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 <ebo...@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 <ple...@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 You're receiving this email because of your account on salsa.debian.org.
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