##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/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
SLF4J: No SLF4J providers were found.
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See https://www.slf4j.org/codes.html#noProviders for further details.
SLF4J: Class path contains SLF4J bindings targeting slf4j-api versions 1.7.x or earlier.
SLF4J: Ignoring binding found at [jar:file:/usr/local/lib/python3.9/site-packages/pyspark/jars/log4j-slf4j-impl-2.17.2.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: See https://www.slf4j.org/codes.html#ignoredBindings for an explanation.
Setting default log level to "WARN".
To adjust logging level use sc.setLogLevel(newLevel). For SparkR, use setLogLevel(newLevel).

Quitting from lines 77-82 [get1] (gwas_tut.Rmd)
Error: processing vignette 'gwas_tut.Rmd' failed with diagnostics:
py4j.protocol.Py4JJavaError: An error occurred while calling z:is.hail.backend.spark.SparkBackend.apply.
<... omitted ...>a: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:469)
	at io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:503)
	at io.netty.util.concurrent.SingleThreadEventExecutor$4.run(SingleThreadEventExecutor.java:986)
	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)

See `reticulate::py_last_error()` for details
--- failed re-building ‘gwas_tut.Rmd’

--- re-building ‘large_t2t.Rmd’ using rmarkdown

Quitting from lines 69-80 [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.
<... omitted ...>a: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:469)
	at io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:503)
	at io.netty.util.concurrent.SingleThreadEventExecutor$4.run(SingleThreadEventExecutor.java:986)
	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)

See `reticulate::py_last_error()` for details
--- failed re-building ‘large_t2t.Rmd’

--- re-building ‘ukbb.Rmd’ using rmarkdown

Quitting from lines 41-46 [getukbb] (ukbb.Rmd)
Error: processing vignette 'ukbb.Rmd' failed with diagnostics:
py4j.protocol.Py4JJavaError: An error occurred while calling z:is.hail.backend.spark.SparkBackend.apply.
<... omitted ...>a: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:469)
	at io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:503)
	at io.netty.util.concurrent.SingleThreadEventExecutor$4.run(SingleThreadEventExecutor.java:986)
	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)

See `reticulate::py_last_error()` for details
--- failed re-building ‘ukbb.Rmd’

SUMMARY: processing the following files failed:
  ‘gwas_tut.Rmd’ ‘large_t2t.Rmd’ ‘ukbb.Rmd’

Error: Vignette re-building failed.
Execution halted