===> License GPLv3 accepted by the user ===> jalview-2.11.1.4 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by jalview-2.11.1.4 for building ===> Extracting for jalview-2.11.1.4 => SHA256 Checksum OK for jalview_2_11_1_4.tar.gz. => SHA256 Checksum OK for jalview-2.11.1.4-deps.tar.gz. ===> Patching for jalview-2.11.1.4 ===> jalview-2.11.1.4 depends on executable: gradle - found ===> jalview-2.11.1.4 depends on file: /usr/local/openjdk11/bin/java - found ===> Configuring for jalview-2.11.1.4 ===> Building for jalview-2.11.1.4 Starting a Gradle Daemon, 1 incompatible and 1 stopped Daemons could not be reused, use --status for details > Configure project : HEADLESS BUILD Using a LOCAL profile. > Task :compileJava Setting target compatibility to 11 /disk-samsung/freebsd-ports/biology/jalview/work/jalview/src/jalview/ws/dbsources/EmblXmlSource.java:73: warning: [dep-ann] deprecated item is not annotated with @Deprecated public abstract class EmblXmlSource extends EbiFileRetrievedProxy ^ Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 1 warning > Task :processResources > Task :classes > Task :cleanPackageDir UP-TO-DATE > Task :copyHelp > Task :buildIndices > Task :setGitVals UP-TO-DATE > Task :createBuildProperties > Task :compileLinkCheck > Task :cleanBuildingHTML > Task :convertBuildingMD UP-TO-DATE > Task :syncDocs > Task :syncResources > Task :prepare > Task :linkCheck Could not read standard output of command '/usr/local/openjdk11/bin/java'. java.lang.NullPointerException at org.apache.tools.ant.util.TeeOutputStream.write(TeeOutputStream.java:86) at org.gradle.process.internal.streams.ExecOutputHandleRunner.forwardContent(ExecOutputHandleRunner.java:67) at org.gradle.process.internal.streams.ExecOutputHandleRunner.run(ExecOutputHandleRunner.java:53) at org.gradle.internal.operations.CurrentBuildOperationPreservingRunnable.run(CurrentBuildOperationPreservingRunnable.java:42) at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:64) at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:48) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:56) at java.base/java.lang.Thread.run(Thread.java:834) Could not read error output of command '/usr/local/openjdk11/bin/java'. java.lang.NullPointerException at org.apache.tools.ant.util.TeeOutputStream.close(TeeOutputStream.java:51) at org.gradle.internal.concurrent.CompositeStoppable$2.stop(CompositeStoppable.java:90) at org.gradle.internal.concurrent.CompositeStoppable.stop(CompositeStoppable.java:106) at org.gradle.process.internal.streams.ExecOutputHandleRunner.forwardContent(ExecOutputHandleRunner.java:70) at org.gradle.process.internal.streams.ExecOutputHandleRunner.run(ExecOutputHandleRunner.java:53) at org.gradle.internal.operations.CurrentBuildOperationPreservingRunnable.run(CurrentBuildOperationPreservingRunnable.java:42) at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:64) at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:48) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:56) at java.base/java.lang.Thread.run(Thread.java:834) > Task :jar > Task :syncJars > Task :makeDist > Task :shadowJar Deprecated Gradle features were used in this build, making it incompatible with Gradle 7.0. Use '--warning-mode all' to show the individual deprecation warnings. See https://docs.gradle.org/6.8.3/userguide/command_line_interface.html#sec:command_line_warnings BUILD SUCCESSFUL in 55s 15 actionable tasks: 13 executed, 2 up-to-date ===> Staging for jalview-2.11.1.4 ===> jalview-2.11.1.4 depends on file: /usr/local/openjdk11/bin/java - found ===> Generating temporary packing list install -m 555 /disk-samsung/freebsd-ports/biology/jalview/work/jalview.sh /disk-samsung/freebsd-ports/biology/jalview/work/stage/usr/local/bin/jalview install -m 0644 /disk-samsung/freebsd-ports/biology/jalview/work/jalview/build/libs/jalview-all-2.11.1.4-j11.jar /disk-samsung/freebsd-ports/biology/jalview/work/stage/usr/local/share/java/jalview/jalview.jar ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa)