This is an automated email from the git hooks/post-receive script. misterc-guest pushed a commit to branch master in repository jalview.
commit b42f7b51dac884f1fdcb06fe07679bd4e430e863 Author: Michael R. Crusoe <[email protected]> Date: Sun Feb 7 12:26:39 2016 -0800 v2.9, refresh patches, add testng --- debian/changelog | 7 +- debian/control | 4 +- debian/patches/drop-lib | 100 ++++++++++ debian/patches/encoding-fix | 11 ++ debian/patches/mutilate-build-system.diff | 58 +++--- debian/patches/newer-jmol-api.diff | 304 +++--------------------------- debian/patches/newer-mime4j-api.diff | 8 +- debian/patches/series | 4 +- debian/patches/testng | 11 ++ 9 files changed, 183 insertions(+), 324 deletions(-) diff --git a/debian/changelog b/debian/changelog index 4181047..80917a2 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,11 +1,14 @@ -jalview (2.7.dfsg-5) UNRELEASED; urgency=low +jalview (2.9+dfsg-1) UNRELEASED; urgency=low [ Steffen Moeller and Hervé Ménager ] * Updated Standards-Version to 3.6 * Introduced EDAM annotation to debian/upstream/edam - -- Steffen Moeller <[email protected]> Fri, 05 Feb 2016 13:47:26 +0100 + [ Michael R. Crusoe ] + * Update to version 2.9 + + -- Michael R. Crusoe <[email protected]> Sun, 07 Feb 2016 12:26:10 -0800 jalview (2.7.dfsg-4) unstable; urgency=low diff --git a/debian/control b/debian/control index 8e70e37..066cc27 100644 --- a/debian/control +++ b/debian/control @@ -26,7 +26,9 @@ Build-Depends: ant, liblog4j1.2-java, libmiglayout-java, libvamsas-client-java, - libwsdl4j-java + libwsdl4j-java, + testng, + varna Standards-Version: 3.9.6 Vcs-Git: git://anonscm.debian.org/git/pkg-java/jalview.git Vcs-Browser: http://anonscm.debian.org/gitweb/?p=pkg-java/jalview.git diff --git a/debian/patches/drop-lib b/debian/patches/drop-lib new file mode 100644 index 0000000..f7f3b28 --- /dev/null +++ b/debian/patches/drop-lib @@ -0,0 +1,100 @@ +--- jalview.orig/build.xml ++++ jalview/build.xml +@@ -102,7 +102,7 @@ + <property name="applet.caller-codebase" value="${applet.codebase}" /> + + <!-- build directory configuration --> +- <property name="libDir" value="lib" /> ++ <property name="libDir" value="/usr/share/java" /> + <property name="resourceDir" value="resources" /> + <property name="helpDir" value="help" /> + <property name="docDir" value="doc" /> +@@ -143,7 +143,7 @@ + <fileset dir="${java.home}/lib"> + <include name="plugin.jar"/> + </fileset> +- <fileset dir="appletlib"> ++ <fileset dir="/usr/share/java"> + <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages + --> + <include name="${jmolJar}" /> +@@ -168,7 +168,7 @@ + <fileset dir="${java.home}/lib"> + <include name="plugin.jar"/> + </fileset> +- <pathelement location="appletlib/${jmolJar}" /> ++ <pathelement location="/usr/share/java/${jmolJar}" /> + <pathelement location="lib/${varnaJar}" /> + <pathelement location="lib/${jsoup}" /> + <pathelement location="lib/${jsonSimple}" /> +@@ -246,6 +246,7 @@ + <target name="build" depends="prepare"> + <!-- not efficient yet. --> + <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath"> ++ <compilerarg line="-encoding utf-8"/> + <exclude name="jalview/*applet*" /> + <exclude name="jalview/appletgui/**" /> + <exclude name="com/stevesoft/**" /> +@@ -273,10 +274,12 @@ + + <target name="buildTests" depends="prepareTests"> + <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${testOutputDir}" +- debug="${javac.debug}" classpathref="build.classpath" includeantruntime="false" > ++ debug="${javac.debug}" classpathref="build.classpath" includeantruntime="false" > ++ <compilerarg line="-encoding utf-8"/> + </javac> + <javac source="${javac.source}" target="${javac.target}" srcdir="${testDir}" destdir="${testOutputDir}" + debug="${javac.debug}" classpathref="build.classpath" includeantruntime="false" > ++ <compilerarg line="-encoding utf-8"/> + </javac> + </target> + +@@ -554,6 +557,7 @@ + <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" + classpathref="jalviewlite.deps" includes="jalview/appletgui/**" + excludes="ext/**,gui/**,jbgui/**,MCview/**,org/**,vamsas/**,jalview/ext/rbvi/**,jalview/ext/paradise/**" /> ++ <compilerarg line="-encoding utf-8"/> + </target> + + <target name="packageApplet" depends="compileApplet, buildPropertiesFile"> +@@ -591,9 +595,9 @@ + + <path id="obfuscateDeps.path"> + <pathelement location="${applet.jre.tools}" /> +- <pathelement location="appletlib/${jmolJar}" /> +- <pathelement location="appletlib/${jsonSimple}" /> +- <pathelement location="appletlib/${javaJson}" /> ++ <pathelement location="/usr/share/java/${jmolJar}" /> ++ <pathelement location="/usr/share/java/${jsonSimple}" /> ++ <pathelement location="/usr/share/java/${javaJson}" /> + </path> + <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" /> + +@@ -665,7 +669,7 @@ + <include name="${libDir}/**/*" /> + <include name="${resourceDir}/**/*" /> + <include name="${helpDir}/**/*" /> +- <include name="appletlib/${jmolJar}" /> ++ <include name="/usr/share/java/${jmolJar}" /> + <exclude name="**/*locales" /> + <exclude name="*locales/**" /> + <exclude name="utils/InstallAnywhere/**Build.iap_xml" /> +@@ -690,9 +694,6 @@ + <fileset dir="."> + <include name="${jalviewLiteJar}" /> + </fileset> +- <fileset dir="appletlib"> +- <include name="**/*"/> +- </fileset> + </copy> + <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}"/> + <jar update="true" index="true" jarfile="${packageDir}/examples/${javaJson}"/> +@@ -833,7 +834,7 @@ + </fileset> + </signjar> + <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly --> +- <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" /> ++ <copy file="/usr/share/java/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" /> + <!-- finally, replace any launchApp servlet tags with a version specification --> + <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}"";> + <replacetoken><![CDATA[http://www.jalview.org/services/launchApp";]]></replacetoken> diff --git a/debian/patches/encoding-fix b/debian/patches/encoding-fix new file mode 100644 index 0000000..6bfdb7e --- /dev/null +++ b/debian/patches/encoding-fix @@ -0,0 +1,11 @@ +--- jalview.orig/src/jalview/json/binding/biojson/v1/SequencePojo.java ++++ jalview/src/jalview/json/binding/biojson/v1/SequencePojo.java +@@ -28,7 +28,7 @@ + required = true, + minLength = 3, + maxLength = 2147483647, +- description = "Sequence residue characters. An aligned sequence may contain <br>one of the following gap characters “.�?, “-�? or “ �?") ++ description = "Sequence residue characters. An aligned sequence may contain <br>one of the following gap characters “.”, “-” or “ ”") + private String seq; + + @Attributes(required = true, description = "Sequence name") diff --git a/debian/patches/mutilate-build-system.diff b/debian/patches/mutilate-build-system.diff index 742adc5..0e54c8c 100644 --- a/debian/patches/mutilate-build-system.diff +++ b/debian/patches/mutilate-build-system.diff @@ -1,38 +1,22 @@ -Index: jalview-2.7.dfsg~almost/build.xml -=================================================================== ---- jalview-2.7.dfsg~almost.orig/build.xml 2011-09-27 16:50:20.000000000 +0200 -+++ jalview-2.7.dfsg~almost/build.xml 2011-10-16 00:25:56.823058139 +0200 -@@ -18,13 +18,6 @@ - --> - <project name="jalviewX" default="usage" basedir="."> - <!-- we use jalopy to format our sources --> -- <taskdef name="jalopy" classname="de.hunsicker.jalopy.plugin.ant.AntPlugin"> -- <classpath> -- <fileset dir="utils/jalopy/lib"> -- <include name="*.jar" /> -- </fileset> -- </classpath> -- </taskdef> +--- jalview.orig/build.xml ++++ jalview/build.xml +@@ -136,10 +136,6 @@ + <property name="wsdl.ClientNS" value="ext.vamsas" /> + <!-- the class path for building the application --> + <path id="build.classpath"> +- <fileset dir="utils"> +- <include name="*.jar" /> +- <include name="**/*.jar" /> +- </fileset> + <fileset dir="${libDir}"> + <include name="*.jar" /> + <include name="**/*.jar" /> +@@ -503,7 +499,7 @@ + </axis-wsdl2java> + </target> - <target name="help" depends="usage" /> - <target name="usage"> -@@ -114,10 +107,6 @@ - <property name="wsdl.ClientNS" value="ext.vamsas" /> - <!-- the class path for building the application --> - <path id="build.classpath"> -- <fileset dir="utils"> -- <include name="*.jar" /> -- <include name="**/*.jar" /> -- </fileset> - <fileset dir="${libDir}"> - <include name="*.jar" /> - <include name="**/*.jar" /> -@@ -407,7 +396,7 @@ - </axis-wsdl2java> - </target> - -- <target name="makedist" depends="build, buildPropertiesFile, buildindices"> -+ <target name="makedist" depends="build, buildindices"> - <!-- make the package jar if not already existing --> - <mkdir dir="${packageDir}" /> - <!-- clean dir if it already existed --> +-<target name="makedist" depends="build, buildPropertiesFile, buildindices"> ++<target name="makedist" depends="build, buildindices"> + <!-- make the package jar if not already existing --> + <mkdir dir="${packageDir}" /> + <!-- clean dir if it already existed --> diff --git a/debian/patches/newer-jmol-api.diff b/debian/patches/newer-jmol-api.diff index b96436a..8a26183 100644 --- a/debian/patches/newer-jmol-api.diff +++ b/debian/patches/newer-jmol-api.diff @@ -3,299 +3,45 @@ Description: fix build with newer Jmol API Patch from 12808bb..a60375a of http://source.jalview.org/git/jalview.git -Index: jalview-2.7.dfsg/build.xml -=================================================================== ---- jalview-2.7.dfsg.orig/build.xml 2011-11-07 20:46:31.000000000 +0100 -+++ jalview-2.7.dfsg/build.xml 2011-11-07 20:46:54.096166723 +0100 -@@ -92,7 +92,7 @@ - <property name="packageDir" value="dist" /> - <property name="outputJar" value="jalview.jar" /> - <!-- Jalview Applet JMol Jar Dependency --> -- <property name="jmolJar" value="JmolApplet-12.1.13.jar" /> -+ <property name="jmolJar" value="JmolApplet-12.2.4.jar" /> - <property name="jalviewLiteJar" value="jalviewApplet.jar" /> - <!-- switch to indicate if we should obfuscate jalviewLite --> - <!--<property name="donotobfuscate" value="true"/> --> -Index: jalview-2.7.dfsg/nbproject/project.properties -=================================================================== ---- jalview-2.7.dfsg.orig/nbproject/project.properties 2011-09-27 16:50:21.000000000 +0200 -+++ jalview-2.7.dfsg/nbproject/project.properties 2011-11-07 20:46:54.096166723 +0100 +--- jalview.orig/build.xml ++++ jalview/build.xml +@@ -112,7 +112,7 @@ + <property name="packageDir" value="dist" /> + <property name="outputJar" value="jalview.jar" /> + <!-- Jalview Applet JMol Jar Dependency --> +- <property name="jmolJar" value="JmolApplet-14.2.14_2015.06.11.jar" /> ++ <property name="jmolJar" value="JmolApplet.jar" /> + <property name="varnaJar" value="VARNAv3-93.jar" /> + <property name="jsoup" value="jsoup-1.8.1.jar" /> + <property name="jsonSimple" value="json_simple-1.1.jar" /> +--- jalview.orig/nbproject/project.properties ++++ jalview/nbproject/project.properties @@ -59,8 +59,8 @@ file.reference.jaxrpc.jar=lib/jaxrpc.jar file.reference.JGoogleAnalytics_0.3.jar=lib/JGoogleAnalytics_0.3.jar file.reference.jhall.jar=lib/jhall.jar --file.reference.Jmol-12.1.13.jar=lib/Jmol-12.1.13.jar --file.reference.JmolApplet-12.1.13.jar=appletlib/JmolApplet-12.1.13.jar -+file.reference.Jmol-12.2.4.jar=lib/Jmol-12.2.4.jar -+file.reference.JmolApplet-12.2.4.jar=appletlib/JmolApplet-12.2.4.jar +-file.reference.Jmol-14.2.14_2015.06.11.jar=lib/Jmol-14.2.14_2015.06.11.jar +-file.reference.JmolApplet-14.2.14_2015.06.11.jar=appletlib/JmolApplet-14.2.14_2015.06.11.jar ++file.reference.Jmol-12.2.32.jar=lib/Jmol-12.2.32.jar ++file.reference.JmolApplet-12.2.32.jar=appletlib/JmolApplet-12.2.32jar file.reference.log4j-1.2.8.jar=lib/log4j-1.2.8.jar file.reference.mail.jar=lib/mail.jar - file.reference.min-jaba-client.jar=lib/min-jaba-client.jar -@@ -91,7 +91,7 @@ + file.reference.min-jaba-client.jar=lib/min-jaba-client-2.0.jar +@@ -92,7 +92,7 @@ ${file.reference.jaxrpc.jar}:\ ${file.reference.JGoogleAnalytics_0.3.jar}:\ ${file.reference.jhall.jar}:\ -- ${file.reference.Jmol-12.1.13.jar}:\ -+ ${file.reference.Jmol-12.2.4.jar}:\ +- ${file.reference.Jmol-14.2.14_2015.06.11.jar}:\ ++ ${file.reference.Jmol-12.2.32.jar}:\ ${file.reference.miglayout-4.0-swing.jar}:\ ${file.reference.log4j-1.2.8.jar}:\ ${file.reference.mail.jar}:\ -@@ -100,7 +100,7 @@ +@@ -101,7 +101,7 @@ ${file.reference.xml-apis.jar}:\ ${file.reference.xercesImpl.jar}:\ ${file.reference.wsdl4j.jar}:\ -- ${file.reference.JmolApplet-12.1.13.jar} -+ ${file.reference.JmolApplet-12.2.4.jar} +- ${file.reference.JmolApplet-14.2.14_2015.06.11.jar} \ ++ ${file.reference.JmolApplet-12.2.32.jar} \ + ${file.reference.varna-3.9-dev.jar} # Space-separated list of extra javac options javac.compilerargs= - javac.deprecation=false -Index: jalview-2.7.dfsg/src/jalview/appletgui/AppletJmolBinding.java -=================================================================== ---- jalview-2.7.dfsg.orig/src/jalview/appletgui/AppletJmolBinding.java 2011-09-27 16:50:21.000000000 +0200 -+++ jalview-2.7.dfsg/src/jalview/appletgui/AppletJmolBinding.java 2011-11-07 20:46:54.096166723 +0100 -@@ -17,18 +17,16 @@ - */ - package jalview.appletgui; - --import java.awt.Container; --import java.util.BitSet; -- - import jalview.api.AlignmentViewPanel; --import jalview.datamodel.AlignmentI; - import jalview.datamodel.PDBEntry; - import jalview.datamodel.SequenceI; - import jalview.structure.StructureSelectionManager; - -+import java.awt.Container; -+import java.util.BitSet; -+ - import org.jmol.api.JmolAppConsoleInterface; - import org.jmol.api.JmolViewer; --import org.jmol.applet.AppletConsole; - import org.jmol.popup.JmolPopup; - - class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding -@@ -119,7 +117,8 @@ - boolean asPopup) - { - -- jmolpopup = JmolPopup.newJmolPopup(viewer, translateLocale, menuName, -+ jmolpopup = new JmolPopup(); -+ jmolpopup.initialize(viewer, translateLocale, menuName, - asPopup); - } - -@@ -150,7 +149,9 @@ - protected JmolAppConsoleInterface createJmolConsole(JmolViewer viewer2, - Container consolePanel, String buttonsToShow) - { -- return new AppletConsole(viewer2, consolePanel); -+ //return new org.jmol.console.AppletConsole(viewer2, consolePanel); -+ JmolAppConsoleInterface appc = new org.jmol.console.AppletConsole().getAppConsole(viewer2); -+ return appc; - } - - @Override -@@ -177,5 +178,10 @@ - public void releaseReferences(Object svl) - { - } -- -+ @Override -+ public void resizeInnerPanel(String data) -+ { -+ // TODO Auto-generated method stub -+ -+ } - } -Index: jalview-2.7.dfsg/src/jalview/ext/jmol/JalviewJmolBinding.java -=================================================================== ---- jalview-2.7.dfsg.orig/src/jalview/ext/jmol/JalviewJmolBinding.java 2011-09-27 16:50:21.000000000 +0200 -+++ jalview-2.7.dfsg/src/jalview/ext/jmol/JalviewJmolBinding.java 2011-11-07 20:46:54.096166723 +0100 -@@ -17,32 +17,40 @@ - */ - package jalview.ext.jmol; - --import java.io.File; --import java.net.URL; --import java.util.*; --import java.applet.Applet; --import java.awt.*; --import java.awt.event.*; -- --import javax.swing.JPanel; -- - import jalview.api.AlignmentViewPanel; - import jalview.api.FeatureRenderer; - import jalview.api.SequenceRenderer; - import jalview.api.SequenceStructureBinding; - import jalview.api.StructureSelectionManagerProvider; --import jalview.datamodel.*; --import jalview.structure.*; --import jalview.io.*; -+import jalview.datamodel.AlignmentI; -+import jalview.datamodel.ColumnSelection; -+import jalview.datamodel.PDBEntry; -+import jalview.datamodel.SequenceI; -+import jalview.io.AppletFormatAdapter; -+import jalview.schemes.ColourSchemeI; -+import jalview.schemes.ResidueProperties; -+import jalview.structure.StructureListener; -+import jalview.structure.StructureMapping; -+import jalview.structure.StructureSelectionManager; -+ -+import java.awt.Color; -+import java.awt.Container; -+import java.awt.event.ComponentEvent; -+import java.awt.event.ComponentListener; -+import java.io.File; -+import java.net.URL; -+import java.util.Enumeration; -+import java.util.Hashtable; -+import java.util.Map; -+import java.util.Vector; - --import org.jmol.api.*; - import org.jmol.adapter.smarter.SmarterJmolAdapter; -- --import org.jmol.popup.*; --import org.jmol.viewer.JmolConstants; --import org.jmol.viewer.Viewer; -- --import jalview.schemes.*; -+import org.jmol.api.JmolAppConsoleInterface; -+import org.jmol.api.JmolSelectionListener; -+import org.jmol.api.JmolStatusListener; -+import org.jmol.api.JmolViewer; -+import org.jmol.constant.EnumCallback; -+import org.jmol.popup.JmolPopup; - - public abstract class JalviewJmolBinding implements StructureListener, - JmolStatusListener, SequenceStructureBinding, -@@ -940,47 +948,48 @@ - - } - -- public void notifyCallback(int type, Object[] data) -+ @Override -+ public void notifyCallback(EnumCallback type, Object[] data) - { - try - { - switch (type) - { -- case JmolConstants.CALLBACK_LOADSTRUCT: -+ case LOADSTRUCT: - notifyFileLoaded((String) data[1], (String) data[2], - (String) data[3], (String) data[4], - ((Integer) data[5]).intValue()); - - break; -- case JmolConstants.CALLBACK_PICK: -+ case PICK: - notifyAtomPicked(((Integer) data[2]).intValue(), (String) data[1], - (String) data[0]); - // also highlight in alignment -- case JmolConstants.CALLBACK_HOVER: -+ case HOVER: - notifyAtomHovered(((Integer) data[2]).intValue(), (String) data[1], - (String) data[0]); - break; -- case JmolConstants.CALLBACK_SCRIPT: -+ case SCRIPT: - notifyScriptTermination((String) data[2], - ((Integer) data[3]).intValue()); - break; -- case JmolConstants.CALLBACK_ECHO: -+ case ECHO: - sendConsoleEcho((String) data[1]); - break; -- case JmolConstants.CALLBACK_MESSAGE: -+ case MESSAGE: - sendConsoleMessage((data == null) ? ((String) null) - : (String) data[1]); - break; -- case JmolConstants.CALLBACK_ERROR: -+ case ERROR: - // System.err.println("Ignoring error callback."); - break; -- case JmolConstants.CALLBACK_SYNC: -- case JmolConstants.CALLBACK_RESIZE: -+ case SYNC: -+ case RESIZE: - refreshGUI(); - break; -- case JmolConstants.CALLBACK_MEASURE: -+ case MEASURE: - -- case JmolConstants.CALLBACK_CLICK: -+ case CLICK: - default: - System.err.println("Unhandled callback " + type + " " - + data[1].toString()); -@@ -993,24 +1002,25 @@ - } - } - -- public boolean notifyEnabled(int callbackPick) -+ @Override -+ public boolean notifyEnabled(EnumCallback callbackPick) - { - switch (callbackPick) - { -- case JmolConstants.CALLBACK_ECHO: -- case JmolConstants.CALLBACK_LOADSTRUCT: -- case JmolConstants.CALLBACK_MEASURE: -- case JmolConstants.CALLBACK_MESSAGE: -- case JmolConstants.CALLBACK_PICK: -- case JmolConstants.CALLBACK_SCRIPT: -- case JmolConstants.CALLBACK_HOVER: -- case JmolConstants.CALLBACK_ERROR: -+ case ECHO: -+ case LOADSTRUCT: -+ case MEASURE: -+ case MESSAGE: -+ case PICK: -+ case SCRIPT: -+ case HOVER: -+ case ERROR: - return true; -- case JmolConstants.CALLBACK_RESIZE: -- case JmolConstants.CALLBACK_SYNC: -- case JmolConstants.CALLBACK_CLICK: -- case JmolConstants.CALLBACK_ANIMFRAME: -- case JmolConstants.CALLBACK_MINIMIZATION: -+ case RESIZE: -+ case SYNC: -+ case CLICK: -+ case ANIMFRAME: -+ case MINIMIZATION: - } - return false; - } -@@ -1542,5 +1552,10 @@ - { - return ssm.printMapping(pdbfile); - } -- -+ @Override -+ public void resizeInnerPanel(String data) -+ { -+ // Jalview doesn't honour resize panel requests -+ -+ } - } -Index: jalview-2.7.dfsg/src/jalview/gui/AppJmolBinding.java -=================================================================== ---- jalview-2.7.dfsg.orig/src/jalview/gui/AppJmolBinding.java 2011-09-27 16:50:21.000000000 +0200 -+++ jalview-2.7.dfsg/src/jalview/gui/AppJmolBinding.java 2011-11-07 20:46:54.096166723 +0100 -@@ -152,7 +152,8 @@ - boolean asPopup) - { - -- jmolpopup = JmolPopup.newJmolPopup(viewer, translateLocale, menuName, -+ jmolpopup = new JmolPopup(); -+ jmolpopup.initialize(viewer, translateLocale, menuName, - asPopup); - } - diff --git a/debian/patches/newer-mime4j-api.diff b/debian/patches/newer-mime4j-api.diff index 9dee41d..3f02e6c 100644 --- a/debian/patches/newer-mime4j-api.diff +++ b/debian/patches/newer-mime4j-api.diff @@ -1,9 +1,9 @@ Description: Patch to use the latest version of Apache Mime4J Author: Emmanuel Bourg <[email protected]> Forwarded: no ---- a/src/jalview/ws/io/mime/JalviewMimeContentHandler.java -+++ b/src/jalview/ws/io/mime/JalviewMimeContentHandler.java -@@ -26,9 +26,9 @@ +--- jalview.orig/src/jalview/ws/io/mime/JalviewMimeContentHandler.java ++++ jalview/src/jalview/ws/io/mime/JalviewMimeContentHandler.java +@@ -29,9 +29,9 @@ import java.util.List; import org.apache.james.mime4j.MimeException; @@ -14,4 +14,4 @@ Forwarded: no +import org.apache.james.mime4j.stream.Field; /** - * ContentHandler for parsing mime encoded messages into Jalview objects. + * ContentHandler for parsing mime encoded messages into Jalview objects. TODO: diff --git a/debian/patches/series b/debian/patches/series index e7ff9d4..4deee53 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1,4 +1,6 @@ +encoding-fix mutilate-build-system.diff newer-jmol-api.diff newer-mime4j-api.diff -java8-compatibility.patch +testng +drop-lib diff --git a/debian/patches/testng b/debian/patches/testng new file mode 100644 index 0000000..f7161fe --- /dev/null +++ b/debian/patches/testng @@ -0,0 +1,11 @@ +--- jalview.orig/build.xml ++++ jalview/build.xml +@@ -281,7 +281,7 @@ + </target> + + <taskdef name="testng" classname="org.testng.TestNGAntTask" > +- <classpath location="utils/testnglibs/testng.jar" /> ++ <classpath location="/usr/share/java/testng.jar" /> + </taskdef> + + <target name="testng" depends="buildTests"> -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/pkg-java/jalview.git _______________________________________________ pkg-java-commits mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-java-commits
