############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data BiocHail ### ############################################################################## ############################################################################## * checking for file ‘BiocHail/DESCRIPTION’ ... OK * preparing ‘BiocHail’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘gwas_tut.Rmd’ using rmarkdown --- finished re-building ‘gwas_tut.Rmd’ --- re-building ‘large_t2t.Rmd’ using rmarkdown 2024-07-05 21:35:51.917 WARN NativeCodeLoader:60 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable Setting default log level to "WARN". To adjust logging level use sc.setLogLevel(newLevel). For SparkR, use setLogLevel(newLevel). 2024-07-05 21:35:53.115 WARN Utils:69 - Service 'sparkDriver' could not bind on a random free port. You may check whether configuring an appropriate binding address. 2024-07-05 21:35:53.118 WARN Utils:69 - Service 'sparkDriver' could not bind on a random free port. You may check whether configuring an appropriate binding address. 2024-07-05 21:35:53.122 WARN Utils:69 - Service 'sparkDriver' could not bind on a random free port. You may check whether configuring an appropriate binding address. 2024-07-05 21:35:53.126 WARN Utils:69 - Service 'sparkDriver' could not bind on a random free port. You may check whether configuring an appropriate binding address. 2024-07-05 21:35:53.130 WARN Utils:69 - Service 'sparkDriver' could not bind on a random free port. You may check whether configuring an appropriate binding address. 2024-07-05 21:35:53.135 WARN Utils:69 - Service 'sparkDriver' could not bind on a random free port. You may check whether configuring an appropriate binding address. 2024-07-05 21:35:53.141 WARN Utils:69 - Service 'sparkDriver' could not bind on a random free port. You may check whether configuring an appropriate binding address. 2024-07-05 21:35:53.146 WARN Utils:69 - Service 'sparkDriver' could not bind on a random free port. You may check whether configuring an appropriate binding address. 2024-07-05 21:35:53.149 WARN Utils:69 - Service 'sparkDriver' could not bind on a random free port. You may check whether configuring an appropriate binding address. 2024-07-05 21:35:53.153 WARN Utils:69 - Service 'sparkDriver' could not bind on a random free port. You may check whether configuring an appropriate binding address. 2024-07-05 21:35:53.157 WARN Utils:69 - Service 'sparkDriver' could not bind on a random free port. You may check whether configuring an appropriate binding address. 2024-07-05 21:35:53.194 WARN Utils:69 - Service 'sparkDriver' could not bind on a random free port. You may check whether configuring an appropriate binding address. 2024-07-05 21:35:53.198 WARN Utils:69 - Service 'sparkDriver' could not bind on a random free port. You may check whether configuring an appropriate binding address. 2024-07-05 21:35:53.202 WARN Utils:69 - Service 'sparkDriver' could not bind on a random free port. You may check whether configuring an appropriate binding address. 2024-07-05 21:35:53.206 WARN Utils:69 - Service 'sparkDriver' could not bind on a random free port. You may check whether configuring an appropriate binding address. 2024-07-05 21:35:53.213 WARN Utils:69 - Service 'sparkDriver' could not bind on a random free port. You may check whether configuring an appropriate binding address. 2024-07-05 21:35:53.222 ERROR SparkContext:94 - Error initializing SparkContext. java.net.BindException: Cannot assign requested address: Service 'sparkDriver' failed after 16 retries (on a random free port)! Consider explicitly setting the appropriate binding address for the service 'sparkDriver' (for example spark.driver.bindAddress for SparkDriver) to the correct binding address. at java.base/sun.nio.ch.Net.bind0(Native Method) at java.base/sun.nio.ch.Net.bind(Net.java:555) at java.base/sun.nio.ch.ServerSocketChannelImpl.netBind(ServerSocketChannelImpl.java:337) at java.base/sun.nio.ch.ServerSocketChannelImpl.bind(ServerSocketChannelImpl.java:294) at io.netty.channel.socket.nio.NioServerSocketChannel.doBind(NioServerSocketChannel.java:134) at io.netty.channel.AbstractChannel$AbstractUnsafe.bind(AbstractChannel.java:562) at io.netty.channel.DefaultChannelPipeline$HeadContext.bind(DefaultChannelPipeline.java:1334) at io.netty.channel.AbstractChannelHandlerContext.invokeBind(AbstractChannelHandlerContext.java:506) at io.netty.channel.AbstractChannelHandlerContext.bind(AbstractChannelHandlerContext.java:491) at io.netty.channel.DefaultChannelPipeline.bind(DefaultChannelPipeline.java:973) at io.netty.channel.AbstractChannel.bind(AbstractChannel.java:260) at io.netty.bootstrap.AbstractBootstrap$2.run(AbstractBootstrap.java:356) at io.netty.util.concurrent.AbstractEventExecutor.safeExecute(AbstractEventExecutor.java:164) at io.netty.util.concurrent.SingleThreadEventExecutor.runAllTasks(SingleThreadEventExecutor.java:472) at io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:500) at io.netty.util.concurrent.SingleThreadEventExecutor$4.run(SingleThreadEventExecutor.java:989) at io.netty.util.internal.ThreadExecutorMap$2.run(ThreadExecutorMap.java:74) at io.netty.util.concurrent.FastThreadLocalRunnable.run(FastThreadLocalRunnable.java:30) at java.base/java.lang.Thread.run(Thread.java:833) Initializing Hail with default parameters... 2024-07-05 21:35:53.326 WARN SparkContext:69 - Another SparkContext is being constructed (or threw an exception in its constructor). This may indicate an error, since only one SparkContext should be running in this JVM (see SPARK-2243). The other SparkContext was created at: org.apache.spark.SparkContext.(SparkContext.scala:85) is.hail.backend.spark.SparkBackend$.configureAndCreateSparkContext(SparkBackend.scala:148) is.hail.backend.spark.SparkBackend$.apply(SparkBackend.scala:230) is.hail.backend.spark.SparkBackend.apply(SparkBackend.scala) java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) java.base/java.lang.reflect.Method.invoke(Method.java:568) py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244) py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:357) py4j.Gateway.invoke(Gateway.java:282) py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132) py4j.commands.CallCommand.execute(CallCommand.java:79) py4j.GatewayConnection.run(GatewayConnection.java:238) java.base/java.lang.Thread.run(Thread.java:833) 2024-07-05 21:35:53.361 WARN Utils:69 - Service 'sparkDriver' could not bind on a random free port. You may check whether configuring an appropriate binding address. 2024-07-05 21:35:53.364 WARN Utils:69 - Service 'sparkDriver' could not bind on a random free port. You may check whether configuring an appropriate binding address. 2024-07-05 21:35:53.368 WARN Utils:69 - Service 'sparkDriver' could not bind on a random free port. You may check whether configuring an appropriate binding address. 2024-07-05 21:35:53.372 WARN Utils:69 - Service 'sparkDriver' could not bind on a random free port. You may check whether configuring an appropriate binding address. 2024-07-05 21:35:53.376 WARN Utils:69 - Service 'sparkDriver' could not bind on a random free port. You may check whether configuring an appropriate binding address. 2024-07-05 21:35:53.383 WARN Utils:69 - Service 'sparkDriver' could not bind on a random free port. You may check whether configuring an appropriate binding address. 2024-07-05 21:35:53.388 WARN Utils:69 - Service 'sparkDriver' could not bind on a random free port. You may check whether configuring an appropriate binding address. 2024-07-05 21:35:53.393 WARN Utils:69 - Service 'sparkDriver' could not bind on a random free port. You may check whether configuring an appropriate binding address. 2024-07-05 21:35:53.397 WARN Utils:69 - Service 'sparkDriver' could not bind on a random free port. You may check whether configuring an appropriate binding address. 2024-07-05 21:35:53.409 WARN Utils:69 - Service 'sparkDriver' could not bind on a random free port. You may check whether configuring an appropriate binding address. 2024-07-05 21:35:53.412 WARN Utils:69 - Service 'sparkDriver' could not bind on a random free port. You may check whether configuring an appropriate binding address. 2024-07-05 21:35:53.416 WARN Utils:69 - Service 'sparkDriver' could not bind on a random free port. You may check whether configuring an appropriate binding address. 2024-07-05 21:35:53.419 WARN Utils:69 - Service 'sparkDriver' could not bind on a random free port. You may check whether configuring an appropriate binding address. 2024-07-05 21:35:53.422 WARN Utils:69 - Service 'sparkDriver' could not bind on a random free port. You may check whether configuring an appropriate binding address. 2024-07-05 21:35:53.426 WARN Utils:69 - Service 'sparkDriver' could not bind on a random free port. You may check whether configuring an appropriate binding address. 2024-07-05 21:35:53.429 WARN Utils:69 - Service 'sparkDriver' could not bind on a random free port. You may check whether configuring an appropriate binding address. 2024-07-05 21:35:53.434 ERROR SparkContext:94 - Error initializing SparkContext. java.net.BindException: Cannot assign requested address: Service 'sparkDriver' failed after 16 retries (on a random free port)! Consider explicitly setting the appropriate binding address for the service 'sparkDriver' (for example spark.driver.bindAddress for SparkDriver) to the correct binding address. at java.base/sun.nio.ch.Net.bind0(Native Method) at java.base/sun.nio.ch.Net.bind(Net.java:555) at java.base/sun.nio.ch.ServerSocketChannelImpl.netBind(ServerSocketChannelImpl.java:337) at java.base/sun.nio.ch.ServerSocketChannelImpl.bind(ServerSocketChannelImpl.java:294) at io.netty.channel.socket.nio.NioServerSocketChannel.doBind(NioServerSocketChannel.java:134) at io.netty.channel.AbstractChannel$AbstractUnsafe.bind(AbstractChannel.java:562) at io.netty.channel.DefaultChannelPipeline$HeadContext.bind(DefaultChannelPipeline.java:1334) at io.netty.channel.AbstractChannelHandlerContext.invokeBind(AbstractChannelHandlerContext.java:506) at io.netty.channel.AbstractChannelHandlerContext.bind(AbstractChannelHandlerContext.java:491) at io.netty.channel.DefaultChannelPipeline.bind(DefaultChannelPipeline.java:973) at io.netty.channel.AbstractChannel.bind(AbstractChannel.java:260) at io.netty.bootstrap.AbstractBootstrap$2.run(AbstractBootstrap.java:356) at io.netty.util.concurrent.AbstractEventExecutor.safeExecute(AbstractEventExecutor.java:164) at io.netty.util.concurrent.SingleThreadEventExecutor.runAllTasks(SingleThreadEventExecutor.java:472) at io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:500) at io.netty.util.concurrent.SingleThreadEventExecutor$4.run(SingleThreadEventExecutor.java:989) at io.netty.util.internal.ThreadExecutorMap$2.run(ThreadExecutorMap.java:74) at io.netty.util.concurrent.FastThreadLocalRunnable.run(FastThreadLocalRunnable.java:30) at java.base/java.lang.Thread.run(Thread.java:833) Quitting from lines 69-79 [do17] (large_t2t.Rmd) Error: processing vignette 'large_t2t.Rmd' failed with diagnostics: py4j.protocol.Py4JJavaError: An error occurred while calling z:is.hail.backend.spark.SparkBackend.apply. : java.net.BindException: Cannot assign requested address: Service 'sparkDriver' failed after 16 retries (on a random free port)! Consider explicitly setting the appropriate binding address for the service 'sparkDriver' (for example spark.driver.bindAddress for SparkDriver) to the correct binding address. <...truncated...>Executor.java:164) at io.netty.util.concurrent.SingleThreadEventExecutor.runAllTasks(SingleThreadEventExecutor.java:472) at io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:500) at io.netty.util.concurrent.SingleThreadEventExecutor$4.run(SingleThreadEventExecutor.java:989) at io.netty.util.internal.ThreadExecutorMap$2.run(ThreadExecutorMap.java:74) at io.netty.util.concurrent.FastThreadLocalRunnable.run(FastThreadLocalRunnable.java:30) at java.base/java.lang.Thread.run(Thread.java:833) Run `reticulate::py_last_error()` for details. --- failed re-building ‘large_t2t.Rmd’ --- re-building ‘ukbb.Rmd’ using rmarkdown --- finished re-building ‘ukbb.Rmd’ SUMMARY: processing the following file failed: ‘large_t2t.Rmd’ Error: Vignette re-building failed. Execution halted