adding afp as components causes bean shell error · Beginner Questions

I wanted to load and read some theories from afp.
To resolve dependencies,
I decided to clone and use the afl repository.
After cloning it I to a folder, I followed the instructions
https://www.isa-afp.org/using.html
and successfully executed the command
isabelle components -u ~/Dropbox/Workspace/afp/afp-devel
with output
Added component "/Users/cstan/Dropbox/Workspace/afp/afp-devel/thys"

Sourced file: inline evaluation of:

     new isabelle.jedit.Isabelle_Export.VFS();   ;'' : No static field or inner class: VFS of class isabelle.jedit.Isabelle_Export : at Line: 2 :
 in file: inline evaluation of:

new isabelle.jedit.Isabelle_Export.VFS(); ;''
: isabelle .jedit .Isabelle_Export .VFS

at org.gjt.sp.jedit.bsh.UtilEvalError.toEvalError(UtilEvalError.java:84)
at org.gjt.sp.jedit.bsh.UtilEvalError.toEvalError(UtilEvalError.java:89)
at org.gjt.sp.jedit.bsh.BSHAmbiguousName.toObject(BSHAmbiguousName.java:64)
at org.gjt.sp.jedit.bsh.BSHAllocationExpression.objectAllocation(BSHAllocationExpression.java:86)
at org.gjt.sp.jedit.bsh.BSHAllocationExpression.eval(BSHAllocationExpression.java:62)
at org.gjt.sp.jedit.bsh.BSHPrimaryExpression.eval(BSHPrimaryExpression.java:102)
at org.gjt.sp.jedit.bsh.BSHPrimaryExpression.eval(BSHPrimaryExpression.java:47)
at org.gjt.sp.jedit.bsh.Interpreter.eval(Interpreter.java:644)
at org.gjt.sp.jedit.bsh.Interpreter.eval(Interpreter.java:738)
at org.gjt.sp.jedit.bsh.Interpreter.eval(Interpreter.java:727)
at org.gjt.sp.jedit.BeanShellFacade._eval(BeanShellFacade.java:153)
at org.gjt.sp.jedit.BeanShellFacade.eval(BeanShellFacade.java:117)
at org.gjt.sp.jedit.BeanShell.eval(BeanShell.java:382)
at org.gjt.sp.jedit.ServiceManager$Descriptor.getInstance(ServiceManager.java:337)
at org.gjt.sp.jedit.ServiceManager.getService(ServiceManager.java:262)
at org.gjt.sp.jedit.io.VFSManager.getVFSForProtocol(VFSManager.java:158)
at org.gjt.sp.jedit.MiscUtilities.isURL(MiscUtilities.java:590)
at org.gjt.sp.jedit.io.VFSManager.getVFSForPath(VFSManager.java:176)
at org.gjt.sp.jedit.MiscUtilities.pathsEqual(MiscUtilities.java:1206)
at org.gjt.sp.jedit.BufferHistory.getEntry(BufferHistory.java:88)
at org.gjt.sp.jedit.jEdit.composeBufferPropsFromHistory(jEdit.java:4418)
at org.gjt.sp.jedit.jEdit.openTemporary(jEdit.java:1859)
at org.gjt.sp.jedit.jEdit.openTemporary(jEdit.java:1825)
at org.gjt.sp.jedit.jEdit.openTemporary(jEdit.java:1778)
at org.gjt.sp.jedit.BeanShell._runScript(BeanShell.java:328)
at org.gjt.sp.jedit.BeanShell._runScript(BeanShell.java:291)
at org.gjt.sp.jedit.BeanShell.runScript(BeanShell.java:217)
at org.gjt.sp.jedit.Macros$BeanShellHandler.runMacro(Macros.java:1115)
at org.gjt.sp.jedit.jEdit.runStartupScripts(jEdit.java:4001)
at org.gjt.sp.jedit.jEdit.main(jEdit.java:552)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:64)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:564)
at isabelle.Main$.$anonfun$main$4(main.scala:129)
at isabelle.Main$.main(main.scala:138)
at isabelle.Main.main(main.scala)

/Applications/Isabelle2021.app/src/Tools/jEdit/dist/jars/Isabelle-jEdit.jar:
Cannot start:
*** Unknown option "document_preprocessor"
*** The error(s) above occurred in session entry "Huffman" (line 3 of "/Users/cstan/Dropbox/Workspace/afp/afp-devel/thys/Huffman/ROOT")

And after that I could not get isabelle working properly (processing input, giving out messages etc.)
And the jedit interface looks like the below picture.
Screenshot-2021-10-17-at-00.42.18.png

Wenda Li (Oct 17 2021 at 14:59):

Which AFP version are you using? To me, it appears that you are probably using the development version rather than the most recent stable one (that is compatible with Isabelle2021). You can check if your AFP is correctly referenced by Isabelle by typing something like Wendas-MBP:~ wenda$ cat ~/.isabelle/Isabelle2021/ROOTS in you terminal. In my case, the command gives

# Additional session root directories
#
#   * each line contains one directory entry in Isabelle path notation
#   * lines starting with "#" are stripped
#   * changes require application restart
#
#:mode=text:encoding=UTF-8:

/Users/wenda/Workspace/afp2021/thys/

where the last line is the path pointing to the theory directory of the downloaded AFP. You can later manually modify the Isabelle2021/ROOTS file as you see fit.

Stream: Beginner Questions

Topic: adding afp as components causes bean shell error

Chengsong Tan (Oct 16 2021 at 23:43):

Wenda Li (Oct 17 2021 at 14:59):