Brew doctor output

gistfile1.txt

O:~ $ brew doctor
We couldn't detect gcc 4.2.x. Some formulae require this compiler.
NOTE: Versions of XCode newer than 4.2 don't include gcc 4.2.x.

"/usr/X11" was found, but it is a symlink to:
  /opt/X11

Homebrew's X11 support has only be tested with Apple's X11.
In particular, "XQuartz" and "XDarwin" are not known to be compatible.

Your pkg-config is not checking "/usr/X11/lib/pkgconfig" for packages.
Earlier versions of the pkg-config formula did not add this path
to the search path, which means that other formula may not be able
to find certain dependencies.

To resolve this issue, re-brew pkg-config with:
  brew rm pkg-config && brew install pkg-config

Some "config" scripts were found in your path, but not in system or Homebrew folders.

`./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.

/opt/X11/bin
    freetype-config libpng-config libpng15-config

Error: Formula apollo will not import.
Error: Formula autoconf will not import.
Error: Formula automake will not import.
Error: Formula autopano-sift-c will not import.
Error: Formula avidemux will not import.
Error: Formula bsdmake will not import.
Error: Formula bup will not import.
Warning: Cogl -- x11: Using symbols for deps is deprecated; use a string instead
Warning: Crossroads -- automake: Using symbols for deps is deprecated; use a string instead
Warning: Crossroads -- libtool: Using symbols for deps is deprecated; use a string instead
Error: Formula crossroads will not import.
Error: Formula csync will not import.
Warning: Curlftpfs -- automake: Using symbols for deps is deprecated; use a string instead
Warning: Curlftpfs -- libtool: Using symbols for deps is deprecated; use a string instead
Error: Formula dsniff will not import.
Error: Formula elixir will not import.
Error: Formula enscript will not import.
Warning: Fcgiwrap -- autoconf: Using symbols for deps is deprecated; use a string instead
Error: Formula fishfish will not import.
Warning: Freerdp -- x11: Using symbols for deps is deprecated; use a string instead
Warning: Freeswitch -- autoconf: Using symbols for deps is deprecated; use a string instead
Warning: Freeswitch -- automake: Using symbols for deps is deprecated; use a string instead
Warning: Freeswitch -- libtool: Using symbols for deps is deprecated; use a string instead
Warning: Gnumeric -- x11: Using symbols for deps is deprecated; use a string instead
Warning: Gobby -- x11: Using symbols for deps is deprecated; use a string instead
Warning: Goffice -- x11: Using symbols for deps is deprecated; use a string instead
Warning: Grace -- x11: Using symbols for deps is deprecated; use a string instead
Error: Formula grib-api will not import.
Error: Formula gtk+3 will not import.
Warning: GtkChtheme -- x11: Using symbols for deps is deprecated; use a string instead
Warning: Gtkglextmm -- x11: Using symbols for deps is deprecated; use a string instead
Warning: HtopOsx -- automake: Using symbols for deps is deprecated; use a string instead
Error: Formula hyperestraier will not import.
Warning: Intercal -- autoconf: Using symbols for deps is deprecated; use a string instead
Warning: Ipe -- x11: Using symbols for deps is deprecated; use a string instead
Error: Formula ipe will not import.
Error: Formula konoha will not import.
Warning: Libbluray -- automake: Using symbols for deps is deprecated; use a string instead
Warning: Libbluray -- libtool: Using symbols for deps is deprecated; use a string instead
Warning: Libgaiagraphics -- x11: Using symbols for deps is deprecated; use a string instead
Warning: Libglademm -- x11: Using symbols for deps is deprecated; use a string instead
Warning: Libinfinity -- x11: Using symbols for deps is deprecated; use a string instead
Error: Formula libinfinity will not import.
Warning: Libkate -- libpng: Using symbols for deps is deprecated; use a string instead
Error: Formula libkate will not import.
Error: Formula libmatio will not import.
Error: Formula libpgm will not import.
Error: Formula libpqxx will not import.
Error: Formula libqglviewer will not import.
Error: Formula libsoup will not import.
Error: Formula libtool will not import.
Error: Formula libzdb will not import.
Warning: Mame -- x11: Using symbols for deps is deprecated; use a string instead
Warning: Mathgl -- x11: Using symbols for deps is deprecated; use a string instead
Error: Formula md will not import.
Warning: Meld -- x11: Using symbols for deps is deprecated; use a string instead
Warning: MesalibGlw -- x11: Using symbols for deps is deprecated; use a string instead
Warning: Mess -- x11: Using symbols for deps is deprecated; use a string instead
Error: Formula mpfi will not import.
Error: Formula mysql-cluster will not import.
Error: Formula mysql-connector-odbc will not import.
Error: Formula open-babel will not import.
Error: Formula open-scene-graph will not import.
Error: Formula openrtsp will not import.
Warning: Pcb -- automake: Using symbols for deps is deprecated; use a string instead
Warning: Pcb -- x11: Using symbols for deps is deprecated; use a string instead
Warning: Pdf2image -- x11: Using symbols for deps is deprecated; use a string instead
Warning: Pngxx -- libpng: Using symbols for deps is deprecated; use a string instead
Warning: Pngquant -- libpng: Using symbols for deps is deprecated; use a string instead
Warning: Py2cairo -- x11: Using symbols for deps is deprecated; use a string instead
Error: Formula py2cairo will not import.
Error: Formula pygobject will not import.
Warning: Pygtk -- x11: Using symbols for deps is deprecated; use a string instead
Error: Formula pygtk will not import.
Error: Formula rarian will not import.
Warning: RomTools -- x11: Using symbols for deps is deprecated; use a string instead
Warning: Root -- x11: Using symbols for deps is deprecated; use a string instead
Warning: Samba -- automake: Using symbols for deps is deprecated; use a string instead
Warning: Samba -- libtool: Using symbols for deps is deprecated; use a string instead
Warning: SdlRtf -- x11: Using symbols for deps is deprecated; use a string instead
Error: Formula serf will not import.
Error: Formula simgrid will not import.
Error: Formula skytools will not import.
Error: Formula soci will not import.
Error: Formula ssreflect will not import.
Error: Formula texi2html will not import.
Warning: TheSilverSearcher -- automake: Using symbols for deps is deprecated; use a string instead
Warning: TheSilverSearcher -- autoconf: Using symbols for deps is deprecated; use a string instead
Error: Formula tmap will not import.
Warning: Ttfautohint -- freetype: Using symbols for deps is deprecated; use a string instead
Warning: WaitOn -- bsdmake: Using symbols for deps is deprecated; use a string instead
Warning: Wmctrl -- x11: Using symbols for deps is deprecated; use a string instead
Warning: XbeeComm -- automake: Using symbols for deps is deprecated; use a string instead
Warning: Xclip -- x11: Using symbols for deps is deprecated; use a string instead
Warning: Xpa -- x11: Using symbols for deps is deprecated; use a string instead
Error: Formula xplanet will not import.
Error: Formula zeroinstall-injector will not import.
==> You have uncommitted modifications to Homebrew's core.
Unless you know what you are doing, you should run:
cd /usr/local && git reset --hard