Hi, This is very similar to the problem @twagnerdescribed in '17, except I’ve been replacing with v3.5b76. The motivation for the changed version is support for Renjin grDevices and ggplot2, etc (for plot types not support elsewhere). It is working well in a plugin of mine-slow vs JFreeChart but quick enough.
As suggest by @ctrueden in the above mentioned post, I looked at the pom @ scijava/ scripting-renjin to submit a PR, but it wasn’t clear to me where to update the version. Assistance with the best path forward would be appreciated. Thanks.
@winfrees Updating the version of Renjin in SciJava et al. would be great. Did you try changing the version constant here? It’s just updating the <renjin-script.version> value. Does the code still build with passing tests? Does all your Renjin-related code still work? Do you think we have enough unit tests to cover it?
I tried bumping to a newer version of renjin-script-engine here:
… but had to disable a failing assertion to make the test pass.
I didn’t try yet whether the built jar file works fine in a Fiji installation, maybe someone else wants to try it with my changes?!
When running the included template script Compute_Quantile.R on the Blobs sample image, I get the following exceptions in the console:
org.renjin.eval.EvalException: Exception initializing compiled GNU R library class org.renjin.grDevices.grDevices
at org.renjin.primitives.packaging.DllInfo.initialize(DllInfo.java:141)
at org.renjin.primitives.packaging.Namespace.loadDynamicLibrary(Namespace.java:383)
at org.renjin.primitives.packaging.Namespace.importDynamicLibrary(Namespace.java:296)
at org.renjin.primitives.packaging.Namespace.initImports(Namespace.java:274)
at org.renjin.primitives.packaging.NamespaceRegistry.load(NamespaceRegistry.java:175)
at org.renjin.primitives.packaging.NamespaceRegistry.getNamespace(NamespaceRegistry.java:156)
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.Namespace.initImports(Namespace.java:211)
at org.renjin.primitives.packaging.NamespaceRegistry.load(NamespaceRegistry.java:175)
at org.renjin.primitives.packaging.NamespaceRegistry.getNamespace(NamespaceRegistry.java:156)
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.Namespace.initImports(Namespace.java:211)
at org.renjin.primitives.packaging.NamespaceRegistry.load(NamespaceRegistry.java:175)
at org.renjin.primitives.packaging.NamespaceRegistry.getNamespace(NamespaceRegistry.java:156)
at org.renjin.primitives.packaging.NamespaceRegistry.getNamespace(NamespaceRegistry.java:130)
at org.renjin.primitives.io.serialization.SessionReadContext.findNamespace(SessionReadContext.java:55)
at org.renjin.primitives.io.serialization.RDataReader.readNamespace(RDataReader.java:508)
at org.renjin.primitives.io.serialization.RDataReader.readExp(RDataReader.java:177)
at org.renjin.primitives.io.serialization.RDataReader.readTag(RDataReader.java:420)
at org.renjin.primitives.io.serialization.RDataReader.readClosure(RDataReader.java:252)
at org.renjin.primitives.io.serialization.RDataReader.readExp(RDataReader.java:185)
at org.renjin.primitives.io.serialization.RDataReader.readFile(RDataReader.java:81)
at org.renjin.packaging.LazyLoadFrame.readVersion2(LazyLoadFrame.java:85)
at org.renjin.packaging.LazyLoadFrame.load(LazyLoadFrame.java:46)
at org.renjin.primitives.packaging.FileBasedPackage.loadSymbols(FileBasedPackage.java:49)
at org.renjin.primitives.packaging.Namespace.populateNamespace(Namespace.java:174)
at org.renjin.primitives.packaging.NamespaceRegistry.load(NamespaceRegistry.java:169)
at org.renjin.primitives.packaging.NamespaceRegistry.getNamespace(NamespaceRegistry.java:156)
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)
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)
at org.renjin.script.RenjinScriptEngineFactory.getScriptEngine(RenjinScriptEngineFactory.java:110)
at org.renjin.script.RenjinScriptEngineFactory.getScriptEngine(RenjinScriptEngineFactory.java:30)
at org.scijava.script.AdaptedScriptLanguage.getScriptEngine(AdaptedScriptLanguage.java:137)
at org.scijava.script.ScriptModule.getEngine(ScriptModule.java:105)
at org.scijava.script.ScriptModule.run(ScriptModule.java:126)
at org.scijava.module.ModuleRunner.run(ModuleRunner.java:163)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:124)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:63)
at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:225)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.NoSuchMethodError: org.renjin.gcc.runtime.Ptr.setPointer(Lorg/renjin/gcc/runtime/Ptr;)V
at org.renjin.grDevices.Context.colors$$ColorDataBase$$init(Unknown Source)
at org.renjin.grDevices.Context.<init>(Unknown Source)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
at java.lang.Class.newInstance(Class.java:442)
at org.renjin.eval.Session.getSingleton(Session.java:198)
at org.renjin.eval.Context.getSingleton(Context.java:286)
at org.renjin.grDevices.Context.current(Unknown Source)
at org.renjin.grDevices.Context.get__main-devices$R_Devices(Unknown Source)
at org.renjin.grDevices.main_devices__.Rf_InitGraphics(main-devices.c:514)
at org.renjin.grDevices.init__.R_init_grDevices(init.c:140)
at org.renjin.grDevices.grDevices.R_init_grDevices(Unknown Source)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.renjin.primitives.packaging.DllInfo.initialize(DllInfo.java:137)
... 59 more
org.renjin.eval.EvalException: Exception initializing compiled GNU R library class org.renjin.graphics.graphics
at org.renjin.primitives.packaging.DllInfo.initialize(DllInfo.java:141)
at org.renjin.primitives.packaging.Namespace.loadDynamicLibrary(Namespace.java:383)
at org.renjin.primitives.packaging.Namespace.importDynamicLibrary(Namespace.java:296)
at org.renjin.primitives.packaging.Namespace.initImports(Namespace.java:274)
at org.renjin.primitives.packaging.NamespaceRegistry.load(NamespaceRegistry.java:175)
at org.renjin.primitives.packaging.NamespaceRegistry.getNamespace(NamespaceRegistry.java:156)
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.Namespace.initImports(Namespace.java:211)
at org.renjin.primitives.packaging.NamespaceRegistry.load(NamespaceRegistry.java:175)
at org.renjin.primitives.packaging.NamespaceRegistry.getNamespace(NamespaceRegistry.java:156)
at org.renjin.primitives.packaging.NamespaceRegistry.getNamespace(NamespaceRegistry.java:130)
at org.renjin.primitives.io.serialization.SessionReadContext.findNamespace(SessionReadContext.java:55)
at org.renjin.primitives.io.serialization.RDataReader.readNamespace(RDataReader.java:508)
at org.renjin.primitives.io.serialization.RDataReader.readExp(RDataReader.java:177)
at org.renjin.primitives.io.serialization.RDataReader.readTag(RDataReader.java:420)
at org.renjin.primitives.io.serialization.RDataReader.readClosure(RDataReader.java:252)
at org.renjin.primitives.io.serialization.RDataReader.readExp(RDataReader.java:185)
at org.renjin.primitives.io.serialization.RDataReader.readFile(RDataReader.java:81)
at org.renjin.packaging.LazyLoadFrame.readVersion2(LazyLoadFrame.java:85)
at org.renjin.packaging.LazyLoadFrame.load(LazyLoadFrame.java:46)
at org.renjin.primitives.packaging.FileBasedPackage.loadSymbols(FileBasedPackage.java:49)
at org.renjin.primitives.packaging.Namespace.populateNamespace(Namespace.java:174)
at org.renjin.primitives.packaging.NamespaceRegistry.load(NamespaceRegistry.java:169)
at org.renjin.primitives.packaging.NamespaceRegistry.getNamespace(NamespaceRegistry.java:156)
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$library.java:33)
at org.renjin.sexp.BuiltinFunction.apply(BuiltinFunction.java:100)
at org.renjin.primitives.special.InternalFunction.apply(InternalFunction.java:46)
at org.renjin.sexp.FunctionCall.eval(FunctionCall.java:80)
at org.renjin.eval.Context.evaluate(Context.java:282)
at org.renjin.primitives.special.BeginFunction.apply(BeginFunction.java:39)
at org.renjin.sexp.FunctionCall.eval(FunctionCall.java:80)
at org.renjin.sexp.Closure.applyPromised(Closure.java:200)
at org.renjin.sexp.Closure.apply(Closure.java:133)
at org.renjin.sexp.FunctionCall.eval(FunctionCall.java:80)
at org.renjin.eval.Context.evaluate(Context.java:282)
at org.renjin.eval.Context.evaluate(Context.java:209)
at org.renjin.eval.SessionBuilder.build(SessionBuilder.java:187)
at org.renjin.script.RenjinScriptEngineFactory.getScriptEngine(RenjinScriptEngineFactory.java:110)
at org.renjin.script.RenjinScriptEngineFactory.getScriptEngine(RenjinScriptEngineFactory.java:30)
at org.scijava.script.AdaptedScriptLanguage.getScriptEngine(AdaptedScriptLanguage.java:137)
at org.scijava.script.ScriptModule.getEngine(ScriptModule.java:105)
at org.scijava.script.ScriptModule.run(ScriptModule.java:126)
at org.scijava.module.ModuleRunner.run(ModuleRunner.java:163)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:124)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:63)
at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:225)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.NoSuchMethodError: org.renjin.gcc.runtime.BytePtr.of(I)Lorg/renjin/gcc/runtime/Ptr;
at org.renjin.graphics.init__.R_init_graphics(init.c:87)
at org.renjin.graphics.graphics.R_init_graphics(Unknown Source)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.renjin.primitives.packaging.DllInfo.initialize(DllInfo.java:137)
... 54 more
org.renjin.eval.EvalException: Exception initializing compiled GNU R library class org.renjin.stats.stats
at org.renjin.primitives.packaging.DllInfo.initialize(DllInfo.java:141)
at org.renjin.primitives.packaging.Namespace.loadDynamicLibrary(Namespace.java:383)
at org.renjin.primitives.packaging.Namespace.importDynamicLibrary(Namespace.java:296)
at org.renjin.primitives.packaging.Namespace.initImports(Namespace.java:274)
at org.renjin.primitives.packaging.NamespaceRegistry.load(NamespaceRegistry.java:175)
at org.renjin.primitives.packaging.NamespaceRegistry.getNamespace(NamespaceRegistry.java:156)
at org.renjin.primitives.packaging.NamespaceRegistry.getNamespace(NamespaceRegistry.java:130)
at org.renjin.primitives.io.serialization.SessionReadContext.findNamespace(SessionReadContext.java:55)
at org.renjin.primitives.io.serialization.RDataReader.readNamespace(RDataReader.java:508)
at org.renjin.primitives.io.serialization.RDataReader.readExp(RDataReader.java:177)
at org.renjin.primitives.io.serialization.RDataReader.readTag(RDataReader.java:420)
at org.renjin.primitives.io.serialization.RDataReader.readClosure(RDataReader.java:252)
at org.renjin.primitives.io.serialization.RDataReader.readExp(RDataReader.java:185)
at org.renjin.primitives.io.serialization.RDataReader.readFile(RDataReader.java:81)
at org.renjin.packaging.LazyLoadFrame.readVersion2(LazyLoadFrame.java:85)
at org.renjin.packaging.LazyLoadFrame.load(LazyLoadFrame.java:46)
at org.renjin.primitives.packaging.FileBasedPackage.loadSymbols(FileBasedPackage.java:49)
at org.renjin.primitives.packaging.Namespace.populateNamespace(Namespace.java:174)
at org.renjin.primitives.packaging.NamespaceRegistry.load(NamespaceRegistry.java:169)
at org.renjin.primitives.packaging.NamespaceRegistry.getNamespace(NamespaceRegistry.java:156)
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)
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)
at org.renjin.script.RenjinScriptEngineFactory.getScriptEngine(RenjinScriptEngineFactory.java:110)
at org.renjin.script.RenjinScriptEngineFactory.getScriptEngine(RenjinScriptEngineFactory.java:30)
at org.scijava.script.AdaptedScriptLanguage.getScriptEngine(AdaptedScriptLanguage.java:137)
at org.scijava.script.ScriptModule.getEngine(ScriptModule.java:105)
at org.scijava.script.ScriptModule.run(ScriptModule.java:126)
at org.scijava.module.ModuleRunner.run(ModuleRunner.java:163)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:124)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:63)
at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:225)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.NoSuchMethodError: org.renjin.gcc.runtime.Ptr.setPointer(Lorg/renjin/gcc/runtime/Ptr;)V
at org.renjin.stats.init__.ExtEntries$$clinit(init.c)
at org.renjin.stats.init__.<clinit>(init.c)
at org.renjin.stats.stats.R_init_stats(Unknown Source)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.renjin.primitives.packaging.DllInfo.initialize(DllInfo.java:137)
... 49 more
Thanks, @imagejan. Does anyone on this thread have time and interest to dig a little deeper? I’d really like to be shipping the latest version of Renjin with Fiji—but we can’t update it until more thorough testing has been done, and ideally unit tests have been fleshed out a bit in scijava/scripting-renjin.
