I am somewhat confused regarding the exact file system limitations that SIP imposes. Homebrew's packages are generally one or two iterations behind MacPorts's, due to their dependence on OS X's shipped libraries. Homebrew also enjoys a more active user community and its packages (called formulas) are updated quite often. MacPorts provides full support for using your home directory, for example. If you prefer not to use root privileges when installing packages, you should not be using a systemwide directory. Moreover, every user-maintainable systemwide software directory in OS X (/Applications, /Library, etcetera) are root-owned. In every OS that has /usr/local, it is root-owned. In fact, not requiring root privileges to modify a systemwide software directory is a major deviation from traditional best practices. It is a common misconception that this is an advantage of Homebrew. It also installs libraries in the user space (thus, you don't need to use "sudo" to install things). If this is something that users struggle with, then it is simply due to a misconfigured shell environment (although this is one advantage to Homebrew in that it does not require the configuration of one's PATH, MANPATH, etcetera). (For instance, using Puppet plus a Homebrew provider to script a configuration that will automatically build upon running a shell script.) I've been Googling everywhere and can't seem to find any answers to this question.I don't know of any package manager that will overwrite OS X's shipped packages, nor any that will affect OS X's resolution of its shipped dependancies. How would I go about fixing my Homebrew install after an OS X upgrade? I am fine with deleting it and starting from scratch again, as long as I can do so in an automated way. I've heard that OS X upgrades will break Homebrew. However, Homebrew relies on system libraries, and for security reasons, my employer may (and from what I hear, frequently will) upgrade my system at any time. Homebrew looks like a good way in which to install these tools, especially because it looks very hackable (since it uses Ruby MacPorts does not look hackable, because it uses Tcl). My employer gave me a MacBook Pro for development work however, most of the development work I do in my research group is for Linux platforms, and for a host of policy reasons, I can't install virtualization software on this laptop.
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