Are there obvious sources for the Brew Doctor warnings I'm seeing?

Question

I have recently installed Hombrew on Yosemite with Xcode installed and would like to better understand what brew doctor is warning me about. I understand that these warnings are nothing to worry about (until they are) and am not asking how or whether to respond to them; but I would like to do the best I can to understand the likely causes so that I can be prepared when issues come up (and also to head off issues that others in my office may encounter on similar systems).

Are any of the items below from obvious sources on a 10.10 machine with Xcode and non-brew Fortran installed? Do any of these items ring a bell?

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/lib/libasan.dylib
  /usr/local/lib/libatomic.dylib
  /usr/local/lib/libcilkrts.dylib
  /usr/local/lib/libgcc_s_ppc64.1.dylib
  /usr/local/lib/libgcc_s_x86_64.1.dylib
  /usr/local/lib/libgfortran.dylib
  /usr/local/lib/libgmp.dylib
  /usr/local/lib/libgmpxx.dylib
  /usr/local/lib/libgomp.dylib
  /usr/local/lib/libitm.dylib
  /usr/local/lib/libmpc.dylib
  /usr/local/lib/libmpfr.dylib
  /usr/local/lib/libquadmath.dylib
  /usr/local/lib/libssp.dylib
  /usr/local/lib/libstdc++.dylib
  /usr/local/lib/libubsan.dylib
  /usr/local/lib/ppc64/libgfortran.2.0.0.dylib
  /usr/local/lib/ppc64/libgfortran.2.dylib
  /usr/local/lib/ppc64/libgfortran.dylib
  /usr/local/lib/x86_64/libgfortran.2.0.0.dylib
  /usr/local/lib/x86_64/libgfortran.2.dylib
  /usr/local/lib/x86_64/libgfortran.dylib

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/ImageMagick/bin/Magick++-config
  /opt/ImageMagick/bin/Magick-config
  /opt/ImageMagick/bin/MagickCore-config
  /opt/ImageMagick/bin/MagickWand-config
  /opt/ImageMagick/bin/Wand-config

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/fakemysql.h
    /usr/local/include/fakepq.h
    /usr/local/include/fakesql.h
    /usr/local/include/gmp.h
    /usr/local/include/gmpxx.h
    /usr/local/include/graphviz/arith.h
    /usr/local/include/graphviz/cdt.h
    /usr/local/include/graphviz/cgraph.h
    /usr/local/include/graphviz/color.h
    /usr/local/include/graphviz/geom.h
    /usr/local/include/graphviz/graphviz_version.h
    /usr/local/include/graphviz/gvc.h
    /usr/local/include/graphviz/gvcext.h
    /usr/local/include/graphviz/gvcjob.h
    /usr/local/include/graphviz/gvcommon.h
    /usr/local/include/graphviz/gvconfig.h
    /usr/local/include/graphviz/gvplugin.h
    /usr/local/include/graphviz/gvplugin_device.h
    /usr/local/include/graphviz/gvplugin_layout.h
    /usr/local/include/graphviz/gvplugin_loadimage.h
    /usr/local/include/graphviz/gvplugin_render.h
    /usr/local/include/graphviz/gvplugin_textlayout.h
    /usr/local/include/graphviz/gvpr.h
    /usr/local/include/graphviz/pack.h
    /usr/local/include/graphviz/pathgeom.h
    /usr/local/include/graphviz/pathplan.h
    /usr/local/include/graphviz/textspan.h
    /usr/local/include/graphviz/types.h
    /usr/local/include/graphviz/usershape.h
    /usr/local/include/graphviz/xdot.h
    /usr/local/include/itcl.h
    /usr/local/include/itcl2TclOO.h
    /usr/local/include/itclDecls.h
    /usr/local/include/itclInt.h
    /usr/local/include/itclIntDecls.h
    /usr/local/include/itclMigrate2TclCore.h
    /usr/local/include/itclTclIntStubsFcn.h
    /usr/local/include/mpc.h
    /usr/local/include/mpf2mpfr.h
    /usr/local/include/mpfr.h
    /usr/local/include/mysqlStubs.h
    /usr/local/include/odbcStubs.h
    /usr/local/include/pqStubs.h
    /usr/local/include/tcl.h
    /usr/local/include/tclDecls.h
    /usr/local/include/tclOO.h
    /usr/local/include/tclOODecls.h
    /usr/local/include/tclPlatDecls.h
    /usr/local/include/tclThread.h
    /usr/local/include/tclTomMath.h
    /usr/local/include/tclTomMathDecls.h
    /usr/local/include/tdbc.h
    /usr/local/include/tdbcDecls.h
    /usr/local/include/tdbcInt.h
    /usr/local/include/tk.h
    /usr/local/include/tkDecls.h
    /usr/local/include/tkPlatDecls.h

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

Any specific sentence that you're having trouble understanding? My guess is the latter parts, but currently, there are various different warnings (and most have a different explanation). — , Jan 09 '15 at 13:50
Practical question: have you *only* installed software (other perhaps than default Mac DMG or PKG files) through homebrew (i.e., not "compile from source" software), and did you use `sudo` or not? — , Jan 09 '15 at 13:52
@Evert: I'm just wondering of any of the files mentioned are from obvious sources. I've installed other software for Python (using sudo in some cases) as well as TeX. — orome, Jan 09 '15 at 13:59
They definitely are from something else; the ImageMagick one is the most obvious. You also installed most of the other software as static libraries, as opposed to dynamic libraries, hence the warnings about the `.la` and `.a` files. Or rather, given the broken links, an attempt for dynamic libraries was made, but failed. You can check where the broken links point to (`ls -l /usr/local/lib/libgomp.dylib`, for example), which should give you a pointer what is wrong there. — , Jan 09 '15 at 15:07
Other than that: yes, you only have to worry about when you try to install the same library through brew; then conflicts can arise. You could (be very careful though) opt to figure out what software you installed, remove (make a copy/backup of /usr/local/ first!) all those files with warnings, and then install the software through homebrew. ImageMagick, graphviz and a few sciency packages are obvious contenders. It doesn't answer your question; I'll try that later below. — , Jan 09 '15 at 15:10
@Evert: Thanks, that helps. Unfortunately I don't even know what `.la` or `.a` files are (I just have Xcode installed to play with Swift and for the command line tools as required by other things) or what a static or dynamic library is really. Is there any obvious source for any of these things; something that generally installs them? — orome, Jan 09 '15 at 16:07
Any unix-like software that is installed from source and needs to be compiled (using C or Fortran) can result in `dylib`, `la` or `a` files. Those are (as the directory name indicates) libraries: files containing functions that can be reused by various programs. — , Jan 09 '15 at 16:12
Have you, at some point, tried to install a C compiler *not through XCode*? Perhaps gcc, or even the Intel compiler. The library files point to a C compiler. Perhaps because you wanted gfortran? — , Jan 09 '15 at 16:58
@Evert: That sounds right. I think when I first installed gfortran I installed it along with gcc (by mistake). — orome, Jan 09 '15 at 17:16
Actually, now thinking about a previous comment: why use Homebrew when you only want to play with Swift & XCode? There's nothing on the command line that I can think you'd need. I'm asking, because you could think about removing all those (gfortran etc) files, and if wanted, re-install gfortran through Homebrew. But only if you need it (because Homebrew then installs its own `gcc`, next to the XCode C compiler). — , Jan 09 '15 at 21:20
@Evert: Sorry, I meant that I only installed Xcode to play with Swift. Homebrew is there for Heroku, AWS-EB, MySQL — and whatever else turns out to be easier to install that way. — orome, Jan 09 '15 at 21:27

score 2 · Accepted Answer · answered Jan 09 '15 at 16:54

There is a variety of warnings here, probably all with a very similar cause: having installed software from source (by compiling with configure; make; make install, or sometimes unpacking a very specific (e.g. scientific) package, such as fortran). That would be mostly software with a unix background, and the software decided to install itself in /usr/local.

I don't know your background, so I'm going to expand somewhat (I'll probably miss a few things or may have a few things (somewhat) incorrect):

In unix & linux, a piece of software is often distributed across various subdirectories, and not inside a single package (which is more Mac style). It can consist of binary that goes into /usr/local/bin/, a library with routines used by the binary that is put in /usr/local/lib/, some header file for function declarations that lives in /usr/local/include/, a manual page that is put in /usr/local/man/ or additional (e.g. configuration) data that could go into /usr/local/share/. Practically any combination can exist.

That looks a bit scattered, but it works. It does mean that pieces of different software live in the same subdirectory, as you can see form the various lists of filenames.

Note that /usr/local/ is in so far unique, that it tends to be a preferred directory to install extra software: software that the system (OS) can do without. This is also why Homebrew likes to install software there. Other software managers avoid the unix default of /usr/local/ and install in /opt/local/ (Macports) or /sw/ (Fink). But the fact that Homebrew picks the default "extra" software installation part can mean it clashes with other installed software.

Your system software lives in plain /usr/, or /System/ and /Library/, and stays out of /usr/local/; if you remove /usr/local/ completely, your system will still work.

So, with that in mind, the warnings:

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

Other software installed its manual pages here, likely with the sudo command (you may simply have had a dialog asking for your password; sudo then happened under the hood). In that case, those specific directories are "owned" by "root", and not by the usual Homebrew user (your login). That would mean Homebrew can't, in a future event, not write in those directories, if it ever comes across software that likes its manual pages there, since it's not owned by the Homebrew user.

You can alleviate this by changing the permissions to yourself:

$ sudo chown -R <user>:<group> /usr/local/share/man/de
$ sudo chown -R <user>:<group> /usr/local/share/man/mann

(do an $ ls -l $HOME to find your <user> and <group> to fill in: it's the hopefully obvious columns.)

Warning: Broken symlinks were found. Remove them with `brew prune`:

A sym(bolic )link is just a pointer to a file that exist somewhere else. If it's broken, the original file doesn't exist anymore, or the symlink is pointing to the wrong place. You can see what it is pointing at by doing for example:

ls -l   /usr/local/lib/libasan.dylib

The .dylib files are all dynamic libraries: library files that contain functions, and are meant to be used by other programs (but, specifically, not fully included inside that program; see later on static libraries). A broken library file is a potentially bad thing: new software that wants to use those files may think "ah, I can use this library" and then things go bad during compilation, when it turns out the file doesn't exist anymore. So, it may be wise to prune (remove) the symbolic links. (A symbolic link can normally be safely removed, even if it points correctly: it's only a pointer, the original file is left untouched.)

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:

configure is part of the chain to build software from source on the command line. It looks around on your system for existing libraries, and also ask for the configuration of programs using these -config scripts. Homebrew had a look around, and found such scripts outside the usual directories. Thus, configure could find multiple versions of the same config script, get confused which one to use and use the wrong one.

In this case, it's all ImageMagick stuff. Depending how you use it, you could opt to remove the entire /opt/ImageMagick/ directory (and perhaps you're then left with an empty /opt/ directory, in which case you can also remove /opt/; it's not part of the usual system).

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.

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.

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.

These are all related, and related to the dynamic libraries mentioned before. The .a files are static libraries: they (also) contain often-used functions, but those files get included inside the binary when compiling software from source (thus, the binary becomes bigger than with dynamic libraries). The .h files are header files, which tell programs what the library files contain; the .la have some extra information on the .a library files.

The warning tells you that Homebrew may get confused when installing new software: perhaps it will try to use these libraries, but they happen to be the (oh so slightly) wrong version and things don't work. You don't know until you bump into it, unfortunately.

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.

pkgconfig files are similar to those config scripts mentioned earlier: they contain configuration information if you need some earlier installed software to build new software. Again, as before: versions may mismatch slightly and then things could not work as intended (it doesn't install, or crashes, or makes your computer pass the Turing test).

As for how you may have gotten all those files in /usr/local.? Probably you installed a package that puts everything in /usr/local/ as well. As mentioned, it is a default place to put things. Since it features libgfortran and libgomp, I'm inclined to think about some scientific package.

All in all, most warnings are about potential incompatibilities: Homebrew, like most package/software managers, tries to hold some grip (not too tight though) on what it installs and what is around, because backwards incompatibilities and such can mean that newly installed software from source ("brewed" software) doesn't properly install or run. As an example, Macports is more strict (at least it was years ago when I used it), and will download matching, known compatible, versions of required extra software (thus, you could end up with four different versions of a C compiler).

Homebrew tries to be lenient with respect to installed libraries and such, but it does warn you that bad things can happen, either during compilation or later on.

One (major) source appears to be HPC's gfortran, and I have a [follow-up question about how to replace it with Homebrew's](http://stackoverflow.com/q/27906611/656912). — orome, Jan 12 '15 at 16:37
Yes, the unfortunate side effect of installing precompiled packages that live in unix-like directories (instead of their own `/Applications/` directory). Several precompiled Python binaries show similar issues. It's not a problem until you try to install something like a homebrew version. — , Jan 13 '15 at 00:07
FWIW, I've managed to get the doctor's warnings down to just a couple lines by manually removing the files that HPC's gfortran installed and the files installed by ImageMagick, followed by Brew installs of both (followed by some prunes and overwriting of links as suggested by the installs). Except for [`texlive`](http://stackoverflow.com/q/27946302/656912) and `mysql-utilities`, `/usr/local` now seems to be comfortably under Homebrew's control. — orome, Jan 14 '15 at 15:30
Epilogue: I found the source for the final two items that `doctor` found, `/usr/local/lib/libtclstub8.6.a` and `/usr/local/lib/libtkstub8.6.a`: [R](http://cran.r-project.org/doc/manuals/r-release/R-admin.html#Uninstalling-under-OS-X). The Doctor now says: *"Your system is ready to brew."*! — orome, Jan 22 '15 at 19:00

Are there obvious sources for the Brew Doctor warnings I'm seeing?

1 Answers1

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