Your message dated Sun, 07 Feb 2021 06:33:21 +0000
with message-id <e1l8ddj-000d15...@fasolo.debian.org>
and subject line Bug#849025: fixed in jalview 2.11.1.3+dfsg2-1
has caused the Debian Bug report #849025,
regarding jalview: FTBFS: error: cannot find symbol EnumCallback
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)
--
849025: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=849025
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
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
`-
jalview.2.7.dfsg-5.unstable.amd64.log.txt.gz
Description: Binary data
--- End Message ---
--- Begin Message ---
Source: jalview
Source-Version: 2.11.1.3+dfsg2-1
Done: Pierre Gruet <pgtdeb...@free.fr>
We believe that the bug you reported is fixed in the latest version of
jalview, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 849...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Pierre Gruet <pgtdeb...@free.fr> (supplier of updated jalview package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Sat, 06 Feb 2021 23:04:36 +0100
Source: jalview
Architecture: source
Version: 2.11.1.3+dfsg2-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Java Maintainers
<pkg-java-maintain...@lists.alioth.debian.org>
Changed-By: Pierre Gruet <pgtdeb...@free.fr>
Closes: 849025 897294
Changes:
jalview (2.11.1.3+dfsg2-1) unstable; urgency=medium
.
[ Pierre Gruet ]
* New upstream version (Closes: #849025)
* New uploader (Closes: #897294)
* Using version 4 in d/watch to remove files
* Using secure URI in d/watch
* Switching from cdbs to dh
* Depending on debhelper-compat 13
* Making the build with Maven instead of upstream's gradle
* Removing call to classgraph, not needed for a Debian run
* Updating build-dependencies list and d/jalview.classpath
* Modifying the jar launcher by setting properly the jar manifest
* Updating Vcs-* and Homepage fields in d/control
* Refreshing d/copyright
* Bump Standards version to 4.5.1:
- Providing a FreeDesktop entry instead of former menu entry
- Rules-Requires-Root: no
- Using the https form of the copyright-format URL
* Updating manpage
* Deactivating Google Analytics, using a non-packaged and improperly
licensed software
* Adding Mime types in d/jalview.desktop and d/jalview-mime.xml
* Adding autopkgtests
* Integrating the patch of upstream to control the way the web services are
launched
.
[ Steffen Moeller ]
* Reintroduced debian/upstream/edam file
* Created debian/upstream/metadata
- references to papers
- references to registries
* Added prior forgotten PMID in metadata
* d/u/metadata: syntax fixed(?) and URLs added
* Added ref to conda, RRID->SciCrunch
.
[ Andreas Tille ]
* d/rules: enforce LC_ALL=C.UTF-8 to cope with UTF-8 characters
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Files:
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--- End Message ---
__
This is the maintainer address of Debian's Java team
<https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/pkg-java-maintainers>.
Please use
debian-j...@lists.debian.org for discussions and questions.
