Back to Multiple platform build/check report for BioC 3.19:   simplified   long
A[B]CDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2024-03-28 11:40:21 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4708
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4446
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4471
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 4426
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 181/2270HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocHail 1.3.0  (landing page)
Vincent Carey
Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/BiocHail
git_branch: devel
git_last_commit: 64b3d77
git_last_commit_date: 2023-10-24 11:48:54 -0400 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64... NOT SUPPORTED ...
lconwaymacOS 12.7.1 Monterey / x86_64... NOT SUPPORTED ...
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    ERROR  skipped

BUILD results for BiocHail on kunpeng2


To the developers/maintainers of the BiocHail package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BiocHail.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results

Summary

Package: BiocHail
Version: 1.3.0
Command: /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD build --keep-empty-dirs --no-resave-data BiocHail
StartedAt: 2024-03-27 21:03:42 -0000 (Wed, 27 Mar 2024)
EndedAt: 2024-03-27 21:04:12 -0000 (Wed, 27 Mar 2024)
EllapsedTime: 30.6 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.4-devel-2024.03.20/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
2024-03-27 21:04:09.862 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).
2024-03-27 21:04:11.020 WARN  Utils:69 - Service 'sparkDriver' could not bind on a random free port. You may check whether configuring an appropriate binding address.
2024-03-27 21:04:11.024 WARN  Utils:69 - Service 'sparkDriver' could not bind on a random free port. You may check whether configuring an appropriate binding address.
2024-03-27 21:04:11.027 WARN  Utils:69 - Service 'sparkDriver' could not bind on a random free port. You may check whether configuring an appropriate binding address.
2024-03-27 21:04:11.031 WARN  Utils:69 - Service 'sparkDriver' could not bind on a random free port. You may check whether configuring an appropriate binding address.
2024-03-27 21:04:11.035 WARN  Utils:69 - Service 'sparkDriver' could not bind on a random free port. You may check whether configuring an appropriate binding address.
2024-03-27 21:04:11.039 WARN  Utils:69 - Service 'sparkDriver' could not bind on a random free port. You may check whether configuring an appropriate binding address.
2024-03-27 21:04:11.044 WARN  Utils:69 - Service 'sparkDriver' could not bind on a random free port. You may check whether configuring an appropriate binding address.
2024-03-27 21:04:11.049 WARN  Utils:69 - Service 'sparkDriver' could not bind on a random free port. You may check whether configuring an appropriate binding address.
2024-03-27 21:04:11.053 WARN  Utils:69 - Service 'sparkDriver' could not bind on a random free port. You may check whether configuring an appropriate binding address.
2024-03-27 21:04:11.057 WARN  Utils:69 - Service 'sparkDriver' could not bind on a random free port. You may check whether configuring an appropriate binding address.
2024-03-27 21:04:11.061 WARN  Utils:69 - Service 'sparkDriver' could not bind on a random free port. You may check whether configuring an appropriate binding address.
2024-03-27 21:04:11.107 WARN  Utils:69 - Service 'sparkDriver' could not bind on a random free port. You may check whether configuring an appropriate binding address.
2024-03-27 21:04:11.111 WARN  Utils:69 - Service 'sparkDriver' could not bind on a random free port. You may check whether configuring an appropriate binding address.
2024-03-27 21:04:11.115 WARN  Utils:69 - Service 'sparkDriver' could not bind on a random free port. You may check whether configuring an appropriate binding address.
2024-03-27 21:04:11.119 WARN  Utils:69 - Service 'sparkDriver' could not bind on a random free port. You may check whether configuring an appropriate binding address.
2024-03-27 21:04:11.126 WARN  Utils:69 - Service 'sparkDriver' could not bind on a random free port. You may check whether configuring an appropriate binding address.
2024-03-27 21:04:11.136 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$2.run(ThreadExecutorMap.java:74)
	at io.netty.util.concurrent.FastThreadLocalRunnable.run(FastThreadLocalRunnable.java:30)
	at java.base/java.lang.Thread.run(Thread.java:833)
Initializing Hail with default parameters...
2024-03-27 21:04:11.200 WARN  SparkContext:69 - Another SparkContext is being constructed (or threw an exception in its constructor). This may indicate an error, since only one SparkContext should be running in this JVM (see SPARK-2243). The other SparkContext was created at:
org.apache.spark.SparkContext.<init>(SparkContext.scala:85)
is.hail.backend.spark.SparkBackend$.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)
2024-03-27 21:04:11.235 WARN  Utils:69 - Service 'sparkDriver' could not bind on a random free port. You may check whether configuring an appropriate binding address.
2024-03-27 21:04:11.239 WARN  Utils:69 - Service 'sparkDriver' could not bind on a random free port. You may check whether configuring an appropriate binding address.
2024-03-27 21:04:11.244 WARN  Utils:69 - Service 'sparkDriver' could not bind on a random free port. You may check whether configuring an appropriate binding address.
2024-03-27 21:04:11.248 WARN  Utils:69 - Service 'sparkDriver' could not bind on a random free port. You may check whether configuring an appropriate binding address.
2024-03-27 21:04:11.252 WARN  Utils:69 - Service 'sparkDriver' could not bind on a random free port. You may check whether configuring an appropriate binding address.
2024-03-27 21:04:11.256 WARN  Utils:69 - Service 'sparkDriver' could not bind on a random free port. You may check whether configuring an appropriate binding address.
2024-03-27 21:04:11.260 WARN  Utils:69 - Service 'sparkDriver' could not bind on a random free port. You may check whether configuring an appropriate binding address.
2024-03-27 21:04:11.266 WARN  Utils:69 - Service 'sparkDriver' could not bind on a random free port. You may check whether configuring an appropriate binding address.
2024-03-27 21:04:11.271 WARN  Utils:69 - Service 'sparkDriver' could not bind on a random free port. You may check whether configuring an appropriate binding address.
2024-03-27 21:04:11.283 WARN  Utils:69 - Service 'sparkDriver' could not bind on a random free port. You may check whether configuring an appropriate binding address.
2024-03-27 21:04:11.290 WARN  Utils:69 - Service 'sparkDriver' could not bind on a random free port. You may check whether configuring an appropriate binding address.
2024-03-27 21:04:11.294 WARN  Utils:69 - Service 'sparkDriver' could not bind on a random free port. You may check whether configuring an appropriate binding address.
2024-03-27 21:04:11.298 WARN  Utils:69 - Service 'sparkDriver' could not bind on a random free port. You may check whether configuring an appropriate binding address.
2024-03-27 21:04:11.302 WARN  Utils:69 - Service 'sparkDriver' could not bind on a random free port. You may check whether configuring an appropriate binding address.
2024-03-27 21:04:11.306 WARN  Utils:69 - Service 'sparkDriver' could not bind on a random free port. You may check whether configuring an appropriate binding address.
2024-03-27 21:04:11.309 WARN  Utils:69 - Service 'sparkDriver' could not bind on a random free port. You may check whether configuring an appropriate binding address.
2024-03-27 21:04:11.314 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