Could you possibly add some more information about this?  In particular, it would be useful to see:

  - The last screen of errors that you get after typing "make"

  - Confirm the platform (i.e. operating system and version) that you're using

  - The output from "git status"

>>The last screen of errors that you get after typing "make":

java/linux-amd64/jdk1.6.0_04/jre/../include/jni.h:1929: error: expected constructor, destructor, or type conversion before ‘void’
fiji.cxx: In function ‘int create_java_vm(JavaVM**, void**, JavaVMInitArgs*)’:
fiji.cxx:220: error: ISO C++ forbids declaration of ‘jint’ with no type
fiji.cxx:220: error: ‘JNI_CreateJavaVM’ was not declared in this scope
fiji.cxx:220: error: expected ‘,’ or ‘;’ before ‘(’ token
fiji.cxx: In function ‘int start_ij()’:
fiji.cxx:778: error: ‘struct JavaVMInitArgs’ has no member named ‘version’
fiji.cxx:780: error: ‘struct JavaVMInitArgs’ has no member named ‘nOptions’
fiji.cxx:815: error: ‘struct JavaVM_’ has no member named ‘DetachCurrentThread’
fiji.cxx:819: error: ‘struct JavaVM_’ has no member named ‘DestroyJavaVM’
Could not compile fiji.cxx: Failed: 1
        in rule (CompileCProgram) fiji <- fiji.cxx
        in rule (All)  <- jdk fiji
make: *** [fiji] Error 1


>>Confirm the platform (i.e. operating system and version) that you're using

I am using fedora, but I don't know the version.

>> The output from "git status"

[albam@localhost fiji]$ git status
# On branch master
# Untracked files:
#   (use "git add <file>..." to include in what will be committed)
#
#       plugins/level_sets.jar
#       src-plugins/BeanShell_Interpreter.jar
#       src-plugins/CLI_.jar
#       src-plugins/Clojure_Interpreter.jar
#       src-plugins/Fiji.jar
#       src-plugins/IO_.jar
#       src-plugins/JRuby_Interpreter.jar
#       src-plugins/Javascript_.jar
#       src-plugins/Jython_Interpreter.jar
#       src-plugins/SplineDeformationGenerator_.jar
#       src-plugins/bUnwarpJ_.jar
#       src-plugins/level_sets.jar
#       src-plugins/register_virtual_stack_slices.jar
#       src-plugins/registration_3d.jar
nothing added to commit but untracked files present (use "git add" to track)


Thanks, Marta.

I have done an update today and now fiji is working.

So, I suppose that the bug is fixed. 

Thanks, Marta.