Re: AstroImageJ_Updater not working on Mac with OS 10.12
URL: http://astroimagej.170.s1.nabble.com/AstroImageJ-Updater-not-working-on-Mac-with-OS-10-12-tp513p518.html
Hi Walter,
I think I misunderstood the problem you are having. My new interpretation is that AIJ and all of its built-in functions work correctly, but you are not able to add a new plugin to AIJ. Is that correct?
If so, it seems like all of your print out issues below are of warning, rather than errors, except the second one, which is a write error:
ij/plugin/filter/PlugInFilter.java(ij/plugin/<a class="moz-txt-link-freetext" href="filter:PlugInFilter.java">filter:PlugInFilter.java):10: error while writing ij.plugin.filter.PlugInFilter: PlugInFilter.class (Read-only file system)
Is your AIstroImageJ folder enabled for writing? If not, maybe that is all that needs to be changed to get your plugin working. I didn't look at all of the warnings, but many of them are "deprecation" warning, which will not typically cause a problem. They are just saying that there is a newer way provided in Java to supersede the code as written.
If fixing the write protection issue doesn't get your plugin working, could you forward it to me at karenacollins (at at) outlook (dot dot) com, so that I can take a look on my end.
If you are actually having a problem with built-in AIJ functions, let me know that too.
Karen
Hello Karen:
Thank you for all of your time that you have put into helping me solve this problem. I did as you suggested and here are the screenshots.I also pasted into the bottom of this email the error report I get if I try to run and install one of the plugins. Just to be clear (maybe I'm getting the wrong version of AstroImageJ) I download my version from http://www.astro.louisville.edu/software/astroimagej/ see my screenshot.
Walter
/Applications/AstroImageJ/plugins/Calculate_Quality.java:27: warning: [deprecation] write(java.lang.String) in ij.IJ has been deprecated
IJ.write("" + slice + "\t" + calculate(ip));
^
ij/plugin/filter/PlugInFilter.java(ij/plugin/<a class="moz-txt-link-freetext" href="filter:PlugInFilter.java">filter:PlugInFilter.java):10: error while writing ij.plugin.filter.PlugInFilter: PlugInFilter.class (Read-only file system)
public interface PlugInFilter {
^
ij/ImagePlus.java(ij:ImagePlus.java):2126: warning: [unchecked] unchecked call to addElement(E) as a member of the raw type java.util.Vector
listeners.addElement(listener);
^
ij/gui/ImageWindow.java(ij/gui:ImageWindow.java):107: warning: [deprecation] show() in java.awt.Window has been deprecated
if (!Prefs.get("Astronomy_Tool.autoConvert", false) || (this instanceof PlotWindow) || (this instanceof HistogramWindow) || this.getTitle().startsWith("Profile of") || this.getTitle().startsWith("About")) show();
^
ij/gui/ImageWindow.java(ij/gui:ImageWindow.java):139: warning: [deprecation] show() in java.awt.Window has been deprecated
if (!Prefs.get("Astronomy_Tool.autoConvert", false) || (this instanceof PlotWindow) || (this instanceof HistogramWindow) || this.getTitle().startsWith("Profile of") || this.getTitle().startsWith("About")) show();
^
ij/gui/Roi.java(ij/gui:Roi.java):876: warning: [deprecation] getDisplayList() in ij.gui.ImageCanvas has been deprecated
if (Interpreter.isBatchMode() && ic!=null && ic.getDisplayList()!=null && strokeColor==null && fillColor==null)
^
ij/ImageJ.java(ij:ImageJ.java):185: warning: [deprecation] show() in java.awt.Window has been deprecated
show();
^
ij/ImageJ.java(ij:ImageJ.java):596: warning: [unchecked] unchecked call to addElement(E) as a member of the raw type java.util.Vector
classes.addElement(c);
^
ij/gui/ImageCanvas.java(ij/gui:ImageCanvas.java):1356: warning: [unchecked] unchecked call to add(E) as a member of the raw type java.util.Vector
displayList.add(overlay.get(i));
^
ij/gui/Overlay.java(ij/gui:Overlay.java):24: warning: [unchecked] unchecked call to add(E) as a member of the raw type java.util.Vector
list.add(roi);
^
ij/gui/Overlay.java(ij/gui:Overlay.java):29: warning: [unchecked] unchecked call to add(E) as a member of the raw type java.util.Vector
list.add(roi);
^
ij/gui/Overlay.java(ij/gui:Overlay.java):49: warning: [unchecked] unchecked call to add(E) as a member of the raw type java.util.Vector
list.add(roi);
^
ij/gui/Overlay.java(ij/gui:Overlay.java):96: warning: [unchecked] unchecked call to <T>toArray(T[]) as a member of the raw type java.util.Vector
return (Roi[])list.toArray(array);
^
ij/plugin/MacroInstaller.java(ij/plugin:MacroInstaller.java):110: warning: [unchecked] unchecked call to add(E) as a member of the raw type java.util.ArrayList
tools.add(name);
^
ij/plugin/MacroInstaller.java(ij/plugin:MacroInstaller.java):293: warning: [unchecked] unchecked call to put(K,V) as a member of the raw type java.util.Hashtable
macroShortcuts.put(new Integer(code), commandPrefix+name);
^
ij/plugin/MacroInstaller.java(ij/plugin:MacroInstaller.java):305: warning: [unchecked] unchecked call to put(K,V) as a member of the raw type java.util.Hashtable
shortcuts.put(new Integer(code), commandPrefix+name);
^
ij/plugin/frame/Editor.java(ij/plugin/frame:Editor.java):233: warning: [deprecation] show() in java.awt.Window has been deprecated
show();
^
ij/plugin/frame/Editor.java(ij/plugin/frame:Editor.java):303: warning: [deprecation] show() in java.awt.Window has been deprecated
show();
^
ij/macro/Interpreter.java(ij/macro:Interpreter.java):1725: warning: [unchecked] unchecked call to addElement(E) as a member of the raw type java.util.Vector
imageTable.addElement(imp);
^
ij/text/TextWindow.java(ij/text:TextWindow.java):98: warning: [deprecation] show() in java.awt.Window has been deprecated
show();
^
ij/text/TextWindow.java(ij/text:TextWindow.java):117: warning: [deprecation] show() in java.awt.Window has been deprecated
show();
^
ij/macro/Functions.java(ij/macro:Functions.java):1374: warning: [unchecked] unchecked call to addElement(E) as a member of the raw type java.util.Vector
vector.addElement(v);
^
ij/macro/Functions.java(ij/macro:Functions.java):2684: warning: [deprecation] show() in java.awt.Window has been deprecated
if (!win.isVisible()) win.show();
^
ij/macro/Functions.java(ij/macro:Functions.java):3356: warning: [deprecation] calculate(java.lang.String,ij.ImagePlus,ij.ImagePlus) in ij.plugin.ImageCalculator has been deprecated
ic.calculate(operator, img1, img2);
^
ij/macro/Functions.java(ij/macro:Functions.java):3646: warning: [unchecked] unchecked call to add(E) as a member of the raw type java.util.Vector
vargs.add(getNextString());
^
ij/macro/Functions.java(ij/macro:Functions.java):3671: warning: [unchecked] unchecked call to getMethod(java.lang.String,java.lang.Class<?>...) as a member of the raw type java.lang.Class
m = c.getMethod(methodName,argClasses);
^
ij/macro/Functions.java(ij/macro:Functions.java):3686: warning: [unchecked] unchecked call to getMethod(java.lang.String,java.lang.Class<?>...) as a member of the raw type java.lang.Class
m = c.getMethod(methodName,argClasses);
^
ij/macro/Functions.java(ij/macro:Functions.java):3809: warning: [unchecked] unchecked call to put(K,V) as a member of the raw type java.util.Hashtable
pgm.menus.put(name, commands);
^
ij/macro/Functions.java(ij/macro:Functions.java):3875: warning: [unchecked] unchecked call to addElement(E) as a member of the raw type java.util.Vector
v.addElement((String)en.nextElement());
^
ij/macro/Functions.java(ij/macro:Functions.java):4013: warning: [unchecked] unchecked call to put(K,V) as a member of the raw type java.util.Hashtable
interp.pgm.extensionRegistry.put(descriptors[i].name, descriptors[i]);
^
ij/macro/Functions.java(ij/macro:Functions.java):4045: warning: [unchecked] unchecked call to add(E) as a member of the raw type java.util.Vector
v.add(arg1);
^
ij/macro/Functions.java(ij/macro:Functions.java):4047: warning: [unchecked] unchecked call to add(E) as a member of the raw type java.util.Vector
v.add(getNextString());
^
ij/macro/Functions.java(ij/macro:Functions.java):4502: warning: [unchecked] unchecked call to addElement(E) as a member of the raw type java.util.Vector
v.addElement(en.nextElement());
^
ij/macro/Functions.java(ij/macro:Functions.java):4770: warning: [unchecked] unchecked call to add(E) as a member of the raw type java.util.ArrayList
list.add((Variable)a[i].clone());
^
ij/macro/Functions.java(ij/macro:Functions.java):4776: warning: [unchecked] unchecked call to add(E) as a member of the raw type java.util.ArrayList
list.add(v);
^
ij/macro/Functions.java(ij/macro:Functions.java):4781: warning: [unchecked] unchecked call to add(E) as a member of the raw type java.util.ArrayList
list.add(v);
^
ij/macro/Functions.java(ij/macro:Functions.java):5209: warning: [deprecation] setLineWidth(int) in ij.gui.Roi has been deprecated
roi.setLineWidth(getProcessor().getLineWidth());
^
ij/plugin/frame/RoiManager.java(ij/plugin/frame:RoiManager.java):133: warning: [deprecation] show() in java.awt.Window has been deprecated
show();
^
ij/plugin/frame/RoiManager.java(ij/plugin/frame:RoiManager.java):331: warning: [unchecked] unchecked call to put(K,V) as a member of the raw type java.util.Hashtable
rois.put(label, roiCopy);
^
ij/plugin/frame/RoiManager.java(ij/plugin/frame:RoiManager.java):366: warning: [unchecked] unchecked call to put(K,V) as a member of the raw type java.util.Hashtable
rois.put(label, (Roi)roi.clone());
^
ij/plugin/frame/RoiManager.java(ij/plugin/frame:RoiManager.java):504: warning: [unchecked] unchecked call to put(K,V) as a member of the raw type java.util.Hashtable
rois.put(name, roi2);
^
ij/plugin/frame/RoiManager.java(ij/plugin/frame:RoiManager.java):506: warning: [unchecked] unchecked call to put(K,V) as a member of the raw type java.util.Hashtable
rois.put(name, roi);
^
ij/plugin/frame/RoiManager.java(ij/plugin/frame:RoiManager.java):523: warning: [unchecked] unchecked call to put(K,V) as a member of the raw type java.util.Hashtable
rois.put(name2, roi);
^
ij/plugin/frame/RoiManager.java(ij/plugin/frame:RoiManager.java):660: warning: [unchecked] unchecked call to put(K,V) as a member of the raw type java.util.Hashtable
rois.put(name, roi);
^
ij/plugin/frame/RoiManager.java(ij/plugin/frame:RoiManager.java):689: warning: [unchecked] unchecked call to put(K,V) as a member of the raw type java.util.Hashtable
rois.put(name, roi);
^
ij/plugin/frame/RoiManager.java(ij/plugin/frame:RoiManager.java):740: warning: [unchecked] unchecked call to put(K,V) as a member of the raw type java.util.Hashtable
rois.put(newName, roi);
^
ij/plugin/frame/RoiManager.java(ij/plugin/frame:RoiManager.java):925: warning: [deprecation] getValue(int,int) in ij.measure.ResultsTable has been deprecated
rtMulti.addValue(head+suffix, rtSys.getValue(j,rtSys.getCounter()-1));
^
ij/plugin/frame/RoiManager.java(ij/plugin/frame:RoiManager.java):1378: warning: [unchecked] unchecked call to put(K,V) as a member of the raw type java.util.Hashtable
rois.put(name2, roi);
^
ij/text/TextPanel.java(ij/text:TextPanel.java):177: warning: [unchecked] unchecked call to addElement(E) as a member of the raw type java.util.Vector
vData.addElement(chars);
^
ij/text/TextPanel.java(ij/text:TextPanel.java):227: warning: [unchecked] unchecked call to addElement(E) as a member of the raw type java.util.Vector
vData.addElement(chars);
^
ij/text/TextPanel.java(ij/text:TextPanel.java):837: warning: [unchecked] unchecked call to setElementAt(E,int) as a member of the raw type java.util.Vector
vData.setElementAt(s.toCharArray(), index);
^
ij/gui/Plot.java(ij/gui:Plot.java):730: warning: [unchecked] unchecked call to add(E) as a member of the raw type java.util.ArrayList
storedData.add(xvalues);
^
ij/gui/Plot.java(ij/gui:Plot.java):731: warning: [unchecked] unchecked call to add(E) as a member of the raw type java.util.ArrayList
storedData.add(yvalues);
^
ij/gui/GenericDialog.java(ij/gui:GenericDialog.java):172: warning: [unchecked] unchecked call to addElement(E) as a member of the raw type java.util.Vector
numberField.addElement(tf);
^
ij/gui/GenericDialog.java(ij/gui:GenericDialog.java):173: warning: [unchecked] unchecked call to addElement(E) as a member of the raw type java.util.Vector
defaultValues.addElement(new Double(defaultValue));
^
ij/gui/GenericDialog.java(ij/gui:GenericDialog.java):174: warning: [unchecked] unchecked call to addElement(E) as a member of the raw type java.util.Vector
defaultText.addElement(tf.getText());
^
ij/gui/GenericDialog.java(ij/gui:GenericDialog.java):208: warning: [unchecked] unchecked call to put(K,V) as a member of the raw type java.util.Hashtable
labels.put(component, label);
^
ij/gui/GenericDialog.java(ij/gui:GenericDialog.java):260: warning: [unchecked] unchecked call to addElement(E) as a member of the raw type java.util.Vector
stringField.addElement(tf);
^
ij/gui/GenericDialog.java(ij/gui:GenericDialog.java):301: warning: [unchecked] unchecked call to addElement(E) as a member of the raw type java.util.Vector
checkbox.addElement(cb);
^
ij/gui/GenericDialog.java(ij/gui:GenericDialog.java):407: warning: [unchecked] unchecked call to addElement(E) as a member of the raw type java.util.Vector
checkbox.addElement(cb);
^
ij/gui/GenericDialog.java(ij/gui:GenericDialog.java):461: warning: [unchecked] unchecked call to addElement(E) as a member of the raw type java.util.Vector
choice.addElement(thisChoice);
^
ij/gui/GenericDialog.java(ij/gui:GenericDialog.java):559: warning: [unchecked] unchecked call to addElement(E) as a member of the raw type java.util.Vector
slider.addElement(s);
^
ij/gui/GenericDialog.java(ij/gui:GenericDialog.java):576: warning: [unchecked] unchecked call to addElement(E) as a member of the raw type java.util.Vector
numberField.addElement(tf);
^
ij/gui/GenericDialog.java(ij/gui:GenericDialog.java):579: warning: [unchecked] unchecked call to addElement(E) as a member of the raw type java.util.Vector
defaultValues.addElement(new Double(defaultValue/scale));
^
ij/gui/GenericDialog.java(ij/gui:GenericDialog.java):580: warning: [unchecked] unchecked call to addElement(E) as a member of the raw type java.util.Vector
defaultText.addElement(tf.getText());
^
ij/gui/GenericDialog.java(ij/gui:GenericDialog.java):725: warning: [unchecked] unchecked call to addElement(E) as a member of the raw type java.util.Vector
dialogListeners.addElement(dl);
^
ij/gui/WaitForUserDialog.java(ij/gui:WaitForUserDialog.java):50: warning: [unchecked] unchecked call to getDeclaredMethod(java.lang.String,java.lang.Class<?>...) as a member of the raw type java.lang.Class
Method setAlwaysOnTop = windowClass.getDeclaredMethod("setAlwaysOnTop", new Class[] {Boolean.TYPE});
^
ij/gui/WaitForUserDialog.java(ij/gui:WaitForUserDialog.java):60: warning: [deprecation] show() in java.awt.Dialog has been deprecated
public void show() {
^
ij/gui/WaitForUserDialog.java(ij/gui:WaitForUserDialog.java):61: warning: [deprecation] show() in java.awt.Dialog has been deprecated
super.show();
^
ij/gui/PlotWindow.java(ij/gui:PlotWindow.java):286: warning: [unchecked] unchecked call to ArrayList(java.util.Collection<? extends E>) as a member of the raw type java.util.ArrayList
ArrayList displayed = new ArrayList(plot.storedData);
^
ij/gui/PlotWindow.java(ij/gui:PlotWindow.java):291: warning: [unchecked] unchecked call to add(int,E) as a member of the raw type java.util.ArrayList
displayed.add(2, plot.errorBars);
^
ij/plugin/filter/PlugInFilterRunner.java(ij/plugin/<a class="moz-txt-link-freetext" href="filter:PlugInFilterRunner.java">filter:PlugInFilterRunner.java):424: warning: [unchecked] unchecked call to put(K,V) as a member of the raw type java.util.Hashtable
sliceForThread.put(Thread.currentThread(), number);
^
ij/plugin/filter/Analyzer.java(ij/plugin/<a class="moz-txt-link-freetext" href="filter:Analyzer.java">filter:Analyzer.java):689: warning: [deprecation] write(java.lang.String) in ij.IJ has been deprecated
IJ.write(rt.getRowAsString(counter-1));
^
ij/plugin/frame/ContrastAdjuster.java(ij/plugin/frame:ContrastAdjuster.java):228: warning: [deprecation] show() in java.awt.Dialog has been deprecated
show();
^
ij/plugin/filter/GaussianBlur.java(ij/plugin/<a class="moz-txt-link-freetext" href="filter:GaussianBlur.java">filter:GaussianBlur.java):58: warning: [deprecation] getBoundingRect() in ij.gui.Roi has been deprecated
Rectangle roiRect = imp.getRoi().getBoundingRect();
^
ij/IJ.java(ij:IJ.java):263: warning: [unchecked] unchecked call to put(K,V) as a member of the raw type java.util.Hashtable
commandTable.put("New...", "Image...");
^
ij/IJ.java(ij:IJ.java):264: warning: [unchecked] unchecked call to put(K,V) as a member of the raw type java.util.Hashtable
commandTable.put("Threshold", "Make Binary");
^
ij/IJ.java(ij:IJ.java):265: warning: [unchecked] unchecked call to put(K,V) as a member of the raw type java.util.Hashtable
commandTable.put("Display...", "Appearance...");
^
ij/IJ.java(ij:IJ.java):266: warning: [unchecked] unchecked call to put(K,V) as a member of the raw type java.util.Hashtable
commandTable.put("Start Animation", "Start Animation [\\]");
^
ij/IJ.java(ij:IJ.java):267: warning: [unchecked] unchecked call to put(K,V) as a member of the raw type java.util.Hashtable
commandTable.put("Convert Images to Stack", "Images to Stack");
^
ij/IJ.java(ij:IJ.java):268: warning: [unchecked] unchecked call to put(K,V) as a member of the raw type java.util.Hashtable
commandTable.put("Convert Stack to Images", "Stack to Images");
^
ij/IJ.java(ij:IJ.java):269: warning: [unchecked] unchecked call to put(K,V) as a member of the raw type java.util.Hashtable
commandTable.put("Convert Stack to RGB", "Stack to RGB");
^
ij/IJ.java(ij:IJ.java):270: warning: [unchecked] unchecked call to put(K,V) as a member of the raw type java.util.Hashtable
commandTable.put("Convert to Composite", "Make Composite");
^
ij/IJ.java(ij:IJ.java):271: warning: [unchecked] unchecked call to put(K,V) as a member of the raw type java.util.Hashtable
commandTable.put("New HyperStack...", "New Hyperstack...");
^
ij/IJ.java(ij:IJ.java):272: warning: [unchecked] unchecked call to put(K,V) as a member of the raw type java.util.Hashtable
commandTable.put("Stack to HyperStack...", "Stack to Hyperstack...");
^
ij/IJ.java(ij:IJ.java):273: warning: [unchecked] unchecked call to put(K,V) as a member of the raw type java.util.Hashtable
commandTable.put("HyperStack to Stack", "Hyperstack to Stack");
^
ij/IJ.java(ij:IJ.java):274: warning: [unchecked] unchecked call to put(K,V) as a member of the raw type java.util.Hashtable
commandTable.put("RGB Split", "Split Channels");
^
ij/IJ.java(ij:IJ.java):275: warning: [unchecked] unchecked call to put(K,V) as a member of the raw type java.util.Hashtable
commandTable.put("RGB Merge...", "Merge Channels...");
^
ij/IJ.java(ij:IJ.java):276: warning: [unchecked] unchecked call to put(K,V) as a member of the raw type java.util.Hashtable
commandTable.put("Channels...", "Channels Tool...");
^
ij/IJ.java(ij:IJ.java):277: warning: [unchecked] unchecked call to put(K,V) as a member of the raw type java.util.Hashtable
commandTable.put("New... ", "Table...");
^
ij/IJ.java(ij:IJ.java):278: warning: [unchecked] unchecked call to put(K,V) as a member of the raw type java.util.Hashtable
commandTable.put("Arbitrarily...", "Rotate... ");
^
ij/IJ.java(ij:IJ.java):279: warning: [unchecked] unchecked call to put(K,V) as a member of the raw type java.util.Hashtable
commandTable.put("Measurements...", "Results... ");
^
ij/IJ.java(ij:IJ.java):280: warning: [unchecked] unchecked call to put(K,V) as a member of the raw type java.util.Hashtable
commandTable.put("List Commands...", "Find Commands...");
^
ij/IJ.java(ij:IJ.java):281: warning: [unchecked] unchecked call to put(K,V) as a member of the raw type java.util.Hashtable
commandTable.put("Capture Screen ", "Capture Screen");
^
ij/IJ.java(ij:IJ.java):282: warning: [unchecked] unchecked call to put(K,V) as a member of the raw type java.util.Hashtable
commandTable.put("Add to Manager ", "Add to Manager");
^
ij/IJ.java(ij:IJ.java):283: warning: [unchecked] unchecked call to put(K,V) as a member of the raw type java.util.Hashtable
commandTable.put("In", "In [+]");
^
ij/IJ.java(ij:IJ.java):284: warning: [unchecked] unchecked call to put(K,V) as a member of the raw type java.util.Hashtable
commandTable.put("Out", "Out [-]");
^
ij/IJ.java(ij:IJ.java):285: warning: [unchecked] unchecked call to put(K,V) as a member of the raw type java.util.Hashtable
commandTable.put("Enhance Contrast", "Enhance Contrast...");
^
ij/IJ.java(ij:IJ.java):286: warning: [unchecked] unchecked call to put(K,V) as a member of the raw type java.util.Hashtable
commandTable.put("XY Coodinates... ", "XY Coordinates... ");
^
ij/IJ.java(ij:IJ.java):287: warning: [unchecked] unchecked call to put(K,V) as a member of the raw type java.util.Hashtable
commandTable.put("Statistics...", "Statistics");
^
ij/IJ.java(ij:IJ.java):288: warning: [unchecked] unchecked call to put(K,V) as a member of the raw type java.util.Hashtable
commandTable.put("Channels Tool... ", "Channels Tool...");
^
Note: Some input files additionally use or override a deprecated API.
Note: Some input files additionally use unchecked or unsafe operations.
1 error
100 warnings
On Sun, Oct 9, 2016 at 4:20 AM, karenacollins [via AstroImageJ] <[hidden email]> wrote:
Hi Walter,
I am running OS X 10.11.6 with Java 7 Update 71, and can't duplicate the problem. I have started the upgrade to the new OS X version, but that looks like it will take a while. I doubt that is the problem, but I need to make sure, and should know tomorrow night. I have students that use Java 8, so I don't think that is the problem either.
In the mean time, this sounds like an installation problem (although there is not much that can go wrong). While I am updating, would you please remove the current AIJ installation and re-download AIJ, unzip it, and move the AstroImageJ folder to the Applications folder. Then double-click AstroImageJ64.app to open AIJ, then click the bottom half of the AIJ toolbar and either send a screen shot of the information reported in the lower half of the toolbar, or type it out exactly. It will look something like this:
Note that the java version may be 1.6.0_65 or similar, even with Java 8 installed. If it will work, also go to Toolbar->Help->About AstroImageJ and send me a screen shot of the window that opens. It will look something like this:
I'll let you know what I find about the new OS X version tomorrow night U.S. time.
Karen
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