On 10/17/2018 11:59 AM, Tony Travis wrote: > On 17/10/2018 10:19, Olivier Sallou wrote: >> [...] >> new IGV needs Java 9 or above. >> The problem is Java 8 to 9 introduced some breaking changes with modules >> support. > Hi, Olivier. > > The default under Ubuntu-MATE 18.04 LTS is Java 10: > >> /usr/lib/jvm/java-11-openjdk-amd64/bin/java -version >> openjdk version "10.0.2" 2018-07-17 >> OpenJDK Runtime Environment (build 10.0.2+13-Ubuntu-1ubuntu0.18.04.2) >> OpenJDK 64-Bit Server VM (build 10.0.2+13-Ubuntu-1ubuntu0.18.04.2, mixed >> mode) > However, IGV did not work with Java 10 because of the missing classes. > > I forced it to Java 8 because that is what the IGV docs said was required: > >> http://software.broadinstitute.org/software/igv/ReleaseNotes/2.4.x > "Java 8 is now required. IGV 2.4 requires Java version 8 to run" > >> /usr/lib/jvm/java-8-openjdk-amd64/bin/java -version >> openjdk version "1.8.0_181" >> OpenJDK Runtime Environment (build 1.8.0_181-8u181-b13-0ubuntu0.18.04.1-b13) >> OpenJDK 64-Bit Server VM (build 25.181-b13, mixed mode) > That also did not work because of the missing classes, so I patched it. > >> For igv (and others), command line is impacted, for example: >> >> Java8: java -cp ... ivg.jar >> Java9: java --add-modules java.xml.bind -cp .. igv.jar >> >> as Java > 9 is default now, we package apps to be Java 9 compliant, not >> Java 8 anymore >> >> in progress (not uploaded) igv packaging *should* be ok, but needs testing > That's a problem for Bio-Linux 9 / Ubuntu 18.04 LTS, because the default > is now Java 10 and the only other Java in the standard repo's is Java 8. well, in my package env for new igv, I use Java 10, so will nto be a pb > >> apt list '*jdk*jre*' >> Listing... Done >> openjdk-11-jre/bionic-updates,bionic-security,now 10.0.2+13-1ubuntu0.18.04.2 >> amd64 [installed,automatic] >> openjdk-11-jre-headless/bionic-updates,bionic-security,now >> 10.0.2+13-1ubuntu0.18.04.2 amd64 [installed,automatic] >> openjdk-11-jre-zero/bionic-updates,bionic-security >> 10.0.2+13-1ubuntu0.18.04.2 amd64 >> openjdk-8-jre/bionic-updates,bionic-security,now 8u181-b13-0ubuntu0.18.04.1 >> amd64 [installed,automatic] >> openjdk-8-jre-dcevm/bionic 8u112-2 amd64 >> openjdk-8-jre-headless/bionic-updates,bionic-security,now >> 8u181-b13-0ubuntu0.18.04.1 amd64 [installed,automatic] >> openjdk-8-jre-zero/bionic-updates,bionic-security 8u181-b13-0ubuntu0.18.04.1 >> amd64 > The stand-alone version of IGV 2.4.14 does not work with Java 10: > >> /usr/lib/jvm/java-11-openjdk-amd64/bin/java -Xmx2000m >> -Dapple.laf.useScreenMenuBar=true -Djava.net.preferIPv4Stack=true -jar >> /usr/local/IGV/lib/igv.jar >> WARN [2018-10-17T10:57:48,211] [Globals.java:138] [AWT-EventQueue-0] >> Development mode is enabled >> Detected an unsupported Java version. Java 8 is required by this release. > I've not tried it with Java 9. > > HTH, > > Tony. > -- Olivier Sallou Univ Rennes, Inria, CNRS, IRISA Irisa, Campus de Beaulieu F-35042 RENNES - FRANCE Tel: 02.99.84.71.95 gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
