Verify

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the version of java

Subject of the issue

Describe your issue here.

trying to get bamstats04 to compile

Your environment

version of jvarkit - cloned 1/3/2018
Java(TM) SE Runtime Environment (build 9.0.1+11)
the value of ${JAVA_HOME} /data/bioinformatics_software/oracleJava/jdk-9.0.1/bin/java
which OS Ubuntu 16.04.3 LTS

Steps to reproduce

Tell us how to reproduce this issue. Please provide an example. make bamstats04

Expected behaviour

Tell us what should happen

it should compile

Actual behaviour

Tell us what happens instead it errors out

$ make bamstats04 mkdir -p /data/marketingGC_bias/jvarkit/src/main/generated-sources/java/com/github/lindenb/jvarkit/util/htsjdk/ echo "package com.github.lindenb.jvarkit.util.htsjdk;" > /data/marketingGC_bias/jvarkit/src/main/generated-sources/java/com/github/lindenb/jvarkit/util/htsjdk/HtsjdkVersion.java echo '@javax.annotation.Generated("jvarkit")' >> /data/marketingGC_bias/jvarkit/src/main/generated-sources/java/com/github/lindenb/jvarkit/util/htsjdk/HtsjdkVersion.java echo 'public class HtsjdkVersion{ private HtsjdkVersion(){}' >> /data/marketingGC_bias/jvarkit/src/main/generated-sources/java/com/github/lindenb/jvarkit/util/htsjdk/HtsjdkVersion.java echo 'public static String getVersion() {return "2.13.0";}' >> /data/marketingGC_bias/jvarkit/src/main/generated-sources/java/com/github/lindenb/jvarkit/util/htsjdk/HtsjdkVersion.java echo -n 'public static String getDate() {return "' >> /data/marketingGC_bias/jvarkit/src/main/generated-sources/java/com/github/lindenb/jvarkit/util/htsjdk/HtsjdkVersion.java && date | tr -d '\n' >> /data/marketingGC_bias/jvarkit/src/main/generated-sources/java/com/github/lindenb/jvarkit/util/htsjdk/HtsjdkVersion.java && echo ')";}' >> /data/marketingGC_bias/jvarkit/src/main/generated-sources/java/com/github/lindenb/jvarkit/util/htsjdk/HtsjdkVersion.java echo 'public static String getHash() {return "2.13.0";}' >> /data/marketingGC_bias/jvarkit/src/main/generated-sources/java/com/github/lindenb/jvarkit/util/htsjdk/HtsjdkVersion.java echo 'public static String getHome() {return "lib/com/github/samtools/htsjdk/2.13.0/htsjdk-2.13.0.jar";}' >> /data/marketingGC_bias/jvarkit/src/main/generated-sources/java/com/github/lindenb/jvarkit/util/htsjdk/HtsjdkVersion.java echo 'public static String getJavadocUrl(final Class<?> clazz) {return "https://samtools.github.io/htsjdk/javadoc/htsjdk/"+clazz.getName().replaceAll("\\.","/")+".html";}' >> /data/marketingGC_bias/jvarkit/src/main/generated-sources/java/com/github/lindenb/jvarkit/util/htsjdk/HtsjdkVersion.java echo '}' >> /data/marketingGC_bias/jvarkit/src/main/generated-sources/java/com/github/lindenb/jvarkit/util/htsjdk/HtsjdkVersion.java mkdir -p /data/marketingGC_bias/jvarkit/dist/ rm -rf "/data/marketingGC_bias/jvarkit/_tmp-2.13.0" mkdir -p /data/marketingGC_bias/jvarkit/_tmp-2.13.0/META-INF/services echo "com.github.lindenb.jvarkit.annotproc.JVarkitAnnotationProcessor" > /data/marketingGC_bias/jvarkit/_tmp-2.13.0/META-INF/services/javax.annotation.processing.Processor echo '### Printing javac version : it should be Oracle 1.8 (NOT OpenJDK). if Not, check your $${PATH}.'

Printing javac version : it should be Oracle 1.8 (NOT OpenJDK). if Not, check your $${PATH}.

javac -version javac 9.0.1

compile

javac -d /data/marketingGC_bias/jvarkit/_tmp-2.13.0 -sourcepath /data/marketingGC_bias/jvarkit/src/main/java:/data/marketingGC_bias/jvarkit/src/main/generated-sources/java /data/marketingGC_bias/jvarkit/src/main/java/com/github/lindenb/jvarkit/annotproc/JVarkitAnnotationProcessor.java /data/marketingGC_bias/jvarkit/src/main/java/com/github/lindenb/semontology/Term.java:11: error: package javax.annotation is not visible @javax.annotation.Generated(value="xslt",date="2017-04-06T09:53:14+02:00",comments="generated from https://github.com/lindenb/semontology") ^ (package javax.annotation is declared in module java.xml.ws.annotation, which is not in the module graph) 1 error Makefile:852: recipe for target '/data/marketingGC_bias/jvarkit/dist/annotproc.jar' failed

lindenb / jvarkit

Can't compile on Ubuntu 16.04.3 LTS w/ Oracle Java 9.0.1+11 #93