[med-svn] [htsjdk] 08/10: Try to adapt gradle build system by removing plugins we can not download

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository htsjdk.

commit f102f23a9cb2cfe3aae305197c5a5706bbf71fa1
Author: Andreas Tille <tille at debian.org>
Date:   Wed Jun 29 10:45:25 2016 +0200

    Try to adapt gradle build system by removing plugins we can not download
---
 debian/patches/10-build.xml       | 66 ---------------------------------------
 debian/patches/10-build.xml.patch | 16 ++++++++++
 debian/patches/series             |  2 +-
 3 files changed, 17 insertions(+), 67 deletions(-)

diff --git a/debian/patches/10-build.xml b/debian/patches/10-build.xml
deleted file mode 100644
index a378084..0000000
--- a/debian/patches/10-build.xml
+++ /dev/null
@@ -1,66 +0,0 @@
-Description: Modifies the upstream build system.
- This patch changes the path to the javac compiler, enables the use
- of the system's testng library, and adds a new target for preparing
- the sam and picard jar files and installing the extra R scripts
- from src/scripts/net/sf/picard/analysis/.
-Origin: vendor
-Forwarded: no
---- a/build.xml
-+++ b/build.xml
-@@ -41,7 +41,10 @@
- 
-     <!-- Get GIT hash, if available, otherwise leave it blank.  -->
- 
--    <property name="repository.revision" value=""/>
-+    <!-- For Debian, do not use GIT hash (it would be the one from the
-+         packaging repo), but use the "dfsg" string as sources are
-+         repacked -->
-+    <property name="repository.revision" value="dfsg"/>
-     <property name="htsjdk-version" value="2.3.0"/>
-     <property name="htsjdk-version-file" value="htsjdk.version.properties"/>
-     <property name="testng.verbosity" value="2"/>
-@@ -76,6 +79,12 @@
-             <fileset dir="${lib}">
-                 <include name="**/*.jar"/>
-             </fileset>
-+            <pathelement path="/usr/share/java/commons-compress.jar"/>
-+            <pathelement path="/usr/share/java/commons-jexl2.jar"/>
-+            <pathelement path="/usr/share/java/jbzip2.jar"/>
-+            <pathelement path="/usr/share/java/snappy-java.jar"/>
-+            <pathelement path="/usr/share/java/testng.jar"/>
-+            <pathelement path="/usr/share/java/ngs-java.jar"/>
-         </path>
-     </target>
- 
-@@ -138,6 +147,7 @@
-                         <pathelement path="${classes}"/>
-                         <pathelement path="${classes.test}"/>
-                         <pathelement path="${scripts}"/>
-+                        <pathelement path="/usr/share/java/jcommander.jar"/>
-                     </classpath>
-                     <classfileset dir="${classes.test}">
-                         <include name="**/Test*.class"/>
-@@ -188,6 +198,7 @@
-                 <pathelement path="${classes}"/>
-                 <pathelement path="${classes.test}"/>
-                 <pathelement path="${scripts}"/>
-+                <pathelement path="/usr/share/java/jcommander.jar"/>
-             </classpath>
-             <classfileset dir="${classes.test}">
-                 <include name="**/${name}.class"/>
-@@ -230,8 +241,14 @@
-                 <fileset dir="${lib}">
-                     <include name="**/*.jar" />
-                 </fileset>
-+                <pathelement path="/usr/share/java/testng.jar"/>
-+                <pathelement path="/usr/share/java/snappy-java.jar"/>
-+                <pathelement path="/usr/share/java/jbzip2.jar"/>
-+                <pathelement path="/usr/share/java/commons-jexl2.jar"/>
-+                <pathelement path="/usr/share/java/commons-compress.jar"/>
-+                <pathelement path="/usr/share/java/ngs-java.jar"/>
-             </classpath>
--            <link href="http://java.sun.com/j2se/1.5.0/docs/api/"/>
-+            <link href="/usr/share/doc/default-jdk-doc/api"/>
-         </javadoc>
-     </target>
- 
diff --git a/debian/patches/10-build.xml.patch b/debian/patches/10-build.xml.patch
new file mode 100644
index 0000000..2bb565f
--- /dev/null
+++ b/debian/patches/10-build.xml.patch
@@ -0,0 +1,16 @@
+Description: Modifies the upstream build system.
+Origin: vendor
+Forwarded: no
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Wed, 29 Jun 2016 10:45:03 +0200
+
+--- a/build.gradle
++++ b/build.gradle
+@@ -9,7 +9,6 @@ plugins {
+     id 'maven'
+     id 'signing'
+     id 'jacoco'
+-    id 'com.palantir.git-version' version '0.5.1'
+     id 'com.github.johnrengelman.shadow' version '1.2.3'
+     id "com.github.kt3k.coveralls" version "2.6.3"
+ }
diff --git a/debian/patches/series b/debian/patches/series
index 11f1a22..57139fb 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,3 @@
-# 10-build.xml
+10-build.xml
 11-snappy-java-compatibility.patch
 13-skip_network_tests

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/htsjdk.git