I was able to fix the problem by going to the afp-devel directory and typing 
“hg fetch". I guess some big incompatible changes had taken place.

> On 6 Dec 2017, at 22:32, Makarius <makar...@sketis.net> wrote:
> On 06/12/17 15:48, Lawrence Paulson wrote:
>> I've just updated to a recent version (fa1173288322) and tried to run a 
>> session by the following command:
>> isabelle jedit -l HOL-Analysis CV.thy 
>> And then I get an alert box containing the appended text. Any idea what's 
>> going wrong here?
> It looks like you have an alien AFP version in your ROOTS or -d options,
> one that does not fit to the Isabelle version.

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