Source: jalview Version: 2.7.dfsg-5 Severity: serious Justification: fails to build from source User: [email protected] Usertags: ftbfs X-Debbugs-Cc: [email protected]
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
`. `'` [email protected] / chris-lamb.co.uk
`-
jalview.2.7.dfsg-5.unstable.amd64.log.txt.gz
Description: Binary data
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