Homebrew reinstall

Research on installing Gnuplot:
Need X-Code and X11.  Apple says:

"X11 is no longer included with OS X, but X11 server and client libraries for OS X are available from the XQuartz project: http://xquartz.macosforge.org. You should use the latest available version of XQuartz. "  (http://support.apple.com/kb/HT5293)

As a test, I downloaded Xcode6-Beta4 and XQuartz 2.7.6.  Both seemed to install fine.  Needed to logout and log back in for X11.

Reinstalled homebrew.  Looks good:

rdominguez5359:~ racheledominguez$ ruby -e "$(curl -fsSL https://raw.github.com/Homebrew/homebrew/go/install)"
==> This script will install:
/usr/local/bin/brew
/usr/local/Library/...
/usr/local/share/man/man1/brew.1

Press RETURN to continue or any other key to abort
==> /usr/bin/sudo /bin/mkdir /Library/Caches/Homebrew
Password:
==> /usr/bin/sudo /bin/chmod g+rwx /Library/Caches/Homebrew
==> Downloading and installing Homebrew...
remote: Counting objects: 188680, done.
remote: Compressing objects: 100% (51573/51573), done.
remote: Total 188680 (delta 135954), reused 188655 (delta 135934)
Receiving objects: 100% (188680/188680), 37.53 MiB | 7.43 MiB/s, done.
Resolving deltas: 100% (135954/135954), done.
From https://github.com/Homebrew/homebrew
 * [new branch]      master     -> origin/master
Checking out files: 100% (3282/3282), done.
HEAD is now at 896dad4 Pathname.binread
==> Installation successful!
==> Next steps
Run `brew doctor` before you install anything
Run `brew help` to get started
rdominguez5359:~ racheledominguez$

Output of brew doctor:

rdominguez5359:~ racheledominguez$ brew doctor
Please note that these warnings are just used to help the Homebrew maintainers
with debugging if you file an issue. If everything you use Homebrew for is
working fine: please don't worry and just ignore them. Thanks!

Warning: Broken symlinks were found. Remove them with `brew prune`:
  /usr/local/etc/bash_completion.d/gdbus-bash-completion.sh
  /usr/local/etc/bash_completion.d/gresource-bash-completion.sh
  /usr/local/etc/bash_completion.d/gsettings-bash-completion.sh
  /usr/local/etc/pango/pango.modules
  /usr/local/etc/pango/pangox.aliases
  /usr/local/lib/pkgconfig/gdlib.pc
  /usr/local/lib/pkgconfig/gio-2.0.pc
  /usr/local/lib/pkgconfig/gio-unix-2.0.pc
  /usr/local/lib/pkgconfig/glib-2.0.pc
  /usr/local/lib/pkgconfig/gmodule-2.0.pc
  /usr/local/lib/pkgconfig/gmodule-export-2.0.pc
  /usr/local/lib/pkgconfig/gmodule-no-export-2.0.pc
  /usr/local/lib/pkgconfig/gobject-2.0.pc
  /usr/local/lib/pkgconfig/gthread-2.0.pc
  /usr/local/lib/pkgconfig/liblzma.pc
  /usr/local/lib/pkgconfig/libtiff-4.pc
  /usr/local/lib/pkgconfig/lua.pc
  /usr/local/lib/pkgconfig/pango.pc
  /usr/local/lib/pkgconfig/pangocairo.pc
  /usr/local/lib/pkgconfig/pangoft2.pc
  /usr/local/lib/pkgconfig/pangox.pc
  /usr/local/lib/pkgconfig/pangoxft.pc
  /usr/local/lib/pkgconfig/pixman-1.pc
  /usr/local/share/locale/af/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/am/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/ar/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/as/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/ast/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/az/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/be/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/be@latin/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/bg/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/bn/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/bn_IN/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/bs/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/ca/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/ca@valencia/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/cs/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/cy/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/da/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/de/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/dz/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/el/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/en@shaw/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/en_CA/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/en_GB/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/eo/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/es/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/et/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/eu/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/fa/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/fi/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/fr/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/ga/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/gl/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/gu/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/he/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/hi/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/hr/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/hu/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/hy/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/id/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/is/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/it/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/ja/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/ka/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/kk/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/kn/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/ko/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/ku/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/lt/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/lv/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/mai/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/mg/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/mk/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/ml/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/mn/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/mr/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/ms/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/nb/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/nds/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/ne/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/nl/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/nn/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/oc/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/or/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/pa/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/pl/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/ps/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/pt/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/pt_BR/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/ro/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/ru/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/rw/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/si/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/sk/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/sl/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/sq/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/sr/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/sr@ije/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/sr@latin/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/sv/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/ta/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/te/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/th/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/tl/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/tr/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/tt/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/ug/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/uk/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/vi/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/wa/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/xh/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/yi/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/zh_CN/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/zh_HK/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/zh_TW/LC_MESSAGES/glib20.mo
  /usr/local/Library/LinkedKegs/gd
  /usr/local/Library/LinkedKegs/glib
  /usr/local/Library/LinkedKegs/gnuplot
  /usr/local/Library/LinkedKegs/jasper
  /usr/local/Library/LinkedKegs/jpeg
  /usr/local/Library/LinkedKegs/latex2rtf
  /usr/local/Library/LinkedKegs/libtiff
  /usr/local/Library/LinkedKegs/lua
  /usr/local/Library/LinkedKegs/pango
  /usr/local/Library/LinkedKegs/pixman
  /usr/local/Library/LinkedKegs/pkg-config
  /usr/local/Library/LinkedKegs/wget
  /usr/local/Library/LinkedKegs/xz

Warning: Enthought Python was found in your PATH.
This can cause build problems, as this software installs its own
copies of iconv and libxml2 into directories that are picked up by
other build systems.

Warning: Python is installed at /Library/Frameworks/Python.framework

Homebrew only supports building against the System-provided Python or a
brewed Python. In particular, Pythons installed to /Library can interfere
with other software installs.

Warning: You have MacPorts or Fink installed:
  /opt/local/bin/port

This can cause trouble. You don't have to uninstall them, but you may want to
temporarily move them out of the way, e.g.

  sudo mv /opt/local ~/macports

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 -d -f

Warning: /usr/bin occurs before /usr/local/bin
This means that system-provided programs will be used instead of those
provided by Homebrew. The following tools exist at both paths:

    2to3
    2to3-2.7
    idle
    idle2.7
    pydoc
    pydoc2.7
    python
    python-config
    python2.7
    python2.7-config
    pythonw
    pythonw2.7
    smtpd.py
    smtpd2.7.py

Consider setting your PATH so that /usr/local/bin
occurs before /usr/bin. Here is a one-liner:
    echo export PATH='/usr/local/bin:$PATH' >> ~/.bash_profile

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.
rdominguez5359:~ racheledominguez$


I did two suggestions:

rdominguez5359:~ racheledominguez$   sudo mv /opt/local ~/macports
Password:
rdominguez5359:~ racheledominguez$     cd /usr/local/Library && git stash && git clean -d -f
No local changes to save
Removing Aliases/firefly
Removing Aliases/fsa
Removing Aliases/gjstest
Removing Aliases/hugs
Removing Aliases/jslint
Removing Aliases/oiio
Removing Aliases/omake
Removing Aliases/p4
Removing Aliases/p4d
Removing Aliases/rbx
Removing Aliases/ree
Removing Aliases/saga
Removing Aliases/umfpack
Removing Contributions/cmds/
Removing Contributions/install_homebrew.rb
Removing Formula/abiword.rb
Removing Formula/abyss.rb
Removing Formula/adol-c.rb
Removing Formula/agrep.rb
Removing Formula/aimage.rb
Removing Formula/ann.rb
Removing Formula/apiextractor.rb
Removing Formula/aplus.rb
Removing Formula/appledoc.rb
Removing Formula/appswitch.rb
Removing Formula/armadillo.rb
Removing Formula/asymptote.rb
Removing Formula/atlassian-plugin-sdk.rb
Removing Formula/avanor.rb
Removing Formula/aws-iam-tools.rb
Removing Formula/bali-phy.rb
Removing Formula/bedtools.rb
Removing Formula/blackbox.rb
Removing Formula/blast.rb
Removing Formula/bonnie.rb
Removing Formula/bowtie.rb
Removing Formula/bwa.rb
Removing Formula/cantera.rb
Removing Formula/cast.rb
Removing Formula/catdoc.rb
Removing Formula/cdo.rb
Removing Formula/cheops.rb
Removing Formula/chmox.rb
Removing Formula/clam.rb
Removing Formula/cliweather.rb
Removing Formula/clojure-contrib.rb
Removing Formula/clojure.rb
Removing Formula/clustal-w.rb
Removing Formula/cminpack.rb
Removing Formula/cmucl.rb
Removing Formula/colloquypush.rb
Removing Formula/color-code.rb
Removing Formula/colpack.rb
Removing Formula/connect.rb
Removing Formula/crossroads.rb
Removing Formula/cufflinks.rb
Removing Formula/curlpp.rb
Removing Formula/darwinbuild.rb
Removing Formula/denyhosts.rb
Removing Formula/despotify.rb
Removing Formula/dia.rb
Removing Formula/diffpdf.rb
Removing Formula/dotwrp.rb
Removing Formula/drizzle.rb
Removing Formula/dsniff.rb
Removing Formula/emboss.rb
Removing Formula/erviz.rb
Removing Formula/exonerate.rb
Removing Formula/fann.rb
Removing Formula/fast-statistical-alignment.rb
Removing Formula/fastri.rb
Removing Formula/fastx_toolkit.rb
Removing Formula/field3d.rb
Removing Formula/fiwalk.rb
Removing Formula/flann.rb
Removing Formula/flare.rb
Removing Formula/flex_sdk.rb
Removing Formula/flume.rb
Removing Formula/flvtool++.rb
Removing Formula/fuego.rb
Removing Formula/gccxml.rb
Removing Formula/generatorrunner.rb
Removing Formula/gerrit-tools.rb
Removing Formula/gfortran.rb
Removing Formula/git-diffall.rb
Removing Formula/git-hg.rb
Removing Formula/git-subtree.rb
Removing Formula/git-svn-abandon.rb
Removing Formula/git-utils.rb
Removing Formula/glfw.rb
Removing Formula/glpk.rb
Removing Formula/gmap-gsnap.rb
Removing Formula/gmock.rb
Removing Formula/gmt.rb
Removing Formula/gnu-arch.rb
Removing Formula/gnu-shogi.rb
Removing Formula/google-js-test.rb
Removing Formula/grads.rb
Removing Formula/gremlin.rb
Removing Formula/gromacs.rb
Removing Formula/gst-ffmpeg.rb
Removing Formula/gst-rtsp.rb
Removing Formula/gsutil.rb
Removing Formula/gtest.rb
Removing Formula/gtkglextmm.rb
Removing Formula/hdf5.rb
Removing Formula/hllib.rb
Removing Formula/hmmer.rb
Removing Formula/hugs98.rb
Removing Formula/igraph.rb
Removing Formula/ipopt.rb
Removing Formula/jscoverage.rb
Removing Formula/jsl.rb
Removing Formula/jstalk.rb
Removing Formula/justniffer.rb
Removing Formula/kelbt.rb
Removing Formula/kismet.rb
Removing Formula/kiwi.rb
Removing Formula/knife-completion.rb
Removing Formula/lastfm_fplib.rb
Removing Formula/ldid.rb
Removing Formula/libdrizzle.rb
Removing Formula/libemu.rb
Removing Formula/libgarmin.rb
Removing Formula/libgsasl.rb
Removing Formula/libgtextutils.rb
Removing Formula/libpar2.rb
Removing Formula/libpurple.rb
Removing Formula/librets.rb
Removing Formula/libspotify.rb
Removing Formula/libunique.rb
Removing Formula/lmutil.rb
Removing Formula/mafft.rb
Removing Formula/mathgl.rb
Removing Formula/mathomatic.rb
Removing Formula/maxima.rb
Removing Formula/mcl.rb
Removing Formula/metapixel.rb
Removing Formula/metasploit.rb
Removing Formula/metis.rb
Removing Formula/minc.rb
Removing Formula/mira.rb
Removing Formula/mlton.rb
Removing Formula/mod_python.rb
Removing Formula/mod_wsgi.rb
Removing Formula/mosh.rb
Removing Formula/mosml.rb
Removing Formula/mpio.rb
Removing Formula/mpsolve.rb
Removing Formula/mrfast.rb
Removing Formula/msgpack-rpc.rb
Removing Formula/mt-daapd.rb
Removing Formula/muscle.rb
Removing Formula/mydumper.rb
Removing Formula/nailgun.rb
Removing Formula/nauty.rb
Removing Formula/ncview.rb
Removing Formula/net-nuclear.rb
Removing Formula/netcdf.rb
Removing Formula/netsed.rb
Removing Formula/o-make.rb
Removing Formula/obby.rb
Removing Formula/octave.rb
Removing Formula/odt2txt.rb
Removing Formula/omega.rb
Removing Formula/oorexx.rb
Removing Formula/open-sg.rb
Removing Formula/opencv.rb
Removing Formula/openimageio.rb
Removing Formula/openmeeg.rb
Removing Formula/opentracker.rb
Removing Formula/otx.rb
Removing Formula/paml.rb
Removing Formula/parmetis.rb
Removing Formula/perforce-proxy.rb
Removing Formula/perforce-server.rb
Removing Formula/perforce.rb
Removing Formula/phyml.rb
Removing Formula/pil.rb
Removing Formula/play.rb
Removing Formula/playdar.rb
Removing Formula/plink.rb
Removing Formula/pngrewrite.rb
Removing Formula/pos.rb
Removing Formula/ppl.rb
Removing Formula/primer3.rb
Removing Formula/prodigal.rb
Removing Formula/qfits.rb
Removing Formula/qhull.rb
Removing Formula/qrupdate.rb
Removing Formula/qt-mobility.rb
Removing Formula/quickfix.rb
Removing Formula/quicktree.rb
Removing Formula/r.rb
Removing Formula/rails-completion.rb
Removing Formula/readpst.rb
Removing Formula/redis-tools.rb
Removing Formula/riak-search.rb
Removing Formula/rogue.rb
Removing Formula/rubinius.rb
Removing Formula/ruby-enterprise-edition.rb
Removing Formula/ruby-odbc.rb
Removing Formula/saga-core.rb
Removing Formula/samtools.rb
Removing Formula/scalate.rb
Removing Formula/scalpel.rb
Removing Formula/scotch.rb
Removing Formula/scrotwm.rb
Removing Formula/scummvm.rb
Removing Formula/shaper-probe.rb
Removing Formula/shark.rb
Removing Formula/sigar.rb
Removing Formula/ski.rb
Removing Formula/smpeg.rb
Removing Formula/staticrouted.rb
Removing Formula/stp.rb
Removing Formula/strategoxt.rb
Removing Formula/suite-sparse.rb
Removing Formula/sundials.rb
Removing Formula/symphony.rb
Removing Formula/synergy.rb
Removing Formula/syslog-ng.rb
Removing Formula/tabix.rb
Removing Formula/tcpstat.rb
Removing Formula/titlecase.rb
Removing Formula/tmap.rb
Removing Formula/tophat.rb
Removing Formula/transcode.rb
Removing Formula/triangle.rb
Removing Formula/uif2iso.rb
Removing Formula/unafold.rb
Removing Formula/ungif.rb
Removing Formula/unyaffs.rb
Removing Formula/urweb.rb
Removing Formula/v8cgi.rb
Removing Formula/vcftools.rb
Removing Formula/velvet.rb
Removing Formula/vimeo-downloader.rb
Removing Formula/vips.rb
Removing Formula/vtk.rb
Removing Formula/willgit.rb
Removing Formula/wkhtmltopdf.rb
Removing Formula/wol.rb
Removing Formula/wp-cli.rb
Removing Formula/xaw3d.rb
Removing Formula/xml2rfc.rb
Removing Homebrew/LICENSE
Removing Homebrew/cmd/--config.rb
Removing Homebrew/cmd/versions.rb
Removing Homebrew/compat/brewkit.rb
Removing Homebrew/compat/compatibility.rb
Removing Homebrew/patches.rb
Removing Homebrew/test/tarballs/configure_fails.tar.gz
Removing Homebrew/test/test_bucket.rb
Removing Homebrew/test/test_checksums.rb
Removing Homebrew/test/test_compilers.rb
Removing Homebrew/test/test_external_deps.rb
Removing Homebrew/test/test_patches.rb
Removing Homebrew/test/test_pathname_install.rb
Removing Homebrew/vendor/LICENSE
Removing Homebrew/vendor/multi_json.rb
Removing Homebrew/vendor/multi_json/
rdominguez5359:Library racheledominguez$

rdominguez5359:Library racheledominguez$ brew prune
Pruned 0 dead formulae
Pruned 130 symbolic links and 199 directories from /usr/local

I don't want to screw up my caanopy install, so I'm not going to change paths.  Output from brew doctor now:

rdominguez5359:Library racheledominguez$ brew doctor
Please note that these warnings are just used to help the Homebrew maintainers
with debugging if you file an issue. If everything you use Homebrew for is
working fine: please don't worry and just ignore them. Thanks!

Warning: Enthought Python was found in your PATH.
This can cause build problems, as this software installs its own
copies of iconv and libxml2 into directories that are picked up by
other build systems.

Warning: Python is installed at /Library/Frameworks/Python.framework

Homebrew only supports building against the System-provided Python or a
brewed Python. In particular, Pythons installed to /Library can interfere
with other software installs.

Warning: /usr/bin occurs before /usr/local/bin
This means that system-provided programs will be used instead of those
provided by Homebrew. The following tools exist at both paths:

    2to3
    2to3-2.7
    idle
    idle2.7
    pydoc
    pydoc2.7
    python
    python-config
    python2.7
    python2.7-config
    pythonw
    pythonw2.7
    smtpd.py
    smtpd2.7.py

Consider setting your PATH so that /usr/local/bin
occurs before /usr/bin. Here is a one-liner:
    echo export PATH='/usr/local/bin:$PATH' >> ~/.bash_profile