[med-svn] [Git][med-team/picard-tools][master] 5 commits: Fixed the build failure with Java 9 (Closes: #894329)
Emmanuel Bourg
gitlab at salsa.debian.org
Fri Apr 6 16:36:30 BST 2018
Emmanuel Bourg pushed to branch master at Debian Med / picard-tools
Commits:
d3eb9023 by Emmanuel Bourg at 2018-04-06T12:13:51+02:00
Fixed the build failure with Java 9 (Closes: #894329)
- - - - -
dd4c4b64 by Emmanuel Bourg at 2018-04-06T12:14:05+02:00
Standards-Version updated to 4.1.4
- - - - -
12315b01 by Emmanuel Bourg at 2018-04-06T12:14:09+02:00
Switch to debhelper level 11
- - - - -
f9300c67 by Emmanuel Bourg at 2018-04-06T17:32:05+02:00
Use salsa.debian.org Vcs-* URLs
- - - - -
e77131a1 by Emmanuel Bourg at 2018-04-06T17:36:14+02:00
Upload to unstable
- - - - -
5 changed files:
- debian/changelog
- debian/compat
- debian/control
- debian/patches/10-build.xml.patch
- debian/patches/40-tests-fix-testng.patch
Changes:
=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,13 @@
+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 at 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
=====================================
--- a/debian/compat
+++ b/debian/compat
@@ -1 +1 @@
-10
+11
=====================================
debian/control
=====================================
--- a/debian/control
+++ b/debian/control
@@ -8,7 +8,7 @@ Uploaders: Charles Plessy <plessy at 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
=====================================
--- a/debian/patches/10-build.xml.patch
+++ b/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
=====================================
--- a/debian/patches/40-tests-fix-testng.patch
+++ b/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'
}
View it on GitLab: https://salsa.debian.org/med-team/picard-tools/compare/afdbd8d7e74b79d3498ccde28b37376fe63394e5...e77131a1bc920e0851e0ac3fd85530b047278399
---
View it on GitLab: https://salsa.debian.org/med-team/picard-tools/compare/afdbd8d7e74b79d3498ccde28b37376fe63394e5...e77131a1bc920e0851e0ac3fd85530b047278399
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