cms2, webp, pillow
==> Installing matplotlib-basemap dependency: numpy
==> Using Homebrew-provided fortran compiler.
This may be changed by setting the FC environment variable.
==> Downloading https://downloads.sourceforge.net/project/numpy/NumPy/1.9.1/numpy-1.9.1.tar.gz
Already downloaded: /Library/Caches/Homebrew/numpy-1.9.1.tar.gz
==> Patching
==> python setup.py build --fcompiler=gnu95 install --prefix=/usr/local/Cellar/numpy/1.9.1
  File "/private/tmp/numpy-PSE07t/numpy-1.9.1/numpy/distutils/fcompiler/gnu.py", line 197, in get_flags_opt
    v = self.get_version()
  File "/private/tmp/numpy-PSE07t/numpy-1.9.1/numpy/distutils/fcompiler/__init__.py", line 434, in get_version
    raise CompilerNotFound()
numpy.distutils.fcompiler.CompilerNotFound
couldn't understand kern.osversion `14.0.0'

even though I have the ScyPy stack and gfortran already installed and working fine.

Is there a way out of this mess? How do I get from a working configuration (Xcode, Python, Python packages maintained in site-packages with pip, etc.) to one that also uses Homebrew (and continues to work)? Do I really need to follow all of the Doctor's recommendations and delete all those files in order to proceed; is it safe to do so?

And I should add that (4) once I did finally get Homebrew to install something, it [turned out to be outdated](http://stackoverflow.com/q/27747455/656912) (and available through `pip`), causing no end of confusion. Really not getting where the brew-love is coming from. — orome, Jan 04 '15 at 13:27
re 3: ``couldn't understand kern.osversion `14.0.0'`` is an indication that gfortran is misbehaving on Yosemite and the numpy distutils are choking. You will need to upgrade gfortran to successfully compile numpy. — Tim Smith, Jan 12 '15 at 01:15
@TimSmith: No problem there with any of the SciPy stack or basemap (via pip) if I use non-brew gfortran. — orome, Jan 12 '15 at 01:18
re 1, 2: If you already have substantial investments of software in /usr/local you might be happier using another prefix; it will avoid build conflicts. Homebrew's website has advice warning that non-standard prefixes can break things; this is mostly untrue, but you'll miss out on some of the precompiled packages. — Tim Smith, Jan 12 '15 at 01:19
When you install the scipy stack with pip on OS X you're probably getting precompiled binary wheels. Ideally, the homebrew-python formulae would not insist on using a brewed numpy; pip is now (but wasn't always) a great way to install numpy on OS X. — Tim Smith, Jan 12 '15 at 01:22
@TimSmith: Indeed: if I try to compile scipy from source I get errors. I don't have a big investment in /usr/local and would like to move more things over to Homebrew. I think the place to start is with gfortran, and [follow on question about how to proceed](http://stackoverflow.com/q/27906611/656912). — orome, Jan 12 '15 at 16:35

score 1 · Answer 1 · answered Jan 11 '15 at 23:15

The issues you show aren't indicative of a general problem.

The fact that Homebrew "takes over" /usr/local/ is a well-documented design decision. It might be "scary" at first, but it works that way for everybody. It is possible to install Homebrew into a different directory, if you really want to do that.
brew doctor warnings are also normal if you have existing non-brewed software installed under /usr/local/. Note that these are warnings that say something to the effect of, if you are having problems, these could be causes. It doesn't say, delete all of these files before doing anything else. (plenty of questions on SO on this issue)
and 4. are just bad luck AFAICT. These are somewhat off-the-beaten-path packages, so they might be having some issues right now.

If you can install mainstream packages like, I don't know, git or make or lynx, then everything is probably fine and you just need to work out the issues with the individual packages.

How can I set up Homebrew without destroying my system?

1 Answers1