NetCDF: Update to 4.2

Starting with the 4.2 release, NetCDF has a new distribution model where the
core C library and command line utilities are shipped as one package and the
C++ and Fortran libraries are shipped as seperate packages.

For now, we're handling this by including the C++ and Fortran libraries as
sub-brews so there is no need for a bunch of `netcdf-cxx` and `netcdf-fortran`
packages. The C++ library is also built by default to mirror the behavior of
the pre-4.2 formula.

These changes preserve the status quo as much as possible.
ncview: Patch rpath settings out of configure

The configure script tries to be clever with figuring out rpath flags for the
compilers. It fails epically.

Also, use `ENV.x11` which removes the need for a couple of configure arguments
and allows libpng to be found.
GDAL: Temporarily disable Poppler

GDAL can't compile against Poppler 0.20.0 so it is explicitly disabled for the
time being in order to prevent compilation errors. This commit can be reverted
once a fix goes in upstream.
GDAL: Fix missing comma

Argh. Forgot a comma when adding the flag to disable Poppler.
gtk-doc: find the libxml2 python site-packages directory

Add an explicit dependency on libxml2 for clarity. Previously it was
implicit in the gnome-doc-utils dep. Prepend its site-packages directory
to the PYTHONPATH.

Signed-off-by: Jack Nagel <jacknagel@gmail.com>
NetCDF: Disable Doxygen

Configure fails to disable make tasks when Doxygen is not installed and this
causes the build to fail. We don't install Doxygen docs anyway.

Also, move `ENV.fortran` to the top of the install block so that the build will
fail early if a fortran compiler is not installed.

Fixes #12406.
MuPDF: Update to 1.0

Make requirement on Snow Leopard or newer fatal.

Remove code that prefixes command line tools with `mu` as this has been done
upstream.
coda-cli 1.0.3

Closes #12405.

Signed-off-by: Jack Nagel <jacknagel@gmail.com>
Update path of nagios-plugins

Change path from sbin/nagios-plugins to sbin in order to avoid hacks in
related formulae.

Closes #12181.

Signed-off-by: Jack Nagel <jacknagel@gmail.com>
gst-ffmpeg: fix clang compile error

GST-ffmpeg comes bundled with an internal ffmpeg that suffers from
the known issue of a hardcoded gcc unless the right configure arg
is thrown.  When building with clang, the hardcoded gcc in the
libav subdirectory causes an error where gcc doesn't recognize
`-march=native`.  GST-ffmpeg offers a configure flag to fix that.
Add a flag to use our ENV.cc.

Fixes #12312

Closes #12390.

Signed-off-by: Jack Nagel <jacknagel@gmail.com>
weechat: make bindings optional, patch to fix perl

The weechat saga continues...  This commit makes all the language
modules optional rather than the default.  It adds a dep on guile
if the user options for that module.  It adds a patch from HEAD
to fix the perl segfault on exit and a removal comment for 0.3.8.
This commit does not patch the ruby-1.9.3+rvm issue other than
not building that module by default.  Still waiting on the
upstream patch.

cf. #12377

Closes #12392.

Signed-off-by: Jack Nagel <jacknagel@gmail.com>
dnscrypt-proxy 0.9.4

Closes #12343.

Signed-off-by: Jack Nagel <jacknagel@gmail.com>
dnscrypt-proxy: remove broken HEAD

The GitHub checkout needs an autotools bootstrap. Patches welcome to
enable it, but removing it until then.

Signed-off-by: Jack Nagel <jacknagel@gmail.com>
wiggle 0.9

Upgrade wiggle to version 0.9.
Patch OSX compile errors using the developer's git repo.
Patch two functionality issues released the day after 0.9.
Include patch removal information in the comments.
Remove the `malloc` patches.  They are fixed in this version.
Remove the `-w` from cflags lets the developer use `-Werror`.
Use our `cflags` and `-g` rather than `-ggdb` to support clang.
Add the `test` make target (~2sec) to verify the build because
we are trusting wiggle to do complex patching.

Closes #12305.

Signed-off-by: Jack Nagel <jacknagel@gmail.com>
git 1.7.10.3

Signed-off-by: Jack Nagel <jacknagel@gmail.com>
eigen: fix build type
Grails 2.0.4

Signed-off-by: Adam Vandenberg <flangy@gmail.com>
Move agrep to homebrew-boneyard

Closes #10140.

Signed-off-by: Jack Nagel <jacknagel@gmail.com>
net-snmp - fix compile error on Lion

net-snmp-5.7.1 is missing a darwin11.h header that can be copied
from the existing darwin10.h, if the 10s are changed to 11s.
Configure also warns that mibII/icmp is required but disabled.

* remove the configure flag --with-out-mib-modules=mibII/icmp
* if lion, cp the darwin10.h to darwin11.h
* patch the darwin11.h to replace the 10s with 11s.

This builds again on Lion without error.  The patch has been
reported upstream, and its url is in the formula comments.

Closes #11378.

Signed-off-by: Adam Vandenberg <flangy@gmail.com>
Subversion: update to 1.7.5

Signed-off-by: Adam Vandenberg <flangy@gmail.com>