[med-svn] [Git][med-team/picard-tools][master] 3 commits: disable java version check, method used is deprecated
Olivier Sallou
gitlab at salsa.debian.org
Tue Sep 18 09:38:08 BST 2018
Olivier Sallou pushed to branch master at Debian Med / picard-tools
Commits:
7c90f01b by Olivier Sallou at 2018-09-18T07:41:10Z
disable java version check, method used is deprecated
- - - - -
387ba245 by Olivier Sallou at 2018-09-18T07:44:17Z
add libcommons-math3-java dependency
- - - - -
ebd57409 by Olivier Sallou at 2018-09-18T08:08:37Z
disable some tests
testng below or equal to 6.9.13.4 does not correctly map
long and Integers. This leads to test issues when provider [0,9] values
and methods expects a long (testng sends an Integer).
This patch disable some tests around this
- - - - -
3 changed files:
- debian/control
- debian/patches/10-build.xml.patch
- debian/patches/40-tests-fix-testng.patch
Changes:
=====================================
debian/control
=====================================
@@ -14,6 +14,7 @@ Build-Depends: default-jdk (>= 2:1.9~),
maven-repo-helper,
libguava-java (>= 15.0),
libcommons-lang3-java,
+ libcommons-math3-java,
libbarclay-java,
libgkl-java,
libgatk-native-bindings-java,
@@ -92,6 +93,7 @@ Depends: ${misc:Depends},
libbarclay-java,
libgkl-java,
libcommons-lang3-java,
+ libcommons-math3-java,
libgatk-native-bindings-java
# avoid ${java:Depends} that contains openjdk-8-jdk-headless
# due to tools.jar in classpath
=====================================
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"
-@@ -31,6 +25,7 @@ repositories {
+@@ -31,6 +25,7 @@
}
}
@@ -26,7 +26,7 @@ Last-Updated: 2016-07-07
jacocoTestReport {
dependsOn test
group = "Reporting"
-@@ -46,6 +41,7 @@ jacocoTestReport {
+@@ -46,21 +41,22 @@
jacoco {
toolVersion = "0.7.5.201505241946"
}
@@ -34,7 +34,31 @@ Last-Updated: 2016-07-07
final requiredJavaVersion = "8"
final buildPrerequisitesMessage = "See https://github.com/broadinstitute/picard/blob/master/README.md#building-picard for information on how to build picard"
-@@ -73,7 +69,7 @@ final googleNio = 'org.broadinstitute:go
+ // Ensure that we have the right JDK version, a clone of the git repository
+ def ensureBuildPrerequisites(requiredJavaVersion, buildPrerequisitesMessage) {
+ // Make sure we can get a ToolProvider class loader. If not we may have just a JRE, or a JDK from the future.
+- if (ToolProvider.getSystemToolClassLoader() == null) {
+- throw new GradleException(
+- "The ClassLoader obtained from the Java ToolProvider is null. "
+- + "A Java $requiredJavaVersion JDK must be installed. $buildPrerequisitesMessage")
+- }
+- if (!file(".git").isDirectory()) {
+- throw new GradleException("The Picard Github repository must be cloned using \"git clone\" to run the build. "
+- + "$buildPrerequisitesMessage")
+- }
++ //if (ToolProvider.getSystemToolClassLoader() == null) {
++ // throw new GradleException(
++ // "The ClassLoader obtained from the Java ToolProvider is null. "
++ // + "A Java $requiredJavaVersion JDK must be installed. $buildPrerequisitesMessage")
++ //}
++ //if (!file(".git").isDirectory()) {
++ // throw new GradleException("The Picard Github repository must be cloned using \"git clone\" to run the build. "
++ // + "$buildPrerequisitesMessage")
++ //}
+ }
+ ensureBuildPrerequisites(requiredJavaVersion, buildPrerequisitesMessage)
+
+@@ -73,7 +69,7 @@
// Get the jdk files we need to run javaDoc. We need to use these during compile, testCompile,
// test execution, and gatkDoc generation, but we don't want them as part of the runtime
// classpath and we don't want to redistribute them in the uber jar.
@@ -43,7 +67,7 @@ Last-Updated: 2016-07-07
configurations {
cloudConfiguration {
-@@ -95,8 +91,8 @@ dependencies {
+@@ -95,8 +91,8 @@
compileOnly googleNio
// javadoc utilities; compile/test only to prevent redistribution of sdk jars
@@ -54,7 +78,7 @@ Last-Updated: 2016-07-07
testCompile 'org.testng:testng:6.9.10'
testCompile 'org.apache.commons:commons-lang3:3.6'
-@@ -112,9 +108,18 @@ configurations.all {
+@@ -112,9 +108,18 @@
sourceCompatibility = 1.8
targetCompatibility = 1.8
@@ -75,7 +99,7 @@ Last-Updated: 2016-07-07
logger.info("build for version:" + version)
group = 'com.github.broadinstitute'
-@@ -166,6 +171,8 @@ jar {
+@@ -166,6 +171,8 @@
tasks.withType(Javadoc) {
// do this for all javadoc tasks, including gatkDoc
options.addStringOption('Xdoclint:none')
@@ -84,7 +108,7 @@ Last-Updated: 2016-07-07
}
javadoc {
-@@ -192,7 +199,8 @@ task picardDoc(type: Javadoc, dependsOn:
+@@ -192,7 +199,8 @@
// The gatkDoc process instantiates any documented feature classes, so to run it we need the entire
// runtime classpath, as well as jdk javadoc files such as tools.jar, where com.sun.javadoc lives.
@@ -94,7 +118,7 @@ Last-Updated: 2016-07-07
options.docletpath = classpath.asType(List)
options.doclet = "picard.util.help.PicardHelpDoclet"
-@@ -279,6 +287,8 @@ tasks.withType(Test) {
+@@ -279,6 +287,8 @@
}
}
@@ -103,7 +127,7 @@ Last-Updated: 2016-07-07
// set heap size for the test JVM(s)
minHeapSize = "1G"
maxHeapSize = "2G"
-@@ -415,6 +425,7 @@ task copyPicardDoc(dependsOn: 'picardDoc
+@@ -415,6 +425,7 @@
into "$htmlDir/picarddoc"
}
@@ -111,7 +135,7 @@ Last-Updated: 2016-07-07
task updateGhPages(dependsOn: ['copyJavadoc', 'copyPicardDoc']){
outputs.dir htmlDir
}
-@@ -430,3 +441,4 @@ githubPages {
+@@ -430,3 +441,4 @@
into 'newdocs'
}
}
=====================================
debian/patches/40-tests-fix-testng.patch
=====================================
@@ -1,10 +1,13 @@
Author: Olivier Sallou
-Last-Update: 2017-11-01 08:42:38
-Description: Fix testng version
-
+Last-Update: 2018-09-18 08:42:38
+Description: Fix testng version and disable some tests.
+ testng below or equal to 6.9.13.4 does not correctly map
+ long and Integers. This leads to test issues when provider [0,9] values
+ and methods expects a long (testng sends an Integer).
+ This patch disable some tests around this
--- a/build.gradle
+++ b/build.gradle
-@@ -74,9 +74,6 @@ final googleNio = 'org.broadinstitute:go
+@@ -74,9 +74,6 @@
configurations {
cloudConfiguration {
extendsFrom runtime
@@ -14,7 +17,7 @@ Description: Fix testng version
}
}
-@@ -88,14 +85,13 @@ dependencies {
+@@ -88,14 +85,13 @@
compile 'org.apache.commons:commons-math3:3.5'
compile 'com.github.samtools:htsjdk:' + htsjdkVersion
compile 'org.broadinstitute:barclay:2.0.0'
@@ -31,7 +34,7 @@ Description: Fix testng version
}
configurations.all {
-@@ -234,6 +230,7 @@ shadowJar {
+@@ -234,6 +230,7 @@
}
*/
@@ -39,7 +42,7 @@ Description: Fix testng version
task cloudJar(type: com.github.jengelman.gradle.plugins.shadow.tasks.ShadowJar) {
configurations = [project.configurations.cloudConfiguration]
from project.sourceSets.main.output
-@@ -258,6 +255,7 @@ task barclayShadowJar(type: com.github.j
+@@ -258,6 +255,7 @@
}
archiveName 'picardBarclay.jar'
}
@@ -47,7 +50,7 @@ Description: Fix testng version
// Run the tests using the legacy parser only. Assumes that test code is written using
// legacy command line parser syntax.
-@@ -268,6 +266,8 @@ task legacyTest(type: Test)
+@@ -268,6 +266,8 @@
task barclayTest(type: Test) {
systemProperty 'picard.convertCommandLine', 'true'
systemProperty 'picard.useLegacyParser', 'false'
@@ -56,7 +59,7 @@ Description: Fix testng version
}
// Run tests using both the legacy and barclay command line parsers.
-@@ -279,6 +279,9 @@ tasks.withType(Test) {
+@@ -279,6 +279,9 @@
outputs.upToDateWhen { false } // tests will always rerun
description = "Runs the unit tests"
@@ -68,7 +71,7 @@ Description: Fix testng version
excludeGroups "slow", "broken"
--- a/src/test/java/picard/analysis/directed/CollectHsMetricsTest.java
+++ b/src/test/java/picard/analysis/directed/CollectHsMetricsTest.java
-@@ -41,51 +41,6 @@ public class CollectHsMetricsTest extend
+@@ -41,51 +41,6 @@
};
}
@@ -120,7 +123,7 @@ Description: Fix testng version
@Test
public void testCoverageHistogram() throws IOException {
-@@ -106,7 +61,7 @@ public class CollectHsMetricsTest extend
+@@ -106,7 +61,7 @@
final boolean clipOverlappingReads = true;
final int sampleSize = 10;
@@ -131,7 +134,7 @@ Description: Fix testng version
final String[] args = new String[] {
--- a/src/test/java/picard/analysis/artifacts/TransitionTest.java
+++ b/src/test/java/picard/analysis/artifacts/TransitionTest.java
-@@ -34,13 +34,4 @@ public class TransitionTest {
+@@ -34,13 +34,4 @@
return new Object[][] {{Character.MIN_VALUE}, {Transition.Base.A.base - 1}, {'Z'}, {Character.MAX_VALUE}};
}
@@ -147,7 +150,7 @@ Description: Fix testng version
}
--- a/src/test/java/picard/util/IntervalListToolsTest.java
+++ b/src/test/java/picard/util/IntervalListToolsTest.java
-@@ -80,12 +80,6 @@ public class IntervalListToolsTest exten
+@@ -80,12 +80,6 @@
};
}
@@ -160,3 +163,18 @@ Description: Fix testng version
@DataProvider
public Object[][] actionAndTotalBasesWithInvertData() {
+--- a/src/test/java/picard/analysis/TheoreticalSensitivityTest.java
++++ b/src/test/java/picard/analysis/TheoreticalSensitivityTest.java
+@@ -351,10 +351,11 @@
+ };
+ }
+
++ /*
+ @Test(dataProvider = "callingThresholdDataProvider")
+ public void testCallingThreshold(final int totalDepth, final int altDepth, final double sumOfAltQualities, final double alleleFraction, final double logOddsThreshold, final boolean expectedCall) {
+ Assert.assertEquals(TheoreticalSensitivity.isCalled(totalDepth, altDepth, sumOfAltQualities, alleleFraction, logOddsThreshold), expectedCall);
+- }
++ } */
+
+ @DataProvider(name = "sumOfGaussiansDataProvider")
+ public Object[][] sumOfGaussians() {
View it on GitLab: https://salsa.debian.org/med-team/picard-tools/compare/9325575e20b129e379076ddced7a1583e26ab751...ebd5740983b6575e0977672a2412d1497abef3cd
--
View it on GitLab: https://salsa.debian.org/med-team/picard-tools/compare/9325575e20b129e379076ddced7a1583e26ab751...ebd5740983b6575e0977672a2412d1497abef3cd
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