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 <[email protected]>
+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 <[email protected]>
+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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