Just a thought, but what if you overload the defunct function in your 
.Globalenv ?

.find.package<-function(package, lib.loc = NULL, quiet = FALSE,
             verbose = getOption("verbose") )  find.package(package, lib.loc , 
quiet,  verbose) 

I don't know whether that workaround will be "recognized" by the package 
manager.

Message: 1
Date: Tue, 15 Apr 2014 04:17:24 -0700
From: James Eales <[email protected]>
To: <[email protected]>
Cc: [email protected]
Subject: Re: [R-SIG-Mac] R.app Package Manager Bug?
Message-ID: <[email protected]>
Content-Type: text/plain; charset="utf-8"

+1
I see this too, on both mavericks and ordinary mac build of R.app Its because R 
3.1.0 has made ".find.package" a defunct function We'll need to wait for the 
R.app developers to change the code behind the package manager to use 
"find.package" instead of ".find.package"
Hopefully it'll be a simple fix

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