I have an assay with an R transformation script. This transformation script uses labkey.saveBatch() to create a new assay batch in a second assay before creating a batch in the original assay. (The first assay contains an FK to the second assay.)

I've used a module with such a configuration on Labkey v15.1-v16.1. I recently upgraded to v16.3, skipping v16.2. Now my transformation script never completes. I've stepped through the code, and it get stuck on a BufferedReader.readLine() call here:
      at org.labkey.api.reports.ExternalScriptEngine.runProcess(ExternalScriptEngine.java:296)
      at org.labkey.api.reports.ExternalScriptEngine.eval(ExternalScriptEngine.java:109)
      at org.labkey.api.reports.RScriptEngine.eval(RScriptEngine.java:90)
      at javax.script.AbstractScriptEngine.eval(AbstractScriptEngine.java:264)
      at org.labkey.api.study.assay.DefaultDataTransformer.transformAndValidate(DefaultDataTransformer.java:137)
      at org.labkey.api.study.assay.DefaultAssayRunCreator.transform(DefaultAssayRunCreator.java:102)
      at org.labkey.api.study.assay.DefaultAssayRunCreator.saveExperimentRun(DefaultAssayRunCreator.java:288)
      at org.labkey.api.study.assay.DefaultAssayRunCreator.saveExperimentRun(DefaultAssayRunCreator.java:135)
      at org.labkey.api.study.actions.UploadWizardAction$RunStepHandler.saveExperimentRun(UploadWizardAction.java:759)
      at org.labkey.api.study.actions.UploadWizardAction$RunStepHandler.handleSuccessfulPost(UploadWizardAction.java:734)
      at org.labkey.api.study.actions.UploadWizardAction$RunStepHandler.handleStep(UploadWizardAction.java:724)
      at org.labkey.api.study.actions.UploadWizardAction.getView(UploadWizardAction.java:173)
      at org.labkey.api.study.actions.UploadWizardAction.getView(UploadWizardAction.java:99)
      at org.labkey.api.action.SimpleViewAction.handleRequest(SimpleViewAction.java:80)
      at org.labkey.api.action.BaseViewAction.handleRequest(BaseViewAction.java:177)
      at org.labkey.api.action.SpringActionController.handleRequest(SpringActionController.java:415)
      at org.labkey.api.module.DefaultModule.dispatch(DefaultModule.java:1211)
      at org.labkey.api.view.ViewServlet._service(ViewServlet.java:190)
      at org.labkey.api.view.ViewServlet.service(ViewServlet.java:124)
      at javax.servlet.http.HttpServlet.service(HttpServlet.java:727)
      at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
      at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
      at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
      at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
      at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
      at org.labkey.api.data.TransactionFilter.doFilter(TransactionFilter.java:38)
      at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
      at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
      at org.labkey.core.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:118)
      at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
      at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
      at org.labkey.api.module.ModuleLoader.doFilter(ModuleLoader.java:1144)
      at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
      at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
      at org.labkey.api.security.AuthFilter.doFilter(AuthFilter.java:206)
      at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
      at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
      at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:220)
      at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122)
      at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:501)
      at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:170)
      at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:98)
      at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:950)
      at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
      at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:408)
      at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1040)
      at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:607)
      at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:315)
      - locked <0x2c9a> (a org.apache.tomcat.util.net.SocketWrapper)
      at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
      at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
      at java.lang.Thread.run(Thread.java:745)

Attached is a minimal module for reproducing this behavior with the following steps:
1) activate module testtrans
2) create instance of assay TestTrans1
3) create instance of assay TestTrans2, the assay instance name must be 'TT2'
4) import a random text file into the TestTrans1 instance
5) Note that the import never completes

This breaks one of my modules that is in production, so if anyone has ideas on how to work around this, please let me know.

thanks,
-Will