javac -g -Xlint:unchecked -Xlint:deprecation -extdirs "./external" -d ./ -target 1.6 -source 1.6 -cp ~/test/fairSIM/ij.jar org/fairsim/*/*.java
warning: [options] bootstrap class path not set in conjunction with -source 1.6
org/fairsim/linalg/JTransformsConnector.java:23: error: package org.fairsim.extern.jtransforms does not exist
import org.fairsim.extern.jtransforms.*;
^
org/fairsim/linalg/JTransformsConnector.java:29: error: cannot find symbol
        FloatFFT_1D fft1ds;
        ^
  symbol:   class FloatFFT_1D
  location: class JTransformsConnector
org/fairsim/linalg/JTransformsConnector.java:30: error: cannot find symbol
        FloatFFT_2D fft2ds;
        ^
  symbol:   class FloatFFT_2D
  location: class JTransformsConnector
org/fairsim/linalg/JTransformsConnector.java:34: error: cannot find symbol
                fft1ds = new  FloatFFT_1D(n);
                              ^
  symbol:   class FloatFFT_1D
  location: class JTransformsConnector
org/fairsim/linalg/JTransformsConnector.java:39: error: cannot find symbol
                fft2ds = new  FloatFFT_2D(w,h);
                              ^
  symbol:   class FloatFFT_2D
  location: class JTransformsConnector
org/fairsim/sim_gui/ImageControl.java:121: warning: [unchecked] unchecked call to setPrototypeDisplayValue(E) as a member of the raw type JComboBox
        imgBox.box.setPrototypeDisplayValue("some really long image filename"+
                                           ^
  where E is a type-variable:
    E extends Object declared in class JComboBox
org/fairsim/sim_gui/ImageControl.java:224: warning: [unchecked] unchecked call to setPrototypeDisplayValue(E) as a member of the raw type JComboBox
        sliceBox.box.setPrototypeDisplayValue("123");
                                             ^
  where E is a type-variable:
    E extends Object declared in class JComboBox
org/fairsim/sim_gui/Tiles.java:176: warning: [unchecked] unchecked call to setRenderer(ListCellRenderer<? super E>) as a member of the raw type JComboBox
                box.setRenderer( new DefaultListCellRenderer() {
                               ^
  where E is a type-variable:
    E extends Object declared in class JComboBox
org/fairsim/sim_gui/Tiles.java:243: warning: [unchecked] unchecked call to addItem(E) as a member of the raw type JComboBox
                    box.addItem( a );
                               ^
  where E is a type-variable:
    E extends Object declared in class JComboBox
org/fairsim/sim_gui/Tiles.java:277: warning: [unchecked] unchecked call to JComboBox(E[]) as a member of the raw type JComboBox
            super(e);
                 ^
  where E is a type-variable:
    E extends Object declared in class JComboBox
5 errors
6 warnings
make: *** [Makefile:26: all] Error 1