Olivier Sallou pushed to branch master at Debian Med / igv
Commits: 8e135074 by Olivier Sallou at 2018-10-15T12:44:28Z fix gradle build - - - - - dce682f8 by Olivier Sallou at 2018-10-15T12:48:09Z update gradle build, an issue remains on log4j - - - - - 3 changed files: - debian/changelog - + debian/patches/fix_gradle.patch - debian/patches/series Changes: ===================================== debian/changelog ===================================== @@ -11,6 +11,11 @@ igv (2.4.14+dfsg-1) UNRELEASED; urgency=medium * Standards-Version: 4.2.1 * Upstream switched build system to gradle + [ Olivier Sallou] + * d/patches/fix_gradle.patch: adapt build to Debian + // TODO there is still an issue with log4j, Logger class is not found + though modules and libraries are loaded in classpath + -- Andreas Tille <[email protected]> Mon, 01 Oct 2018 21:14:39 +0200 igv (2.4.6+dfsg-1) unstable; urgency=medium ===================================== debian/patches/fix_gradle.patch ===================================== @@ -0,0 +1,97 @@ +Subject: adapt gradle build for debian +Description: gradle build file needs to add debian based libraries + Needs some adaptation also to support Java 9 modules. + All Debian libraries do not provide Module name in their manifest. In this + case, system tries to get it from Jar name, so module names need also to be + adapted for those libraries to match Debian jar names. +Author: Olivier Sallou <[email protected]> +Last-Updated: 2018-10-15 +Forwarded: no +--- a/build_java9.gradle ++++ b/build_java9.gradle +@@ -20,7 +20,10 @@ + // LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + // OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + // THE SOFTWARE. +-apply plugin: 'java' ++plugins { ++ id 'java' ++ id 'maven' ++} + import org.apache.tools.ant.filters.ReplaceTokens + + ext.moduleName = 'org.broad.igv' +@@ -30,6 +33,12 @@ + // Despite this, it is recommended that Java 8 vs. 9 builds be run in different locations. + buildDir = 'build_java9' + ++repositories { ++ mavenCentral() ++ mavenLocal() ++} ++ ++ + sourceSets { + main { + java { +@@ -45,6 +54,19 @@ + dependencies { + // Use the newer JIDE lib for Java 9 builds + compile fileTree(dir: 'lib', include: '*.jar', exclude: 'jide-oss-3.5.5.jar') + fileTree(dir: 'lib_java9', include: '*.jar') ++ compile "com.google.guava:guava:debian" ++ compile "commons-io:commons-io:debian" ++ compile "org.apache.commons:commons-math:debian" ++ compile "com.google.code.gson:gson:debian" ++ compile "org.openjfx:javafx:debian" ++ compile "org.openjfx:javafx-fxml:debian" ++ compile "org.openjfx:javafx-graphics:debian" ++ compile "org.openjfx:javafx-swing:debian" ++ compile "org.jfree:jfreechart:debian" ++ compile "org.apache.logging.log4j:log4j:debian" ++ compile "org.apache.logging.log4j:log4j-api:debian" ++ compile "org.apache.logging.log4j:log4j-core:debian" ++ compile "org.swinglabs:swing-layout:debian" + testCompile fileTree(dir: 'test/lib', include: '*.jar') + } + +--- a/src/main/java9/module-info.java ++++ b/src/main/java9/module-info.java +@@ -93,11 +93,11 @@ + + requires AbsoluteLayout; + requires ant; +- requires com.google.common; +- requires commons.io; +- requires commons.math; ++ requires guava.debian; ++ requires org.apache.commons.io; ++ requires commons.math.debian; + requires goby.io.igv; +- requires gson; ++ requires gson.debian; + requires htsjdk; + requires java.datatransfer; + requires java.desktop; +@@ -107,15 +107,14 @@ + requires java.sql; + requires java.xml; + requires java.xml.bind; +- requires javafx.base; +- requires javafx.controls; +- requires javafx.fxml; +- requires javafx.graphics; +- requires javafx.swing; ++ requires javafx.baseEmpty; ++ requires javafx.controlsEmpty; ++ requires javafx.fxmlEmpty; ++ requires javafx.graphicsEmpty; ++ requires javafx.swingEmpty; + requires jdk.xml.dom; +- requires jfreechart; +- requires log4j; ++ requires jfreechart.debian; + requires org.apache.logging.log4j; + requires org.apache.logging.log4j.core; +- requires swing.layout; ++ requires swing.layout.debian; + } ===================================== debian/patches/series ===================================== @@ -1 +1,2 @@ # fix_samtools_api +fix_gradle.patch View it on GitLab: https://salsa.debian.org/med-team/igv/compare/1fd85b5d63a43613ee39f7915278e35787438aa2...dce682f881aca91f8737bc9675f970dfd02a5cca -- View it on GitLab: https://salsa.debian.org/med-team/igv/compare/1fd85b5d63a43613ee39f7915278e35787438aa2...dce682f881aca91f8737bc9675f970dfd02a5cca You're receiving this email because of your account on salsa.debian.org.
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