libgit2: Update to 0.17
Armadillo: Update to 3.2.0
GDAL: Update to 1.9.1

The new release contains pre-built man pages.
gpg-agent: set default pinentry program

Fixes #12382.

Signed-off-by: Jack Nagel <jacknagel@gmail.com>
HDF5: Update to 1.8.9

Also clean up arguments and options.
parallel 20120522

Signed-off-by: Jack Nagel <jacknagel@gmail.com>
wdiff 1.1.1

Signed-off-by: Jack Nagel <jacknagel@gmail.com>
Poppler: Update to 0.20.0
DiffPDF: Update to 2.0.0

Also, use a Requirement that references the Poppler Tab to figure out if Qt
support is present.
pdf2svg: Depend on a Requirement for Poppler-Glib

Instead of doing `pkg-config` checks, now use a Requirement that references the
installation Tab for Poppler.
Set close-on-exec on the error pipe

We use a pipe to marshal exceptions from the build script back to the
main Homebrew process; the associated file descriptor is stored in an
environment variable so that the script can figure out which descriptor
to use after being exec'd.

However, any child processes of the build script inherit this
descriptor (i.e. anything spawned via "system" by the formula during
installation). Normally this is not an issue, but if a formula executes
a long-running process such as a daemon, the main Homebrew process will
never see EOF on the error pipe because the daemon still has an open
descriptor.

We can fix this while preserving current behavior by setting the
close-on-exec flag on the build script's error pipe descriptor.

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