debian/changelog

+picard-tools (2.8.1+dfsg-4) unstable; urgency=medium
+
+  * Team upload.
+  * Fixed the build failure with Java 9 (Closes: #894329)
+  * Standards-Version updated to 4.1.4
+  * Switch to debhelper level 11
+  * Use salsa.debian.org Vcs-* URLs
+
+ -- Emmanuel Bourg <ebourg@apache.org>  Fri, 06 Apr 2018 17:36:09 +0200
+
 picard-tools (2.8.1+dfsg-3) unstable; urgency=medium
 
   * debian/upstream/metadata: RRID -> SciCrunch

debian/compat

-10
+11

debian/control

@@ -8,7 +8,7 @@ Uploaders: Charles Plessy <plessy@debian.org>,
 Section: science
 Priority: optional
 Build-Depends: default-jdk (>= 2:1.8),
-               debhelper (>= 10),
+               debhelper (>= 11),
                javahelper,
                gradle-debian-helper,
                maven-repo-helper,
@@ -22,9 +22,9 @@ Build-Depends: default-jdk (>= 2:1.8),
                default-jdk-doc,
                libhtsjdk-java-doc,
                libguava-java-doc
-Standards-Version: 3.9.8
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/picard-tools.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/picard-tools.git
+Standards-Version: 4.1.4
+Vcs-Browser: https://salsa.debian.org/med-team/picard-tools
+Vcs-Git: https://salsa.debian.org/med-team/picard-tools.git
 Homepage: http://broadinstitute.github.io/picard/
 
 Package: picard-tools

debian/patches/10-build.xml.patch

@@ -4,7 +4,7 @@ Forwarded: not-needed
 Last-Updated: 2016-07-07
 --- a/build.gradle
 +++ b/build.gradle
-@@ -12,13 +12,7 @@ plugins {
+@@ -12,13 +12,7 @@
      id "java"
      id 'maven'
      id 'signing'
@@ -18,7 +18,7 @@ Last-Updated: 2016-07-07
  }
  
  mainClassName = "picard.cmdline.PicardCommandLine"
-@@ -31,22 +25,6 @@ repositories {
+@@ -31,38 +25,31 @@
      }
  }
  
@@ -41,7 +41,14 @@ Last-Updated: 2016-07-07
  final htsjdkVersion = System.getProperty('htsjdk.version', '2.8.0')
  
  dependencies {
-@@ -60,9 +38,18 @@ dependencies {
+     compile 'com.google.guava:guava:15.0'
+     compile 'com.github.samtools:htsjdk:' + htsjdkVersion
+     //tools dependency for doclet requires sdk devel
+-    compile(files(((URLClassLoader) ToolProvider.getSystemToolClassLoader()).getURLs()))
++    //compile(files(((URLClassLoader) ToolProvider.getSystemToolClassLoader()).getURLs()))
+     testCompile 'org.testng:testng:6.9.10'
+ }
+ 
  sourceCompatibility = 1.8
  targetCompatibility = 1.8
  
@@ -62,7 +69,16 @@ Last-Updated: 2016-07-07
  
  logger.info("build for version:" + version)
  group = 'com.github.broadinstitute'
-@@ -323,19 +310,3 @@ task copyJavadoc(dependsOn: 'javadoc', t
+@@ -176,7 +163,7 @@
+ 
+ //generate documentation
+ 
+-task documentAll(dependsOn: ['documentCommands', 'createMetricsDoc', 'documentStandardOptions']){
++task documentAll(dependsOn: ['documentCommands', 'documentStandardOptions']){
+   doFirst{
+     htmlDirInc.mkdirs()
+   }
+@@ -323,19 +310,3 @@
      from 'build/docs/javadoc'
      into "$htmlDir/javadoc"
  }

debian/patches/40-tests-fix-testng.patch

@@ -3,7 +3,7 @@
 @@ -32,7 +32,7 @@
      compile 'com.github.samtools:htsjdk:' + htsjdkVersion
      //tools dependency for doclet requires sdk devel
-     compile(files(((URLClassLoader) ToolProvider.getSystemToolClassLoader()).getURLs()))
+     //compile(files(((URLClassLoader) ToolProvider.getSystemToolClassLoader()).getURLs()))
 -    testCompile 'org.testng:testng:6.9.10'
 +    testCompile 'org.testng:testng:debian'
  }