Repairing a broken development environment with mavericks migration (Note)

Maybe the same thing will happen the next time I update the OS ...

The sloppy update notifications got in the way, so I decided to run the mavericks update while I was sleeping. When I woke up in the morning, it was restarted as if nothing had happened ... tmux doesn't start.

$ brew uninstall tmux && brew install tmux

It started up for the time being, but it seems that various other parts were broken ...

The pip was also broken, so heal it

$ sudo easy_install pip

When I ran the brew doctor, I was angry that there was no veclibfort, so ...

$ brew install veclibfort
==> make all
==> make check
dyld: Library not loaded: /usr/local/lib/libcloog-isl.4.dylib
  Referenced from: /usr/local/Cellar/gcc/4.8.3_1/libexec/gcc/x86_64-apple-darwin13.2.0/4.8.3/f951
  Reason: image not found
gfortran: internal compiler error: Trace/BPT trap: 5 (program f951)
make: *** [check] Abort trap: 6

READ THIS: https://github.com/Homebrew/homebrew/wiki/troubleshooting
If reporting this issue please do so at (not Homebrew/homebrew):
  https://github.com/homebrew/homebrew-science/issues

Without cloog

$ brew uninstall cloog && brew install cloog

Isn't there a command line tool?

$ xcode-select --install

Gnuplot too ...

==> Installing gnuplot
==> Downloading https://downloads.sourceforge.net/project/gnuplot/gnuplot/4.6.5/gnuplot-4.6.5.tar.gz
######################################################################## 100.0%
==> ./configure --disable-silent-rules --prefix=/usr/local/Cellar/gnuplot/4.6.5 --with-readline=/usr/local/opt/readline --with-pdf=/usr/local/opt/pdflib-lite --with-gd=/usr/local/opt/gd --disable-wxwidgets --with-aquaterm --with-x --witho
==> make
  Referenced from: /private/tmp/gnuplot-7jMx/gnuplot-4.6.5/docs/./doc2gih
  Reason: image not found
make[2]: *** [gnuplot.gih] Trace/BPT trap: 5
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2

READ THIS: https://github.com/Homebrew/homebrew/wiki/troubleshooting

Error: Class is not a module
Please report this bug:
    https://github.com/Homebrew/homebrew/wiki/troubleshooting
/System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/lib/ruby/2.0.0/rubygems/core_ext/kernel_require.rb:55:in `require'
/System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/lib/ruby/2.0.0/rubygems/core_ext/kernel_require.rb:55:in `require'
/System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/lib/ruby/2.0.0/net/http.rb:390:in `<class:HTTP>'
/System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/lib/ruby/2.0.0/net/http.rb:384:in `<module:Net>'
/System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/lib/ruby/2.0.0/net/http.rb:25:in `<top (required)>'
/System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/lib/ruby/2.0.0/rubygems/core_ext/kernel_require.rb:55:in `require'
/System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/lib/ruby/2.0.0/rubygems/core_ext/kernel_require.rb:55:in `require'
/System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/lib/ruby/2.0.0/net/https.rb:21:in `<top (required)>'
/System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/lib/ruby/2.0.0/rubygems/core_ext/kernel_require.rb:55:in `require'
/System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/lib/ruby/2.0.0/rubygems/core_ext/kernel_require.rb:55:in `require'
/usr/local/Library/Homebrew/utils.rb:311:in `open'
/usr/local/Library/Homebrew/utils.rb:353:in `issues_matching'
/usr/local/Library/Homebrew/utils.rb:381:in `issues_for_formula'
/usr/local/Library/Homebrew/exceptions.rb:171:in `fetch_issues'
/usr/local/Library/Homebrew/exceptions.rb:167:in `issues'
/usr/local/Library/Homebrew/exceptions.rb:207:in `dump'
/usr/local/Library/Homebrew/cmd/upgrade.rb:84:in `rescue in upgrade_formula'
/usr/local/Library/Homebrew/cmd/upgrade.rb:92:in `upgrade_formula'
/usr/local/Library/Homebrew/cmd/upgrade.rb:43:in `block in upgrade'
/usr/local/Library/Homebrew/cmd/upgrade.rb:43:in `each'
/usr/local/Library/Homebrew/cmd/upgrade.rb:43:in `upgrade'
/usr/local/Library/brew.rb:131:in `<main>'

Or rather, it's Apple's gcc LLVM clang that's bad ...

$ brew install gcc49
$ brew install --cc=gcc-4.9 gnuplot
==> Downloading https://downloads.sf.net/project/machomebrew/Bottles/gnuplot-4.6.5.mavericks.bottle.tar.gz
######################################################################## 100.0%
==> Pouring gnuplot-4.6.5.mavericks.bottle.tar.gz
Warning: gnuplot dependency jpeg was built with a different C++ standard
library (libstdc++ from clang). This could cause problems at runtime.
==> Caveats
AquaTerm support will only be built into Gnuplot if the standard AquaTerm
package from SourceForge has already been installed onto your system.
If you subsequently remove AquaTerm, you will need to uninstall and then
reinstall Gnuplot.
==> Summary
/usr/local/Cellar/gnuplot/4.6.5: 45 files, 4.2M

When you start ipython ...

******************************************************************************
libedit detected - readline will not be well behaved, including but not limited to:
   * crashes on tab completion
   * incorrect history navigation
   * corrupting long-lines
   * failure to wrap or indent lines properly
It is highly recommended that you install readline, which is easy_installable:
     easy_install readline
Note that `pip install readline` generally DOES NOT WORK, because
it installs to site-packages, which come *after* lib-dynload in sys.path,
where readline is located.  It must be `easy_install readline`, or to a custom
location on your PYTHONPATH (even --user comes after lib-dyload).
******************************************************************************

It is solved by easy_install readline.

X11 reinstall http://xquartz.macosforge.org/landing/

Come back to virtualenv

$ python easy_install.py virtualenv

Continue ... maybe

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