[jalview] 03/03: Update d/changelog, patches, and add some dependencies
Ximin Luo
infinity0 at debian.org
Sat Dec 10 15:13:27 UTC 2016
This is an automated email from the git hooks/post-receive script.
infinity0 pushed a commit to branch master
in repository jalview.
commit f6ce144f1ee9a52c39b164e3fbf896720bc861d9
Author: Ximin Luo <infinity0 at debian.org>
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 <moeller at debian.org> Wed, 22 Jun 2016 21:33:44 +0200
+ [ Ximin Luo ]
+ * New upstream release.
+
+ -- Ximin Luo <infinity0 at debian.org> 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 <ebourg at apache.org>
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 \
--
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