brew output for "Missing .inc files when installing LLVM"

gistfile1.txt

$ brew doctor
Warning: An "autoconf" in your path blocks the Xcode-provided version at:
  /opt/local/bin/autoconf

This custom autoconf may cause some Homebrew formulae to fail to compile.
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/curl-config
    /opt/local/bin/freetype-config
    /opt/local/bin/gdlib-config
    /opt/local/bin/gts-config
    /opt/local/bin/icu-config
    /opt/local/bin/libpng-config
    /opt/local/bin/libpng14-config
    /opt/local/bin/libusb-legacy-config
    /opt/local/bin/ncurses5-config
    /opt/local/bin/ncursesw5-config
    /opt/local/bin/pkg-config
    /opt/local/bin/python2.7-config
    /opt/local/bin/xml2-config
    /Applications/MAMP/Library/bin/curl-config
    /Applications/MAMP/Library/bin/freetype-config
    /Applications/MAMP/Library/bin/libmcrypt-config
    /Applications/MAMP/Library/bin/libpng-config
    /Applications/MAMP/Library/bin/libpng15-config
    /Applications/MAMP/Library/bin/sablot-config
    /Applications/MAMP/Library/bin/xml2-config
    /Applications/MAMP/Library/bin/xslt-config
    /Applications/MAMP/Library/bin/yaz-config
Warning: Your Xcode (3.2.5) is outdated
Please install Xcode 3.2.6.
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Warning: Your Homebrew is outdated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: 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/libcdt.4.dylib    /usr/local/lib/libcgraph.5.dylib    /usr/local/lib/libEnhancedDisassembly.dylib    /usr/local/lib/libgraph.4.dylib    /usr/local/lib/libgvc.5.dylib    /usr/local/lib/libgvpr.1.dylib    /usr/local/lib/libmysql.16.0.0.dylib    /usr/local/lib/libmysql.16.dylib    /usr/local/lib/libmysql.dylib    /usr/local/lib/libmysqlclient.dylib    /usr/local/lib/libmysqlclient_r.dylib    /usr/local/lib/libopencv_calib3d.2.2.0.dylib    /usr/local/lib/libopencv_contrib.2.2.0.dylib    /usr/local/lib/libopencv_core.2.2.0.dylib    /usr/local/lib/libopencv_features2d.2.2.0.dylib    /usr/local/lib/libopencv_flann.2.2.0.dylib    /usr/local/lib/libopencv_gpu.2.2.0.dylib    /usr/local/lib/libopencv_highgui.2.2.0.dylib    /usr/local/lib/libopencv_imgproc.2.2.0.dylib    /usr/local/lib/libopencv_legacy.2.2.0.dylib    /usr/local/lib/libopencv_ml.2.2.0.dylib    /usr/local/lib/libopencv_objdetect.2.2.0.dylib    /usr/local/lib/libopencv_video.2.2.0.dylib    /usr/local/lib/libusb-0.1.4.4.4.dylib    /usr/local/lib/libusbpp-0.1.4.4.4.dylib    /usr/local/lib/profile_rt.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/libcdt.la    /usr/local/lib/libcgraph.la    /usr/local/lib/libgraph.la    /usr/local/lib/libgvc.la    /usr/local/lib/libgvpr.la    /usr/local/lib/libpathplan.la    /usr/local/lib/libusb.la    /usr/local/lib/libusbpp.la    /usr/local/lib/libxdot.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/libusb.pc    /usr/local/lib/pkgconfig/opencv.pc    /usr/local/lib/pkgconfig/soundtouch-1.4.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/libCompilerDriver.a    /usr/local/lib/libEnhancedDisassembly.a    /usr/local/lib/libmysqlclient.a    /usr/local/lib/libUnitTestMain.a    /usr/local/lib/libusb.a    /usr/local/lib/libusbpp.a    /usr/local/lib/libyasm.a
Warning: Some installed formula are missing dependencies.
You should `brew install` the missing dependencies:

    brew install gd jpeg

Run `brew missing` for more details.
Warning: You have a non-Homebrew 'pkg-config' in your PATH:
  /opt/local/bin/pkg-config

`./configure` may have problems finding brew-installed packages using
this other pkg-config.