Source: jalview
Version: 2.7.dfsg-5
Severity: serious
Justification: fails to build from source
User: reproducible-bui...@lists.alioth.debian.org
Usertags: ftbfs
X-Debbugs-Cc: reproducible-b...@lists.alioth.debian.org

Dear Maintainer,

jalview fails to build from source in unstable/amd64:

  […]

      [javac] «BUILDDIR»/src/jalview/ext/jmol/JalviewJmolBinding.java:952: 
error: cannot find symbol
      [javac]   public void notifyCallback(EnumCallback type, Object[] data)
      [javac]                              ^
      [javac]   symbol:   class EnumCallback
      [javac]   location: class JalviewJmolBinding
      [javac] «BUILDDIR»/src/jalview/ext/jmol/JalviewJmolBinding.java:1006: 
error: cannot find symbol
      [javac]   public boolean notifyEnabled(EnumCallback callbackPick)
      [javac]                                ^
      [javac]   symbol:   class EnumCallback
      [javac]   location: class JalviewJmolBinding
      [javac] «BUILDDIR»/src/jalview/ws/EnfinEnvision2OneWay.java:67: error: 
package com.lowagie.text.html does not exist
      [javac] import com.lowagie.text.html.HtmlEncoder;
      [javac]                             ^
      [javac] «BUILDDIR»/src/jalview/ws/rest/params/SeqVector.java:37: error: 
cannot find symbol
      [javac] import org.jmol.util.ArrayUtil;
      [javac]                     ^
      [javac]   symbol:   class ArrayUtil
      [javac]   location: package org.jmol.util
      [javac] «BUILDDIR»/src/jalview/appletgui/AppletJmol.java:32: error: 
cannot find symbol
      [javac] import org.jmol.viewer.JmolConstants;
      [javac]                       ^
      [javac]   symbol:   class JmolConstants
      [javac]   location: package org.jmol.viewer
      [javac] «BUILDDIR»/src/jalview/appletgui/AppletJmolBinding.java:30: 
error: cannot find symbol
      [javac] import org.jmol.popup.JmolPopup;
      [javac]                      ^
      [javac]   symbol:   class JmolPopup
      [javac]   location: package org.jmol.popup
      [javac] «BUILDDIR»/src/jalview/bin/Jalview.java:756: warning: non-varargs 
call of varargs method with inexact argument type for last parameter;
      [javac]         gbcons = gbindingc.getConstructor(null);
      [javac]                                           ^
      [javac]   cast to Class for a varargs call
      [javac]   cast to Class[] for a non-varargs call and to suppress this 
warning
      [javac] «BUILDDIR»/src/jalview/bin/Jalview.java:757: warning: non-varargs 
call of varargs method with inexact argument type for last parameter;
      [javac]         gbinding = gbcons.newInstance(null);
      [javac]                                       ^
      [javac]   cast to Object for a varargs call
      [javac]   cast to Object[] for a non-varargs call and to suppress this 
warning
      [javac] «BUILDDIR»/src/jalview/gui/Desktop.java:2177: warning: 
non-varargs call of varargs method with inexact argument type for last 
parameter;
      [javac]       Constructor gccons = gcClass.getConstructor(null);
      [javac]                                                   ^
      [javac]   cast to Class for a varargs call
      [javac]   cast to Class[] for a non-varargs call and to suppress this 
warning
      [javac] «BUILDDIR»/src/jalview/gui/Desktop.java:2181: warning: 
non-varargs call of varargs method with inexact argument type for last 
parameter;
      [javac]       java.lang.reflect.Method run = gcClass.getMethod("run", 
null);
      [javac]                                                               ^
      [javac]   cast to Class for a varargs call
      [javac]   cast to Class[] for a non-varargs call and to suppress this 
warning
      [javac] «BUILDDIR»/src/jalview/gui/Desktop.java:2182: warning: 
non-varargs call of varargs method with inexact argument type for last 
parameter;
      [javac]       Object gc = gccons.newInstance(null);
      [javac]                                      ^
      [javac]   cast to Object for a varargs call
      [javac]   cast to Object[] for a non-varargs call and to suppress this 
warning
      [javac] «BUILDDIR»/src/jalview/gui/Desktop.java:2185: warning: 
non-varargs call of varargs method with inexact argument type for last 
parameter;
      [javac]       run.invoke(gc, null);
      [javac]                      ^
      [javac]   cast to Object for a varargs call
      [javac]   cast to Object[] for a non-varargs call and to suppress this 
warning
      [javac] «BUILDDIR»/src/jalview/ext/jmol/JalviewJmolBinding.java:1556: 
error: resizeInnerPanel(String) in JalviewJmolBinding cannot implement 
resizeInnerPanel(String) in JmolStatusListener
      [javac]   public void resizeInnerPanel(String data)
      [javac]               ^
      [javac]   return type void is not compatible with int[]
      [javac] «BUILDDIR»/src/jalview/ext/jmol/JalviewJmolBinding.java:239: 
error: cannot find symbol
      [javac]     viewer.setModeMouse(org.jmol.viewer.JmolConstants.MOUSE_NONE);
      [javac]                                        ^
      [javac]   symbol:   class JmolConstants
      [javac]   location: package org.jmol.viewer
      [javac] «BUILDDIR»/src/jalview/ext/jmol/JalviewJmolBinding.java:636: 
error: cannot find symbol
      [javac]     return new Color(viewer.getAtomArgb(atomIndex));
      [javac]                            ^
      [javac]   symbol:   method getAtomArgb(int)
      [javac]   location: variable viewer of type JmolViewer
      [javac] «BUILDDIR»/src/jalview/ext/jmol/JalviewJmolBinding.java:690: 
error: cannot find symbol
      [javac]       String mset[] = new String[viewer.getModelCount()];
      [javac]                                        ^
      [javac]   symbol:   method getModelCount()
      [javac]   location: variable viewer of type JmolViewer
      [javac] «BUILDDIR»/src/jalview/ext/jmol/JalviewJmolBinding.java:693: 
error: cannot find symbol
      [javac]       mset[0] = viewer.getModelFileName(0);
      [javac]                       ^
      [javac]   symbol:   method getModelFileName(int)
      [javac]   location: variable viewer of type JmolViewer
      [javac] «BUILDDIR»/src/jalview/ext/jmol/JalviewJmolBinding.java:696: 
error: cannot find symbol
      [javac]         mset[j] = viewer.getModelFileName(i);
      [javac]                         ^
      [javac]   symbol:   method getModelFileName(int)
      [javac]   location: variable viewer of type JmolViewer
      [javac] «BUILDDIR»/src/jalview/ext/jmol/JalviewJmolBinding.java:873: 
error: cannot find symbol
      [javac]                 .getModelFileName(new Integer(mdlId).intValue() - 
1);
      [javac]                 ^
      [javac]   symbol:   method getModelFileName(int)
      [javac]   location: variable viewer of type JmolViewer
      [javac] «BUILDDIR»/src/jalview/ext/jmol/JalviewJmolBinding.java:956: 
error: strings in switch are not supported in -source 1.5
      [javac]       switch (type)
      [javac]              ^
      [javac]   (use -source 7 or higher to enable strings in switch)
      [javac] «BUILDDIR»/src/jalview/ext/jmol/JalviewJmolBinding.java:958: 
error: cannot find symbol
      [javac]       case LOADSTRUCT:
      [javac]            ^
      [javac]   symbol:   variable LOADSTRUCT
      [javac]   location: class JalviewJmolBinding
      [javac] «BUILDDIR»/src/jalview/ext/jmol/JalviewJmolBinding.java:964: 
error: cannot find symbol
      [javac]       case PICK:
      [javac]            ^
      [javac]   symbol:   variable PICK
      [javac]   location: class JalviewJmolBinding
      [javac] «BUILDDIR»/src/jalview/ext/jmol/JalviewJmolBinding.java:968: 
error: cannot find symbol
      [javac]       case HOVER:
      [javac]            ^
      [javac]   symbol:   variable HOVER
      [javac]   location: class JalviewJmolBinding
      [javac] «BUILDDIR»/src/jalview/ext/jmol/JalviewJmolBinding.java:972: 
error: cannot find symbol
      [javac]       case SCRIPT:
      [javac]            ^
      [javac]   symbol:   variable SCRIPT
      [javac]   location: class JalviewJmolBinding
      [javac] «BUILDDIR»/src/jalview/ext/jmol/JalviewJmolBinding.java:976: 
error: cannot find symbol
      [javac]       case ECHO:
      [javac]            ^
      [javac]   symbol:   variable ECHO
      [javac]   location: class JalviewJmolBinding
      [javac] «BUILDDIR»/src/jalview/ext/jmol/JalviewJmolBinding.java:979: 
error: cannot find symbol
      [javac]       case MESSAGE:
      [javac]            ^
      [javac]   symbol:   variable MESSAGE
      [javac]   location: class JalviewJmolBinding
      [javac] «BUILDDIR»/src/jalview/ext/jmol/JalviewJmolBinding.java:983: 
error: cannot find symbol
      [javac]       case ERROR:
      [javac]            ^
      [javac]   symbol:   variable ERROR
      [javac]   location: class JalviewJmolBinding
      [javac] «BUILDDIR»/src/jalview/ext/jmol/JalviewJmolBinding.java:986: 
error: cannot find symbol
      [javac]       case SYNC:
      [javac]            ^
      [javac]   symbol:   variable SYNC
      [javac]   location: class JalviewJmolBinding
      [javac] «BUILDDIR»/src/jalview/ext/jmol/JalviewJmolBinding.java:987: 
error: cannot find symbol
      [javac]       case RESIZE:
      [javac]            ^
      [javac]   symbol:   variable RESIZE
      [javac]   location: class JalviewJmolBinding
      [javac] «BUILDDIR»/src/jalview/ext/jmol/JalviewJmolBinding.java:990: 
error: cannot find symbol
      [javac]       case MEASURE:
      [javac]            ^
      [javac]   symbol:   variable MEASURE
      [javac]   location: class JalviewJmolBinding
      [javac] «BUILDDIR»/src/jalview/ext/jmol/JalviewJmolBinding.java:992: 
error: cannot find symbol
      [javac]       case CLICK:
      [javac]            ^
      [javac]   symbol:   variable CLICK
      [javac]   location: class JalviewJmolBinding
      [javac] «BUILDDIR»/src/jalview/ext/jmol/JalviewJmolBinding.java:1008: 
error: strings in switch are not supported in -source 1.5
      [javac]     switch (callbackPick)
      [javac]            ^
      [javac]   (use -source 7 or higher to enable strings in switch)
      [javac] «BUILDDIR»/src/jalview/ext/jmol/JalviewJmolBinding.java:1010: 
error: cannot find symbol
      [javac]     case ECHO:
      [javac]          ^
      [javac]   symbol:   variable ECHO
      [javac]   location: class JalviewJmolBinding
      [javac] «BUILDDIR»/src/jalview/ext/jmol/JalviewJmolBinding.java:1011: 
error: cannot find symbol
      [javac]     case LOADSTRUCT:
      [javac]          ^
      [javac]   symbol:   variable LOADSTRUCT
      [javac]   location: class JalviewJmolBinding
      [javac] «BUILDDIR»/src/jalview/ext/jmol/JalviewJmolBinding.java:1012: 
error: cannot find symbol
      [javac]     case MEASURE:
      [javac]          ^
      [javac]   symbol:   variable MEASURE
      [javac]   location: class JalviewJmolBinding
      [javac] «BUILDDIR»/src/jalview/ext/jmol/JalviewJmolBinding.java:1013: 
error: cannot find symbol
      [javac]     case MESSAGE:
      [javac]          ^
      [javac]   symbol:   variable MESSAGE
      [javac]   location: class JalviewJmolBinding
      [javac] «BUILDDIR»/src/jalview/ext/jmol/JalviewJmolBinding.java:1014: 
error: cannot find symbol
      [javac]     case PICK:
      [javac]          ^
      [javac]   symbol:   variable PICK
      [javac]   location: class JalviewJmolBinding
      [javac] «BUILDDIR»/src/jalview/ext/jmol/JalviewJmolBinding.java:1015: 
error: cannot find symbol
      [javac]     case SCRIPT:
      [javac]          ^
      [javac]   symbol:   variable SCRIPT
      [javac]   location: class JalviewJmolBinding
      [javac] «BUILDDIR»/src/jalview/ext/jmol/JalviewJmolBinding.java:1016: 
error: cannot find symbol
      [javac]     case HOVER:
      [javac]          ^
      [javac]   symbol:   variable HOVER
      [javac]   location: class JalviewJmolBinding
      [javac] «BUILDDIR»/src/jalview/ext/jmol/JalviewJmolBinding.java:1017: 
error: cannot find symbol
      [javac]     case ERROR:
      [javac]          ^
      [javac]   symbol:   variable ERROR
      [javac]   location: class JalviewJmolBinding
      [javac] «BUILDDIR»/src/jalview/ext/jmol/JalviewJmolBinding.java:1019: 
error: cannot find symbol
      [javac]     case RESIZE:
      [javac]          ^
      [javac]   symbol:   variable RESIZE
      [javac]   location: class JalviewJmolBinding
      [javac] «BUILDDIR»/src/jalview/ext/jmol/JalviewJmolBinding.java:1020: 
error: cannot find symbol
      [javac]     case SYNC:
      [javac]          ^
      [javac]   symbol:   variable SYNC
      [javac]   location: class JalviewJmolBinding
      [javac] «BUILDDIR»/src/jalview/ext/jmol/JalviewJmolBinding.java:1021: 
error: cannot find symbol
      [javac]     case CLICK:
      [javac]          ^
      [javac]   symbol:   variable CLICK
      [javac]   location: class JalviewJmolBinding
      [javac] «BUILDDIR»/src/jalview/ext/jmol/JalviewJmolBinding.java:1022: 
error: cannot find symbol
      [javac]     case ANIMFRAME:
      [javac]          ^
      [javac]   symbol:   variable ANIMFRAME
      [javac]   location: class JalviewJmolBinding
      [javac] «BUILDDIR»/src/jalview/ext/jmol/JalviewJmolBinding.java:1023: 
error: cannot find symbol
      [javac]     case MINIMIZATION:
      [javac]          ^
      [javac]   symbol:   variable MINIMIZATION
      [javac]   location: class JalviewJmolBinding
      [javac] «BUILDDIR»/src/jalview/ext/jmol/JalviewJmolBinding.java:1555: 
error: method does not override or implement a method from a supertype
      [javac]   @Override
      [javac]   ^
      [javac] «BUILDDIR»/src/jalview/gui/AppJmolBinding.java:41: error: 
AppJmolBinding is not abstract and does not override abstract method 
getJSpecViewProperty(String) in JmolStatusListener
      [javac] public class AppJmolBinding extends 
jalview.ext.jmol.JalviewJmolBinding
      [javac]        ^
      [javac] «BUILDDIR»/src/jalview/gui/AppJmolBinding.java:155: error: cannot 
find symbol
      [javac]     jmolpopup = new JmolPopup();
      [javac]                     ^
      [javac]   symbol:   class JmolPopup
      [javac]   location: class AppJmolBinding
      [javac] «BUILDDIR»/src/jalview/gui/AppJmolBinding.java:200: error: cannot 
find symbol
      [javac]     return new AppConsole(viewer, consolePanel, buttonsToShow);
      [javac]                ^
      [javac]   symbol:   class AppConsole
      [javac]   location: class AppJmolBinding
      [javac] «BUILDDIR»/src/jalview/gui/RestInputParamEditDialog.java:55: 
warning: non-varargs call of varargs method with inexact argument type for last 
parameter;
      [javac]               .newInstance(null));
      [javac]                            ^
      [javac]   cast to Object for a varargs call
      [javac]   cast to Object[] for a non-varargs call and to suppress this 
warning
      [javac] «BUILDDIR»/src/jalview/gui/RestInputParamEditDialog.java:173: 
warning: non-varargs call of varargs method with inexact argument type for last 
parameter;
      [javac]         jtype = (InputType) 
(type.getConstructor().newInstance(null));
      [javac]                                                                ^
      [javac]   cast to Object for a varargs call
      [javac]   cast to Object[] for a non-varargs call and to suppress this 
warning
      [javac] «BUILDDIR»/src/jalview/ws/rest/RestServiceDescription.java:836: 
warning: non-varargs call of varargs method with inexact argument type for last 
parameter;
      [javac]         jinput = (InputType) 
(type.getConstructor().newInstance(null));
      [javac]                                                                 ^
      [javac]   cast to Object for a varargs call
      [javac]   cast to Object[] for a non-varargs call and to suppress this 
warning
      [javac] «BUILDDIR»/src/jalview/ws/seqfetcher/ASequenceFetcher.java:239: 
warning: non-varargs call of varargs method with inexact argument type for last 
parameter;
      [javac]       Object proxyObj = dbSourceProxy.getConstructor(null)
      [javac]                                                      ^
      [javac]   cast to Class for a varargs call
      [javac]   cast to Class[] for a non-varargs call and to suppress this 
warning
      [javac] «BUILDDIR»/src/jalview/ws/seqfetcher/ASequenceFetcher.java:240: 
warning: non-varargs call of varargs method with inexact argument type for last 
parameter;
      [javac]               .newInstance(null);
      [javac]                            ^
      [javac]   cast to Object for a varargs call
      [javac]   cast to Object[] for a non-varargs call and to suppress this 
warning
      [javac] «BUILDDIR»/src/jalview/ws/EnfinEnvision2OneWay.java:327: error: 
cannot find symbol
      [javac]       descr = HtmlEncoder.encode(descr);
      [javac]               ^
      [javac]   symbol:   variable HtmlEncoder
      [javac]   location: class EnfinEnvision2OneWay
      [javac] «BUILDDIR»/src/jalview/appletgui/AppletJmolBinding.java:32: 
error: AppletJmolBinding is not abstract and does not override abstract method 
getJSpecViewProperty(String) in JmolStatusListener
      [javac] class AppletJmolBinding extends 
jalview.ext.jmol.JalviewJmolBinding
      [javac] ^
      [javac] «BUILDDIR»/src/jalview/appletgui/AppletJmolBinding.java:182: 
error: resizeInnerPanel(String) in AppletJmolBinding cannot implement 
resizeInnerPanel(String) in JmolStatusListener
      [javac]   public void resizeInnerPanel(String data)
      [javac]               ^
      [javac]   return type void is not compatible with int[]
      [javac] «BUILDDIR»/src/jalview/appletgui/AppletJmolBinding.java:120: 
error: cannot find symbol
      [javac]     jmolpopup = new JmolPopup();
      [javac]                     ^
      [javac]   symbol:   class JmolPopup
      [javac]   location: class AppletJmolBinding
      [javac] «BUILDDIR»/src/jalview/appletgui/AppletJmolBinding.java:153: 
error: cannot find symbol
      [javac]     JmolAppConsoleInterface appc = new 
org.jmol.console.AppletConsole().getAppConsole(viewer2);
      [javac]                                                                   
     ^
      [javac]   symbol:   method getAppConsole(JmolViewer)
      [javac]   location: class AppletConsole
      [javac] «BUILDDIR»/src/jalview/appletgui/ExtJmol.java:42: error: ExtJmol 
is not abstract and does not override abstract method 
getJSpecViewProperty(String) in 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] 54 errors
      [javac] 20 warnings
  
  BUILD FAILED
  «BUILDDIR»/build.xml:202: Compile failed; see the compiler error output for 
details.
  
  Total time: 9 seconds
  /usr/share/cdbs/1/class/ant.mk:39: recipe for target 'debian/stamp-ant-build' 
failed
  make: *** [debian/stamp-ant-build] Error 1
  dpkg-buildpackage: error: debian/rules build gave error exit status 2

  […]

The full build log is attached.


Regards,

-- 
      ,''`.
     : :'  :     Chris Lamb
     `. `'`      la...@debian.org / chris-lamb.co.uk
       `-

Attachment: jalview.2.7.dfsg-5.unstable.amd64.log.txt.gz
Description: Binary data

__
This is the maintainer address of Debian's Java team
<http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-java-maintainers>. 
Please use
debian-j...@lists.debian.org for discussions and questions.

Reply via email to