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commit f6ce144f1ee9a52c39b164e3fbf896720bc861d9 Author: Ximin Luo <[email protected]> Date: Sat Dec 10 16:12:31 2016 +0100 Update d/changelog, patches, and add some dependencies Others are not documented in Debian, added to d/TODO --- debian/TODO | 58 +++++++++++++++++++++++++++++++ debian/changelog | 10 ++++-- debian/control | 7 ++++ debian/patches/mutilate-build-system.diff | 58 +++++++++++-------------------- debian/patches/newer-mime4j-api.diff | 4 +-- debian/patches/series | 3 +- debian/rules | 4 ++- 7 files changed, 100 insertions(+), 44 deletions(-) diff --git a/debian/TODO b/debian/TODO new file mode 100644 index 0000000..63c0c6d --- /dev/null +++ b/debian/TODO @@ -0,0 +1,58 @@ +The following dependencies appear not to be in Debian: + + [javac] src/jalview/datamodel/SequenceI.java:26: error: package fr.orsay.lri.varna.models.rna does not exist + [javac] src/jalview/datamodel/Sequence.java:37: error: package fr.orsay.lri.varna.models.rna does not exist + [javac] src/jalview/util/ImageMaker.java:39: error: package org.jfree.graphics2d.svg does not exist + [javac] src/jalview/util/ImageMaker.java:40: error: package org.jfree.graphics2d.svg does not exist + [javac] src/jalview/gui/DasSourceBrowser.java:50: error: package org.biodas.jdas.schema.sources does not exist + [javac] src/jalview/gui/DasSourceBrowser.java:51: error: package org.biodas.jdas.schema.sources does not exist + [javac] src/jalview/gui/DasSourceBrowser.java:52: error: package org.biodas.jdas.schema.sources does not exist + [javac] src/jalview/gui/DasSourceBrowser.java:53: error: package org.biodas.jdas.schema.sources does not exist + [javac] src/jalview/ws/DasSequenceFeatureFetcher.java:51: error: package org.biodas.jdas.client does not exist + [javac] src/jalview/ws/DasSequenceFeatureFetcher.java:52: error: package org.biodas.jdas.client.adapters.features does not exist + [javac] src/jalview/ws/DasSequenceFeatureFetcher.java:53: error: package org.biodas.jdas.client.adapters.features.DasGFFAdapter does not exist + [javac] src/jalview/ws/DasSequenceFeatureFetcher.java:54: error: package org.biodas.jdas.client.threads does not exist + [javac] src/jalview/ws/DasSequenceFeatureFetcher.java:55: error: package org.biodas.jdas.schema.features does not exist + [javac] src/jalview/ws/DasSequenceFeatureFetcher.java:56: error: package org.biodas.jdas.schema.features does not exist + [javac] src/jalview/ws/DasSequenceFeatureFetcher.java:57: error: package org.biodas.jdas.schema.features does not exist + [javac] src/jalview/ws/DasSequenceFeatureFetcher.java:58: error: package org.biodas.jdas.schema.features does not exist + [javac] src/jalview/ws/DasSequenceFeatureFetcher.java:59: error: package org.biodas.jdas.schema.features does not exist + [javac] src/jalview/ws/DasSequenceFeatureFetcher.java:60: error: package org.biodas.jdas.schema.features does not exist + [javac] src/jalview/ws/DasSequenceFeatureFetcher.java:61: error: package org.biodas.jdas.schema.features does not exist + [javac] src/jalview/ws/DasSequenceFeatureFetcher.java:62: error: package org.biodas.jdas.schema.sources does not exist + [javac] src/jalview/ws/dbsources/das/api/jalviewSourceI.java:27: error: package org.biodas.jdas.schema.sources does not exist + [javac] src/jalview/ws/dbsources/das/api/jalviewSourceI.java:28: error: package org.biodas.jdas.schema.sources does not exist + [javac] src/jalview/ws/dbsources/das/api/DasSourceRegistryI.java:25: error: package org.biodas.jdas.client.threads does not exist + [javac] src/jalview/datamodel/SecondaryStructureAnnotation.java:23: error: package fr.orsay.lri.varna.models.rna does not exist + [javac] src/jalview/ext/htsjdk/HtsContigDb.java:23: error: package htsjdk.samtools does not exist + [javac] src/jalview/ext/htsjdk/HtsContigDb.java:24: error: package htsjdk.samtools does not exist + [javac] src/jalview/ext/htsjdk/HtsContigDb.java:25: error: package htsjdk.samtools.reference does not exist + [javac] src/jalview/ext/htsjdk/HtsContigDb.java:26: error: package htsjdk.samtools.reference does not exist + [javac] src/jalview/ext/htsjdk/HtsContigDb.java:27: error: package htsjdk.samtools.reference does not exist + [javac] src/jalview/ext/htsjdk/HtsContigDb.java:28: error: package htsjdk.samtools.util does not exist + [javac] src/jalview/ext/htsjdk/HtsContigDb.java:54: error: package htsjdk.samtools.reference does not exist + [javac] src/jalview/ext/so/SequenceOntology.java:40: error: package org.biojava.nbio.ontology does not exist + [javac] src/jalview/ext/so/SequenceOntology.java:41: error: package org.biojava.nbio.ontology does not exist + [javac] src/jalview/ext/so/SequenceOntology.java:42: error: package org.biojava.nbio.ontology.Term does not exist + [javac] src/jalview/ext/so/SequenceOntology.java:43: error: package org.biojava.nbio.ontology does not exist + [javac] src/jalview/ext/so/SequenceOntology.java:44: error: package org.biojava.nbio.ontology.io does not exist + [javac] src/jalview/ext/so/SequenceOntology.java:45: error: package org.biojava.nbio.ontology.utils does not exist + [javac] src/jalview/ext/varna/RnaModel.java:26: error: package fr.orsay.lri.varna.models.rna does not exist + [javac] src/jalview/gui/AppVarna.java:52: error: package fr.orsay.lri.varna does not exist + [javac] src/jalview/gui/AppVarna.java:53: error: package fr.orsay.lri.varna.exceptions does not exist + [javac] src/jalview/gui/AppVarna.java:54: error: package fr.orsay.lri.varna.exceptions does not exist + [javac] src/jalview/gui/AppVarna.java:55: error: package fr.orsay.lri.varna.exceptions does not exist + [javac] src/jalview/gui/AppVarna.java:56: error: package fr.orsay.lri.varna.interfaces does not exist + [javac] src/jalview/gui/AppVarna.java:57: error: package fr.orsay.lri.varna.models does not exist + [javac] src/jalview/gui/AppVarna.java:58: error: package fr.orsay.lri.varna.models does not exist + [javac] src/jalview/gui/AppVarna.java:59: error: package fr.orsay.lri.varna.models.annotations does not exist + [javac] src/jalview/gui/AppVarna.java:60: error: package fr.orsay.lri.varna.models.rna does not exist + [javac] src/jalview/gui/AppVarna.java:61: error: package fr.orsay.lri.varna.models.rna does not exist + [javac] src/jalview/gui/AppVarnaBinding.java:58: error: package fr.orsay.lri.varna does not exist + [javac] src/jalview/gui/AppVarnaBinding.java:59: error: package fr.orsay.lri.varna.components does not exist + [javac] src/jalview/gui/AppVarnaBinding.java:60: error: package fr.orsay.lri.varna.exceptions does not exist + [javac] src/jalview/gui/AppVarnaBinding.java:61: error: package fr.orsay.lri.varna.exceptions does not exist + [javac] src/jalview/gui/AppVarnaBinding.java:62: error: package fr.orsay.lri.varna.exceptions does not exist + [javac] src/jalview/gui/AppVarnaBinding.java:63: error: package fr.orsay.lri.varna.models does not exist + [javac] src/jalview/gui/AppVarnaBinding.java:64: error: package fr.orsay.lri.varna.models does not exist + [javac] src/jalview/gui/AppVarnaBinding.java:65: error: package fr.orsay.lri.varna.models.rna does not exist diff --git a/debian/changelog b/debian/changelog index b71141f..5afe32a 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,8 +1,14 @@ -jalview (2.7.dfsg-6) UNRELEASED; urgency=medium +jalview (2.10.1.dfsg-1) UNRELEASED; urgency=medium + * Team upload. + + [ Steffen Moeller ] * Reintroduced debian/upstream/edam file - -- Steffen Moeller <[email protected]> Wed, 22 Jun 2016 21:33:44 +0200 + [ Ximin Luo ] + * New upstream release. + + -- Ximin Luo <[email protected]> Sat, 10 Dec 2016 16:06:23 +0100 jalview (2.7.dfsg-5) unstable; urgency=medium diff --git a/debian/control b/debian/control index ba925d3..947b8d0 100644 --- a/debian/control +++ b/debian/control @@ -8,6 +8,7 @@ Build-Depends: ant, cdbs, debhelper (>= 9), default-jdk, + groovy, icedtea-netx-common, javahelp2, javahelper, @@ -21,10 +22,16 @@ Build-Depends: ant, libhttpcore-java, libhttpmime-java, libjaba-client-java, + libjaxrs-api-java, + libjersey1-client-java, + libjetty9-java, libjmol-java (>= 12.1.42), + libjson-simple-java, libjswingreader-java, liblog4j1.2-java, libmiglayout-java, + libservlet3.1-java, + libslf4j-java, libvamsas-client-java, libwsdl4j-java Standards-Version: 3.9.7 diff --git a/debian/patches/mutilate-build-system.diff b/debian/patches/mutilate-build-system.diff index 742adc5..4b780a0 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> +--- a/build.xml ++++ b/build.xml +@@ -152,10 +152,6 @@ + <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="${libDir}"> + <include name="*.jar" /> + <include name="**/*.jar" /> +@@ -521,7 +517,7 @@ + </axis-wsdl2java> + </target> - <target name="help" depends="usage" /> - <target name="usage"> -@@ -114,10 +107,6 @@ - <property name="wsdl.ClientNS" value="ext.vamsas" /> - <!-- the class path for building the application --> - <path id="build.classpath"> -- <fileset dir="utils"> -- <include name="*.jar" /> -- <include name="**/*.jar" /> -- </fileset> - <fileset dir="${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="${packageDir}" /> - <!-- clean dir if it already existed --> +-<target name="makedist" depends="build, buildPropertiesFile, linkcheck, buildindices"> ++<target name="makedist" depends="build, linkcheck, buildindices"> + <!-- make the package jar if not already existing --> + <mkdir dir="${packageDir}" /> + <!-- clean dir if it already existed --> diff --git a/debian/patches/newer-mime4j-api.diff b/debian/patches/newer-mime4j-api.diff index 9dee41d..89985f9 100644 --- a/debian/patches/newer-mime4j-api.diff +++ b/debian/patches/newer-mime4j-api.diff @@ -3,7 +3,7 @@ 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 @@ +@@ -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..bf66c2d 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1,4 +1,3 @@ mutilate-build-system.diff -newer-jmol-api.diff newer-mime4j-api.diff -java8-compatibility.patch +#java8-compatibility.patch diff --git a/debian/rules b/debian/rules index 84c3a87..2e4b48f 100755 --- a/debian/rules +++ b/debian/rules @@ -21,7 +21,9 @@ DEB_JARS := castor-xml commons-logging log4j-1.2 \ castor-core Jmol min-jaba-client axis-jaxrpc commons-discovery \ axis jh vamsas-client /usr/share/jmol-applet/JmolApplet.jar \ jswingreader miglayout /usr/share/icedtea-web/plugin.jar \ - httpmime httpcore apache-mime4j-core httpclient jsearch-indexer + httpmime httpcore apache-mime4j-core httpclient jsearch-indexer \ + json-simple servlet-api-3.1 jetty9-server javax.ws.rs-api \ + jersey1-client slf4j-api groovy ANT_OPTS := -Dbuild.sysclasspath=last \ -- 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
