Jalview 2.7 is incompatible with Jmol-12.2.2

  Hello all !

  I have two pieces of news for you: one good and one bad.

  First, for now more than a week, jalview is part of Debian ! Thanks to all of you who helped me achieve that. You may be interested in the following pages, which are the so called package tracking pages of the various (source) packages jalview is made of in Debian:

http://packages.qa.debian.org/libj/libjaba-client-java.html

http://packages.qa.debian.org/j/jalview.html

http://packages.qa.debian.org/libv/libvamsas-client-java.html

  On these pages, there are a couple of links that may interest you more than other:

  * The bugs box on the right. Some of those may be Debian-specific (i.e. blundering from my side) or packaging-specific (which is probably of no interest to you).

  * The popcon link is the popularity contest in Debian, ie the number of Debian users that have installed jalview. For now, there's hardly anyone, mostly because jalview is in the experimental suite, because it was built against a 'development' version of jmol.

  Some time later, jalview will automatically be imported by Ubuntu, and you'll be able to find similar statistics there, although I can't give you a direct link, I'm aware of none for the time being. You can just look at the raw popcon data at popcon.ubuntu.com.

  This leads me to the bad news: jalview is fresh but already broken. Debian now ships jmol version 12.2.2 (that's the stable release, isn't it ?), and jalview doesn't build against it.

  Although I could tackle porting to the newer jmol, I guess it won't take much time to you. I'm attaching the build failure log in case someone wants to have a look. If no one steps forward, I'll give it a try ;-)...

  Cheers, and thanks again !

    Vincent

jalview-breakage-with-newer-jmol

cd . && /usr/lib/jvm/default-java/bin/java -classpath /usr/share/ant/lib/ant.jar:/usr/share/ant/lib/ant-launcher.jar:/usr/share/java/castor-xml.jar:/usr/share/java/commons-logging.jar:/usr/share/java/log4j-1.2.jar:/usr/share/java/castor-core.jar:/usr/share/java/Jmol.jar:/usr/share/java/min-jaba-client.jar:/usr/share/java/axis-jaxrpc.jar:/usr/share/java/commons-discovery.jar:/usr/share/java/axis.jar:/usr/share/java/jh.jar:/usr/share/java/vamsas-client.jar:/usr/share/jmol-applet/JmolApplet.jar:/usr/share/java/jswingreader.jar:/usr/share/java/miglayout.jar:/usr/share/icedtea-web/plugin.jar:/usr/share/java/httpmime.jar:/usr/share/java/httpcore.jar:/usr/share/java/apache-mime4j.jar:/usr/share/java/httpclient.jar:/usr/lib/jvm/default-java/lib/tools.jar -Dbuild.sysclasspath=last -DJALVIEW_VERSION=2.7 -Dant.home=/usr/share/ant org.apache.tools.ant.Main -Dcompile.debug=true -Dcompile.optimize=true -Dbuild.compiler=modern makedist
Buildfile: /tmp/buildd/jalview-2.7.dfsg/build.xml
  [taskdef] Could not load definitions from resource com/roxes/tools/ant/taskdefs.properties. It could not be found.

init:

prepare:
    [mkdir] Created dir: /tmp/buildd/jalview-2.7.dfsg/classes
     [copy] Copying 163 files to /tmp/buildd/jalview-2.7.dfsg/classes

build:
    [javac] Compiling 561 source files to /tmp/buildd/jalview-2.7.dfsg/classes
    [javac] AppletJmolBinding.java:31: cannot find symbol
    [javac] symbol : class AppletConsole
    [javac] location: package org.jmol.applet
    [javac] import org.jmol.applet.AppletConsole;
    [javac] ^
    [javac] Jalview.java:756: warning: non-varargs call of varargs method with inexact argument type for last parameter;
    [javac] cast to java.lang.Class for a varargs call
    [javac] cast to java.lang.Class[] for a non-varargs call and to suppress this warning
    [javac] gbcons = gbindingc.getConstructor(null);
    [javac] ^
    [javac] Jalview.java:757: warning: non-varargs call of varargs method with inexact argument type for last parameter;
    [javac] cast to java.lang.Object for a varargs call
    [javac] cast to java.lang.Object[] for a non-varargs call and to suppress this warning
    [javac] gbinding = gbcons.newInstance(null);
    [javac] ^
    [javac] Desktop.java:2177: warning: non-varargs call of varargs method with inexact argument type for last parameter;
    [javac] cast to java.lang.Class for a varargs call
    [javac] cast to java.lang.Class[] for a non-varargs call and to suppress this warning
    [javac] Constructor gccons = gcClass.getConstructor(null);
    [javac] ^
    [javac] Desktop.java:2181: warning: non-varargs call of varargs method with inexact argument type for last parameter;
    [javac] cast to java.lang.Class for a varargs call
    [javac] cast to java.lang.Class[] for a non-varargs call and to suppress this warning
    [javac] java.lang.reflect.Method run = gcClass.getMethod("run", null);
    [javac] ^
    [javac] Desktop.java:2182: warning: non-varargs call of varargs method with inexact argument type for last parameter;
    [javac] cast to java.lang.Object for a varargs call
    [javac] cast to java.lang.Object[] for a non-varargs call and to suppress this warning
    [javac] Object gc = gccons.newInstance(null);
    [javac] ^
    [javac] Desktop.java:2185: warning: non-varargs call of varargs method with inexact argument type for last parameter;
    [javac] cast to java.lang.Object for a varargs call
    [javac] cast to java.lang.Object[] for a non-varargs call and to suppress this warning
    [javac] run.invoke(gc, null);
    [javac] ^
    [javac] JalviewJmolBinding.java:949: cannot find symbol
    [javac] symbol : variable CALLBACK_LOADSTRUCT
    [javac] location: class org.jmol.viewer.JmolConstants
    [javac] case JmolConstants.CALLBACK_LOADSTRUCT:
    [javac] ^
    [javac] JalviewJmolBinding.java:955: cannot find symbol
    [javac] symbol : variable CALLBACK_PICK
    [javac] location: class org.jmol.viewer.JmolConstants
    [javac] case JmolConstants.CALLBACK_PICK:
    [javac] ^
    [javac] JalviewJmolBinding.java:959: cannot find symbol
    [javac] symbol : variable CALLBACK_HOVER
    [javac] location: class org.jmol.viewer.JmolConstants
    [javac] case JmolConstants.CALLBACK_HOVER:
    [javac] ^
    [javac] JalviewJmolBinding.java:963: cannot find symbol
    [javac] symbol : variable CALLBACK_SCRIPT
    [javac] location: class org.jmol.viewer.JmolConstants
    [javac] case JmolConstants.CALLBACK_SCRIPT:
    [javac] ^
    [javac] JalviewJmolBinding.java:967: cannot find symbol
    [javac] symbol : variable CALLBACK_ECHO
    [javac] location: class org.jmol.viewer.JmolConstants
    [javac] case JmolConstants.CALLBACK_ECHO:
    [javac] ^
    [javac] JalviewJmolBinding.java:970: cannot find symbol
    [javac] symbol : variable CALLBACK_MESSAGE
    [javac] location: class org.jmol.viewer.JmolConstants
    [javac] case JmolConstants.CALLBACK_MESSAGE:
    [javac] ^
    [javac] JalviewJmolBinding.java:974: cannot find symbol
    [javac] symbol : variable CALLBACK_ERROR
    [javac] location: class org.jmol.viewer.JmolConstants
    [javac] case JmolConstants.CALLBACK_ERROR:
    [javac] ^
    [javac] JalviewJmolBinding.java:977: cannot find symbol
    [javac] symbol : variable CALLBACK_SYNC
    [javac] location: class org.jmol.viewer.JmolConstants
    [javac] case JmolConstants.CALLBACK_SYNC:
    [javac] ^
    [javac] JalviewJmolBinding.java:978: cannot find symbol
    [javac] symbol : variable CALLBACK_RESIZE
    [javac] location: class org.jmol.viewer.JmolConstants
    [javac] case JmolConstants.CALLBACK_RESIZE:
    [javac] ^
    [javac] JalviewJmolBinding.java:981: cannot find symbol
    [javac] symbol : variable CALLBACK_MEASURE
    [javac] location: class org.jmol.viewer.JmolConstants
    [javac] case JmolConstants.CALLBACK_MEASURE:
    [javac] ^
    [javac] JalviewJmolBinding.java:983: cannot find symbol
    [javac] symbol : variable CALLBACK_CLICK
    [javac] location: class org.jmol.viewer.JmolConstants
    [javac] case JmolConstants.CALLBACK_CLICK:
    [javac] ^
    [javac] JalviewJmolBinding.java:1000: cannot find symbol
    [javac] symbol : variable CALLBACK_ECHO
    [javac] location: class org.jmol.viewer.JmolConstants
    [javac] case JmolConstants.CALLBACK_ECHO:
    [javac] ^
    [javac] JalviewJmolBinding.java:1001: cannot find symbol
    [javac] symbol : variable CALLBACK_LOADSTRUCT
    [javac] location: class org.jmol.viewer.JmolConstants
    [javac] case JmolConstants.CALLBACK_LOADSTRUCT:
    [javac] ^
    [javac] JalviewJmolBinding.java:1002: cannot find symbol
    [javac] symbol : variable CALLBACK_MEASURE
    [javac] location: class org.jmol.viewer.JmolConstants
    [javac] case JmolConstants.CALLBACK_MEASURE:
    [javac] ^
    [javac] JalviewJmolBinding.java:1003: cannot find symbol
    [javac] symbol : variable CALLBACK_MESSAGE
    [javac] location: class org.jmol.viewer.JmolConstants
    [javac] case JmolConstants.CALLBACK_MESSAGE:
    [javac] ^
    [javac] JalviewJmolBinding.java:1004: cannot find symbol
    [javac] symbol : variable CALLBACK_PICK
    [javac] location: class org.jmol.viewer.JmolConstants
    [javac] case JmolConstants.CALLBACK_PICK:
    [javac] ^
    [javac] JalviewJmolBinding.java:1005: cannot find symbol
    [javac] symbol : variable CALLBACK_SCRIPT
    [javac] location: class org.jmol.viewer.JmolConstants
    [javac] case JmolConstants.CALLBACK_SCRIPT:
    [javac] ^
    [javac] JalviewJmolBinding.java:1006: cannot find symbol
    [javac] symbol : variable CALLBACK_HOVER
    [javac] location: class org.jmol.viewer.JmolConstants
    [javac] case JmolConstants.CALLBACK_HOVER:
    [javac] ^
    [javac] JalviewJmolBinding.java:1007: cannot find symbol
    [javac] symbol : variable CALLBACK_ERROR
    [javac] location: class org.jmol.viewer.JmolConstants
    [javac] case JmolConstants.CALLBACK_ERROR:
    [javac] ^
    [javac] JalviewJmolBinding.java:1009: cannot find symbol
    [javac] symbol : variable CALLBACK_RESIZE
    [javac] location: class org.jmol.viewer.JmolConstants
    [javac] case JmolConstants.CALLBACK_RESIZE:
    [javac] ^
    [javac] JalviewJmolBinding.java:1010: cannot find symbol
    [javac] symbol : variable CALLBACK_SYNC
    [javac] location: class org.jmol.viewer.JmolConstants
    [javac] case JmolConstants.CALLBACK_SYNC:
    [javac] ^
    [javac] JalviewJmolBinding.java:1011: cannot find symbol
    [javac] symbol : variable CALLBACK_CLICK
    [javac] location: class org.jmol.viewer.JmolConstants
    [javac] case JmolConstants.CALLBACK_CLICK:
    [javac] ^
    [javac] JalviewJmolBinding.java:1012: cannot find symbol
    [javac] symbol : variable CALLBACK_ANIMFRAME
    [javac] location: class org.jmol.viewer.JmolConstants
    [javac] case JmolConstants.CALLBACK_ANIMFRAME:
    [javac] ^
    [javac] JalviewJmolBinding.java:1013: cannot find symbol
    [javac] symbol : variable CALLBACK_MINIMIZATION
    [javac] location: class org.jmol.viewer.JmolConstants
    [javac] case JmolConstants.CALLBACK_MINIMIZATION:
    [javac] ^
    [javac] AppJmolBinding.java:41: jalview.gui.AppJmolBinding is not abstract and does not override abstract method resizeInnerPanel(java.lang.String) in org.jmol.api.JmolStatusListener
    [javac] public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
    [javac] ^
    [javac] AppJmolBinding.java:155: cannot find symbol
    [javac] symbol : method newJmolPopup(org.jmol.api.JmolViewer,boolean,java.lang.String,boolean)
    [javac] location: class org.jmol.popup.JmolPopup
    [javac] jmolpopup = JmolPopup.newJmolPopup(viewer, translateLocale, menuName,
    [javac] ^
    [javac] RestInputParamEditDialog.java:55: warning: non-varargs call of varargs method with inexact argument type for last parameter;
    [javac] cast to java.lang.Object for a varargs call
    [javac] cast to java.lang.Object[] for a non-varargs call and to suppress this warning
    [javac] .newInstance(null));
    [javac] ^
    [javac] RestInputParamEditDialog.java:173: warning: non-varargs call of varargs method with inexact argument type for last parameter;
    [javac] cast to java.lang.Object for a varargs call
    [javac] cast to java.lang.Object[] for a non-varargs call and to suppress this warning
    [javac] jtype = (InputType) (type.getConstructor().newInstance(null));
    [javac] ^
    [javac] RestServiceDescription.java:836: warning: non-varargs call of varargs method with inexact argument type for last parameter;
    [javac] cast to java.lang.Object for a varargs call
    [javac] cast to java.lang.Object[] for a non-varargs call and to suppress this warning
    [javac] jinput = (InputType) (type.getConstructor().newInstance(null));
    [javac] ^
    [javac] ASequenceFetcher.java:239: warning: non-varargs call of varargs method with inexact argument type for last parameter;
    [javac] cast to java.lang.Class for a varargs call
    [javac] cast to java.lang.Class[] for a non-varargs call and to suppress this warning
    [javac] Object proxyObj = dbSourceProxy.getConstructor(null)
    [javac] ^
    [javac] ASequenceFetcher.java:240: warning: non-varargs call of varargs method with inexact argument type for last parameter;
    [javac] cast to java.lang.Object for a varargs call
    [javac] cast to java.lang.Object[] for a non-varargs call and to suppress this warning
    [javac] .newInstance(null);
    [javac] ^
    [javac] AppletJmolBinding.java:34: jalview.appletgui.AppletJmolBinding is not abstract and does not override abstract method resizeInnerPanel(java.lang.String) in org.jmol.api.JmolStatusListener
    [javac] class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
    [javac] ^
    [javac] AppletJmolBinding.java:122: cannot find symbol
    [javac] symbol : method newJmolPopup(org.jmol.api.JmolViewer,boolean,java.lang.String,boolean)
    [javac] location: class org.jmol.popup.JmolPopup
    [javac] jmolpopup = JmolPopup.newJmolPopup(viewer, translateLocale, menuName,
    [javac] ^
    [javac] AppletJmolBinding.java:153: cannot find symbol
    [javac] symbol : class AppletConsole
    [javac] location: class jalview.appletgui.AppletJmolBinding
    [javac] return new AppletConsole(viewer2, consolePanel);
    [javac] ^
    [javac] ExtJmol.java:42: jalview.appletgui.ExtJmol is not abstract and does not override abstract method resizeInnerPanel(java.lang.String) in org.jmol.api.JmolStatusListener
    [javac] public class ExtJmol extends JalviewJmolBinding
    [javac] ^
    [javac] Note: Some input files use or override a deprecated API.
    [javac] Note: Recompile with -Xlint:deprecation for details.
    [javac] Note: Some input files use unchecked or unsafe operations.
    [javac] Note: Recompile with -Xlint:unchecked for details.
    [javac] 31 errors
    [javac] 11 warnings

BUILD FAILED
/tmp/buildd/jalview-2.7.dfsg/build.xml:202: Compile failed; see the compiler error output for details.