[med-svn] [Git][med-team/htsjdk][master] 3 commits: add patch for Java 9 support

[Olivier Sallou]

Olivier Sallou pushed to branch master at Debian Med / htsjdk


Commits:
08ecca67 by Olivier Sallou at 2018-04-17T08:43:41+00:00
add patch for Java 9 support

- - - - -
2bbfe997 by Olivier Sallou at 2018-04-17T10:03:12+00:00
fix javadoc generation

- - - - -
855b9b6a by Olivier Sallou at 2018-04-17T10:06:12+00:00
update modifications done and pending

- - - - -


4 changed files:

- debian/changelog
- + debian/patches/40-fix-java9
- + debian/patches/50-fix-javadoc
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -12,11 +12,10 @@ htsjdk (2.14.3+dfsg-1) UNRELEASED-targeting-experimental; urgency=medium
   * d/rules
     Disable unit testing due to gradle+testng errors in gradle 3.2
     gradle 3.4 will fix the problem
+  * Fix JDK9 with --add-modules java.xml.bind in javadoc generation
+  * Fix javadoc generation
     
   [TODO - O. Sallou in progress]
-  * Fix JDK9 with --add-modules java.xml.bind in javadoc generation and test, need a new patch
-  * Javadoc generation failure: certainly due to openjdk issues (exits with error
-    on warnings, would need to patch a lot of files to workaround the issue or disable javadoc package)
   * Reintroduce unit tests now that gradle 3.4 is available in sid
     - new patch is needed for latest upstream, referencing junit classes
     - add testng() call in build.gradle with a patch and set test call in d/rules back


=====================================
debian/patches/40-fix-java9
=====================================
--- /dev/null
+++ b/debian/patches/40-fix-java9
@@ -0,0 +1,16 @@
+Subject: add support for java9
+Description: Java 9 uses modules, code makes use fo some modules,
+ need to add them
+Author: Olivier Sallou <osallou at debian.org>
+Last-Updated: 17-04-2018
+Forwarded: no
+--- a/build.gradle
++++ b/build.gradle
+@@ -115,6 +115,7 @@
+ if (JavaVersion.current().isJava8Compatible()) {
+     tasks.withType(Javadoc) {
+         options.addStringOption('Xdoclint:none', '-quiet')
++        options.addStringOption('-add-modules', 'java.xml.bind')
+     }
+ }
+ 


=====================================
debian/patches/50-fix-javadoc
=====================================
--- /dev/null
+++ b/debian/patches/50-fix-javadoc
@@ -0,0 +1,25 @@
+Subject: javadoc exception
+Description: some exception is raised by javadoc
+ looks like an openjdk issue, this patch removes impacted
+ comments
+Author: Olivier Sallou <osallou at debian.org>
+Last-Updated: 2018-04-17
+Forwarded: no
+--- a/src/main/java/htsjdk/samtools/util/MergingIterator.java
++++ b/src/main/java/htsjdk/samtools/util/MergingIterator.java
+@@ -88,7 +88,6 @@
+ 	}
+ 
+ 	/**
+-	 * @see java.util.Iterator<T>.hasNext
+ 	 */
+ 	@Override
+ 	public boolean hasNext() {
+@@ -96,7 +95,6 @@
+ 	}
+ 
+ 	/**
+-	 * @see java.util.Iterator<T>.next
+ 	 */
+ 	@Override
+ 	public T next() {


=====================================
debian/patches/series
=====================================
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -2,3 +2,5 @@
 13-skip_network_tests
 20-fix-version.patch
 30-disable-scalatest.patch
+40-fix-java9
+50-fix-javadoc



View it on GitLab: https://salsa.debian.org/med-team/htsjdk/compare/a49f8588499169413b73161dec26c9f293ab7db2...855b9b6a8385212bdb87c3274f27069443b05fcc

---
View it on GitLab: https://salsa.debian.org/med-team/htsjdk/compare/a49f8588499169413b73161dec26c9f293ab7db2...855b9b6a8385212bdb87c3274f27069443b05fcc
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