In a new post to his site Christian Weiske shares his interaction with the Open Source group at Apple concerning his Structures_Graph PEAR package. While they were interested in the package and its functionality but with one issue.

Fact is that Structures_Graph is used in the PEAR installer, which is shipped as part of OSX's PHP packages. Apple simply wanted to continue their current setup without changing anything

Unfortunately, Apple had issues with the package being under the LGPLv3 license. They had a concern that, in certain circumstances, the license could allow the owner access to other potentially sensitive information from the user. He lists out his options - bascially either changing the license, asking Apple for compensation or just tell them "no". Unfortunately, if they decide that having it under that license isn't acecptable, they may drop PEAR all together (as the package is a part of the installer itself).