Fix brew doctor

brew doctor

## guide for mavericks 10.9 configuration + python development environment setup
http://hackercodex.com/guide/mac-osx-mavericks-10.9-configuration/
http://hackercodex.com/guide/python-development-environment-on-mac-osx/

## installing xcode command line tools
xcode-select --install

## installing homebrew
ruby -e "$(curl -fsSL https://raw.github.com/mxcl/homebrew/go/install)"
brew doctor

  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: 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: 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/libtcl8.6.dylib
      /usr/local/lib/libtk8.6.dylib
      /usr/local/lib/libusb-1.0.0.dylib
  
  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/tcl.pc
      /usr/local/lib/pkgconfig/tk.pc
      /usr/local/lib/pkgconfig/valgrind.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/libtclstub8.6.a
      /usr/local/lib/libtkstub8.6.a
  
  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:
  
      ccmake
      cmake
      cmakexbuild
      cpack
      ctest
  
  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

## fix brew errors
http://stackoverflow.com/questions/16462949/homebrew-brew-doctor-throwing-up-a-lot-of-errors-how-can-i-fix-them

## change ownership of certain folders
sudo chown -R graceyeo:admin /usr/local/share/man/de
sudo chown -R graceyeo:admin /usr/local/share/man/de/man1
sudo chown -R graceyeo:admin /usr/local/share/man/mann

## uninstall macports
http://stackoverflow.com/questions/7751427/prevent-warning-about-macports-fink-installation
http://guide.macports.org/chunked/installing.macports.uninstalling.html
sudo port -fp uninstall installed
sudo rm -rf \
    /opt/local \
    /Applications/DarwinPorts \
    /Applications/MacPorts \
    /Library/LaunchDaemons/org.macports.* \
    /Library/Receipts/DarwinPorts*.pkg \
    /Library/Receipts/MacPorts*.pkg \
    /Library/StartupItems/DarwinPortsStartup \
    /Library/Tcl/darwinports1.0 \
    /Library/Tcl/macports1.0 \
    ~/.macports

  ## Removed from .bash_profile
  
  ##
  # Your previous /Users/graceyeo/.bash_profile file was backed up as /Users/graceyeo/.bash_profile.macports-saved_2013-05-30_at_16:54:38
  ##
  
  # MacPorts Installer addition on 2013-05-30_at_16:54:38: adding an appropriate PATH variable for use with MacPorts.
  export PATH=/opt/local/bin:/opt/local/sbin:$PATH
  # Finished adapting your PATH environment variable for use with MacPorts.

## unexpected files and libraries

http://stackoverflow.com/questions/10580813/how-do-i-fix-brew-doctor-errors
mv /usr/local/lib/libtcl8.6.dylib .
mv /usr/local/lib/libtk8.6.dylib .
mv /usr/local/lib/libusb-1.0.0.dylib .
mv /usr/local/lib/pkgconfig/tcl.pc /usr/local/lib/pkgconfig/tk.pc /usr/local/lib/pkgconfig/valgrind.pc /usr/local/lib/libtclstub8.6.a /usr/local/lib/libtkstub8.6.a .

## update brew

brew update
  Updated Homebrew from ff02410f to f74d6141.
  ==> Updated Formulae
  grass    riemann  voms

brew install bash-completion ssh-copy-id wget

## install python
brew install python --with-brewed-openssl

  ==> Installing dependencies for python: pkg-config, readline, sqlite, gdbm, openssl
  ==> Installing python dependency: pkg-config
  ==> Downloading https://downloads.sf.net/project/machomebrew/Bottles/pkg-config-0.28.mavericks.bot
  ######################################################################## 100.0%
  ==> Pouring pkg-config-0.28.mavericks.bottle.2.tar.gz
  🍺  /usr/local/Cellar/pkg-config/0.28: 10 files, 604K
  ==> Installing python dependency: readline
  ==> Downloading https://downloads.sf.net/project/machomebrew/Bottles/readline-6.2.4.mavericks.bott
  ######################################################################## 100.0%
  ==> Pouring readline-6.2.4.mavericks.bottle.1.tar.gz
  ==> Caveats
  This formula is keg-only, so it was not symlinked into /usr/local.
  
  OS X provides the BSD libedit library, which shadows libreadline.
  In order to prevent conflicts when programs look for libreadline we are
  defaulting this GNU Readline installation to keg-only.
  
  Generally there are no consequences of this for you. If you build your
  own software and it requires this formula, you'll need to add to your
  build variables:
  
      LDFLAGS:  -L/usr/local/opt/readline/lib
      CPPFLAGS: -I/usr/local/opt/readline/include
  
  ==> Summary
  🍺  /usr/local/Cellar/readline/6.2.4: 31 files, 1.6M
  ==> Installing python dependency: sqlite
  ==> Downloading https://downloads.sf.net/project/machomebrew/Bottles/sqlite-3.8.1.mavericks.bottle
  ######################################################################## 100.0%
  ==> Pouring sqlite-3.8.1.mavericks.bottle.tar.gz
  ==> Caveats
  This formula is keg-only, so it was not symlinked into /usr/local.
  
  Mac OS X already provides this software and installing another version in
  parallel can cause all kinds of trouble.
  
  OS X provides an older sqlite3.
  
  Generally there are no consequences of this for you. If you build your
  own software and it requires this formula, you'll need to add to your
  build variables:
  
      LDFLAGS:  -L/usr/local/opt/sqlite/lib
      CPPFLAGS: -I/usr/local/opt/sqlite/include
  
  ==> Summary
  🍺  /usr/local/Cellar/sqlite/3.8.1: 9 files, 2.0M
  ==> Installing python dependency: gdbm
  ==> Downloading http://ftpmirror.gnu.org/gdbm/gdbm-1.10.tar.gz
  ######################################################################## 100.0%
  ==> ./configure --prefix=/usr/local/Cellar/gdbm/1.10 --mandir=/usr/local/Cellar/gdbm/1.10/share/ma
  ==> make install
  🍺  /usr/local/Cellar/gdbm/1.10: 11 files, 240K, built in 15 seconds
  ==> Installing python dependency: openssl
  ==> Downloading http://openssl.org/source/openssl-1.0.1e.tar.gz
  ################################################                          67.4%
  curl: (18) transfer closed with 1453980 bytes remaining to read
  Trying a mirror...
  ==> Downloading http://mirrors.ibiblio.org/openssl/source/openssl-1.0.1e.tar.gz
  ######################################################################## 100.0%
  ==> perl ./Configure --prefix=/usr/local/Cellar/openssl/1.0.1e --openssldir=/usr/local/etc/openssl
  ==> make depend
  ==> make
  ==> make test
  ==> make install MANDIR=/usr/local/Cellar/openssl/1.0.1e/share/man MANSUFFIX=ssl
  ==> security find-certificate -a -p /Library/Keychains/System.keychain > '/usr/local/etc/openssl/o
  ==> security find-certificate -a -p /System/Library/Keychains/SystemRootCertificates.keychain >> '
  ==> mv -f /usr/local/etc/openssl/osx_cert.pem.tmp /usr/local/etc/openssl/osx_cert.pem
  ==> Caveats
  This formula is keg-only, so it was not symlinked into /usr/local.
  
  Mac OS X already provides this software and installing another version in
  parallel can cause all kinds of trouble.
  
  The OpenSSL provided by OS X is too old for some software.
  
  Generally there are no consequences of this for you. If you build your
  own software and it requires this formula, you'll need to add to your
  build variables:
  
      LDFLAGS:  -L/usr/local/opt/openssl/lib
      CPPFLAGS: -I/usr/local/opt/openssl/include
  
  ==> Summary
  🍺  /usr/local/Cellar/openssl/1.0.1e: 429 files, 15M, built in 4.4 minutes
  ==> Installing python
  ==> Downloading http://www.python.org/ftp/python/2.7.6/Python-2.7.6.tgz
  ######################################################################## 100.0%
  ==> ./configure --prefix=/usr/local/Cellar/python/2.7.6 --enable-ipv6 --datarootdir=/usr/local/Cel
  ==> make
  ==> make install PYTHONAPPSDIR=/usr/local/Cellar/python/2.7.6
  ==> make frameworkinstallextras PYTHONAPPSDIR=/usr/local/Cellar/python/2.7.6/share/python
  ==> Downloading https://pypi.python.org/packages/source/s/setuptools/setuptools-1.3.2.tar.gz
  ######################################################################## 100.0%
  ==> /usr/local/Cellar/python/2.7.6/bin/python -s setup.py --no-user-cfg install --force --verbose
  ==> Downloading https://pypi.python.org/packages/source/p/pip/pip-1.4.1.tar.gz
  ######################################################################## 100.0%
  ==> /usr/local/Cellar/python/2.7.6/bin/python -s setup.py --no-user-cfg install --force --verbose
  ==> Caveats
  Python demo
    /usr/local/share/python/Extras
  
  Setuptools and Pip have been installed. To update them
    pip install --upgrade setuptools
    pip install --upgrade pip
  
  To symlink "Idle" and the "Python Launcher" to ~/Applications
    `brew linkapps`
  
  You can install Python packages with (the outdated easy_install or)
    `pip install <your_favorite_package>`
  
  They will install into the site-package directory
    /usr/local/lib/python2.7/site-packages
  
  See: https://github.com/mxcl/homebrew/wiki/Homebrew-and-Python
  Warning: Could not link python. Unlinking...
  Error: The `brew link` step did not complete successfully
  The formula built, but is not symlinked into /usr/local
  You can try again using `brew link python'
  
  Possible conflicting files are:
  /usr/local/bin/pip-2.7
  /usr/local/bin/pip
  ==> Summary
  🍺  /usr/local/Cellar/python/2.7.6: 5225 files, 80M, built in 2.6 minutes


## resolving errors from brew python installation
http://stackoverflow.com/questions/13088998/homebrew-python-installing

sudo chown -R graceyeo /usr/local
brew uninstall -f python
rm -rf 'brew --cache'
brew cleanup
brew prune
brew doctor
brew install python --with-brewed-openssl

http://stackoverflow.com/questions/19340871/how-to-link-home-brew-python-version-and-set-it-as-default
http://stackoverflow.com/questions/13354207/how-to-symlink-python-in-homebrew

brew link --overwrite --dry-run python
  Would remove:
  /usr/local/bin/pip-2.7
  /usr/local/bin/pip

## key command for making the link work
brew link --overwrite python
  Linking /usr/local/Cellar/python/2.7.6... 34 symlinks created

pip install --upgrade setuptools
pip install --upgrade pip

## already have git installed
brew install git

which git
  /usr/local/bin/git
/usr/bin/git --version
  git version 1.8.3.4 (Apple Git-47)

http://www.lowindata.com/2013/installing-scientific-python-on-mac-os-x/
which python
  /usr/local/bin/python

## installing virtualenv
pip install virtualenv
http://stackoverflow.com/questions/18396210/installing-virtualenv-using-homebrew-and-pip-on-mac-os-x-10-8-4
pip install virtualenvwrapper
http://virtualenvwrapper.readthedocs.org/en/latest/
source /usr/local/bin/virtualenvwrapper.sh

  add source /usr/local/bin/virtualenvwrapper.sh to ~/.bash_profile

## superhero-themed environments
mkvirtualenv wintersoldier
pip install numpy
brew install gfortran
pip install scipy
brew install freetype
pip install matplotlib

export LDFLAGS="-L/usr/local/opt/freetype/lib"
export CFLAGS="-I/usr/local/opt/freetype/include"

http://stackoverflow.com/questions/12363557/matplotlib-install-failure-on-mac-osx-10-8-mountain-lion
LDFLAGS="-L/usr/local/opt/freetype/lib -L/usr/local/opt/libpng/lib" CPPFLAGS="-I/usr/local/opt/freetype/include -I/usr/local/opt/libpng/include -I/usr/local/opt/freetype/include/freetype2" pip install matplotlib

pip install ipython

## install qtconsole

## download library from
https://qt-project.org/downloads

brew install pyqt

  add to .bash_profile
  export PYTHONPATH=/usr/local/lib/python2.7/site-packages:$PYTHONPATH

brew install zmq

  To install the zmq gem on 10.6 with the system Ruby on a 64-bit machine,
  you may need to do:
  
      ARCHFLAGS="-arch x86_64" gem install zmq -- --with-zmq-dir=/usr/local/opt/zeromq

pip install pyzmq
pip install pygments

## for more libraries that could be useful e.g. pandas, BeautifulSoup
http://joernhees.de/blog/2013/06/08/mac-os-x-10-8-scientific-python-with-homebrew/

sudo rm -rf /Library/Frameworks/R.framework /Applications/R.app \
>    /usr/bin/R /usr/bin/Rscript

brew tap homebrew/science
brew install R

  R.framework was installed to:
  /usr/local/opt/r/R.framework
  
  To use this Framework with IDEs such as RStudio, it must be linked
  to the standard OS X location:
  sudo ln -s "/usr/local/opt/r/R.framework" /Library/Frameworks
  
  To enable rJava support, run the following command:
    R CMD javareconf JAVA_CPPFLAGS=-I/System/Library/Frameworks/JavaVM.framework/Headers
  
    Bash completion has been installed to:
      /usr/local/etc/bash_completion.d
  
## is there an advantage/disadvantage to using homebrew/science to install numpy, scipy etc. vs pip? 
## does brew install scipy (with homebrew/science) == pip install scipy for all intents and purposes?