Renjin cannot install (default) packages

Question

I am new to Renjin and cannot install packages with the AetherPackageLoader. I am getting the same error as in Renjin can't load pckages but with a seemingly correct Gradle file (please notice the a4Base dependency):

testCompile group: 'junit', name: 'junit', version: '4.12'
compile "org.renjin:renjin-script-engine:3.5-beta43";
//    compile group: 'org.renjin.cran', name: 'e1071', version: '1.7-2-b1'
compile group: 'org.renjin', name: 'renjin-aether-package-loader', version: '0.8.1938'
compile "org.renjin.bioconductor:a4Base:1.27.0-b3"

The full error is:

18:08:35: Executing task 'PackageTest.main()'...

Starting Gradle Daemon...
Gradle Daemon started in 1 s 867 ms
> Task :compileJava
> Task :processResources NO-SOURCE
> Task :classes

> Task :PackageTest.main() FAILED
Using local repository: /Users/miguel/.m2/repository
Exception in thread "main" java.lang.RuntimeException: org.renjin.eval.EvalException: org.renjin.aether.AetherPackageLoader.load(Lorg/renjin/primitives/packaging/FqPackageName;)Ljava/util/Optional;
    at org.renjin.eval.SessionBuilder.build(SessionBuilder.java:192)
    at PackageTest.main(PackageTest.java:26)
Caused by: org.renjin.eval.EvalException: org.renjin.aether.AetherPackageLoader.load(Lorg/renjin/primitives/packaging/FqPackageName;)Ljava/util/Optional;
    at org.renjin.sexp.Closure.applyPromised(Closure.java:212)
    at org.renjin.sexp.Closure.apply(Closure.java:133)
    at org.renjin.sexp.FunctionCall.eval(FunctionCall.java:80)
    at org.renjin.eval.Context.evaluate(Context.java:282)
    at org.renjin.eval.Context.evaluate(Context.java:209)
    at org.renjin.eval.SessionBuilder.build(SessionBuilder.java:187)
    ... 1 more
Caused by: java.lang.AbstractMethodError: org.renjin.aether.AetherPackageLoader.load(Lorg/renjin/primitives/packaging/FqPackageName;)Ljava/util/Optional;
    at org.renjin.primitives.packaging.NamespaceRegistry.getNamespace(NamespaceRegistry.java:152)
    at org.renjin.primitives.packaging.NamespaceRegistry.getNamespace(NamespaceRegistry.java:130)
    at org.renjin.primitives.packaging.NamespaceRegistry.getNamespace(NamespaceRegistry.java:114)
    at org.renjin.primitives.packaging.Packages.library(Packages.java:39)
    at org.renjin.primitives.R$primitive$library.doApply(R$primitive$library.java:68)
    at org.renjin.primitives.R$primitive$library.applyPromised(R$primitive$library.java:33)
    at org.renjin.sexp.BuiltinFunction.apply(BuiltinFunction.java:100)
    at org.renjin.primitives.special.InternalFunction.apply(InternalFunction.java:46)
    at org.renjin.sexp.FunctionCall.eval(FunctionCall.java:80)
    at org.renjin.eval.Context.evaluate(Context.java:282)
    at org.renjin.primitives.special.BeginFunction.apply(BeginFunction.java:39)
    at org.renjin.sexp.FunctionCall.eval(FunctionCall.java:80)
    at org.renjin.sexp.Closure.applyPromised(Closure.java:200)
    ... 6 more

FAILURE: Build failed with an exception.

* What went wrong:
Execution failed for task ':PackageTest.main()'.
> Process 'command '/Library/Java/JavaVirtualMachines/jdk1.8.0_231.jdk/Contents/Home/bin/java'' finished with non-zero exit value 1

* Try:
Run with --stacktrace option to get the stack trace. Run with --info or --debug option to get more log output. Run with --scan to get full insights.

* Get more help at https://help.gradle.org

BUILD FAILED in 48s
2 actionable tasks: 2 executed
18:09:24: Task execution finished 'PackageTest.main()'.

The example code only configures a session with an instance of AetherPackageLoader and try to execute an R command that loads a library that will need to be installed. The code fails sooner, when the session builder creates the session and loads the default packages.

AetherPackageLoader loader = new AetherPackageLoader();
loader.setRepositoryListener(new ConsoleRepositoryListener(System.out));
loader.setTransferListener(new ConsoleTransferListener(System.out));

Session session = new SessionBuilder()
        .withDefaultPackages()
        .setPackageLoader(loader)
        .build();

RenjinScriptEngineFactory factory = new RenjinScriptEngineFactory();
RenjinScriptEngine engine = factory.getScriptEngine(session);

String code = "library('digest')";

SEXP sexp = (SEXP)engine.eval(code);
System.out.println(sexp);

I'd appreciate any help with AetherPackageLoader. I read the documentation and cannot tell what is missing. Thanks a lot, Miguel

EDIT: I cannot reproduce this error on a Windows PC. I believe this is related to other errors I am getting in RStudio since after the update to MacOS Catalina. I think there is a problem with the permissions after the update.

Answer 1

If you are including your dependencies in your gradle file, then then the libraries will be available on the classpath, and there is no need to use the AetherPackageLoader.