The upcoming 2.2.2 release was submitted to CRAN. I think there are some knows issues on Windows, but does anybody know what the following error with Netty is ?
> WARNING: Illegal reflective access by > io.netty.util.internal.PlatformDependent0$1 > (file:/home/hornik/.cache/spark/spark-2.2.2-bin-hadoop2.7/jars/netty-all-4.0.43.Final.jar) > to field java.nio.Buffer.address Thanks Shivaram ---------- Forwarded message --------- From: <lig...@statistik.tu-dortmund.de> Date: Mon, Jul 9, 2018 at 12:12 PM Subject: [CRAN-pretest-archived] CRAN submission SparkR 2.2.2 To: <shiva...@cs.berkeley.edu> Cc: <cran-submissi...@r-project.org> Dear maintainer, package SparkR_2.2.2.tar.gz does not pass the incoming checks automatically, please see the following pre-tests: Windows: <https://win-builder.r-project.org/incoming_pretest/SparkR_2.2.2_20180709_175630/Windows/00check.log> Status: 1 ERROR, 1 WARNING Debian: <https://win-builder.r-project.org/incoming_pretest/SparkR_2.2.2_20180709_175630/Debian/00check.log> Status: 1 ERROR, 2 WARNINGs Last released version's CRAN status: ERROR: 1, OK: 1 See: <https://CRAN.R-project.org/web/checks/check_results_SparkR.html> CRAN Web: <https://cran.r-project.org/package=SparkR> Please fix all problems and resubmit a fixed version via the webform. If you are not sure how to fix the problems shown, please ask for help on the R-package-devel mailing list: <https://stat.ethz.ch/mailman/listinfo/r-package-devel> If you are fairly certain the rejection is a false positive, please reply-all to this message and explain. More details are given in the directory: <https://win-builder.r-project.org/incoming_pretest/SparkR_2.2.2_20180709_175630/> The files will be removed after roughly 7 days. No strong reverse dependencies to be checked. Best regards, CRAN teams' auto-check service Flavor: r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64 Check: CRAN incoming feasibility, Result: WARNING Maintainer: 'Shivaram Venkataraman <shiva...@cs.berkeley.edu>' New submission Package was archived on CRAN Insufficient package version (submitted: 2.2.2, existing: 2.3.0) Possibly mis-spelled words in DESCRIPTION: Frontend (4:10, 5:28) CRAN repository db overrides: X-CRAN-Comment: Archived on 2018-05-01 as check problems were not corrected despite reminders. Found the following (possibly) invalid URLs: URL: http://spark.apache.org/docs/latest/api/R/mean.html From: inst/doc/sparkr-vignettes.html Status: 404 Message: Not Found Flavor: r-devel-windows-ix86+x86_64 Check: running tests for arch 'x64', Result: ERROR Running 'run-all.R' [175s] Running the tests in 'tests/run-all.R' failed. Complete output: > # > # Licensed to the Apache Software Foundation (ASF) under one or more > # contributor license agreements. See the NOTICE file distributed with > # this work for additional information regarding copyright ownership. > # The ASF licenses this file to You under the Apache License, Version 2.0 > # (the "License"); you may not use this file except in compliance with > # the License. You may obtain a copy of the License at > # > # http://www.apache.org/licenses/LICENSE-2.0 > # > # Unless required by applicable law or agreed to in writing, software > # distributed under the License is distributed on an "AS IS" BASIS, > # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. > # See the License for the specific language governing permissions and > # limitations under the License. > # > > library(testthat) > library(SparkR) Attaching package: 'SparkR' The following object is masked from 'package:testthat': describe The following objects are masked from 'package:stats': cov, filter, lag, na.omit, predict, sd, var, window The following objects are masked from 'package:base': as.data.frame, colnames, colnames<-, drop, endsWith, intersect, rank, rbind, sample, startsWith, subset, summary, transform, union > > # Turn all warnings into errors > options("warn" = 2) > > if (.Platform$OS.type == "windows") { + Sys.setenv(TZ = "GMT") + } > > # Setup global test environment > # Install Spark first to set SPARK_HOME > > # NOTE(shivaram): We set overwrite to handle any old tar.gz files or directories left behind on > # CRAN machines. For Jenkins we should already have SPARK_HOME set. > install.spark(overwrite = TRUE) Overwrite = TRUE: download and overwrite the tar fileand Spark package directory if they exist. Spark not found in the cache directory. Installation will start. MirrorUrl not provided. Looking for preferred site from apache website... Preferred mirror site found: http://mirror.dkd.de/apache/spark Downloading spark-2.2.2 for Hadoop 2.7 from: - http://mirror.dkd.de/apache/spark/spark-2.2.2/spark-2.2.2-bin-hadoop2.7.tgz trying URL 'http://mirror.dkd.de/apache/spark/spark-2.2.2/spark-2.2.2-bin-hadoop2.7.tgz' Content type 'application/x-gzip' length 200743115 bytes (191.4 MB) ================================================== downloaded 191.4 MB Installing to C:\Users\ligges\AppData\Local\Apache\Spark\Cache DONE. SPARK_HOME set to C:\Users\ligges\AppData\Local\Apache\Spark\Cache/spark-2.2.2-bin-hadoop2.7 > > sparkRDir <- file.path(Sys.getenv("SPARK_HOME"), "R") > sparkRWhitelistSQLDirs <- c("spark-warehouse", "metastore_db") > invisible(lapply(sparkRWhitelistSQLDirs, + function(x) { unlink(file.path(sparkRDir, x), recursive = TRUE, force = TRUE)})) > sparkRFilesBefore <- list.files(path = sparkRDir, all.files = TRUE) > > sparkRTestMaster <- "local[1]" > sparkRTestConfig <- list() > if (identical(Sys.getenv("NOT_CRAN"), "true")) { + sparkRTestMaster <- "" + } else { + # Disable hsperfdata on CRAN + old_java_opt <- Sys.getenv("_JAVA_OPTIONS") + Sys.setenv("_JAVA_OPTIONS" = paste("-XX:-UsePerfData", old_java_opt)) + tmpDir <- tempdir() + tmpArg <- paste0("-Djava.io.tmpdir=", tmpDir) + sparkRTestConfig <- list(spark.driver.extraJavaOptions = tmpArg, + spark.executor.extraJavaOptions = tmpArg) + } > > test_package("SparkR") Launching java with spark-submit command C:\Users\ligges\AppData\Local\Apache\Spark\Cache/spark-2.2.2-bin-hadoop2.7/bin/spark-submit2.cmd --driver-java-options "-Djava.io.tmpdir=D:\temp\RtmpABZLQj" sparkr-shell D:\temp\RtmpABZLQj\backend_port16d0838283f7e Picked up _JAVA_OPTIONS: -XX:-UsePerfData Using Spark's default log4j profile: org/apache/spark/log4j-defaults.properties Setting default log level to "WARN". To adjust logging level use sc.setLogLevel(newLevel). For SparkR, use setLogLevel(newLevel). -- 1. Error: create DataFrame from list or data.frame (@test_basic.R#21) ------ cannot open the connection 1: sparkR.session(master = sparkRTestMaster, enableHiveSupport = FALSE, sparkConfig = sparkRTestConfig) at D:/temp/Rtmp8IKu99/RLIBS_77d8215b7bce/SparkR/tests/testthat/test_basic.R:21 2: sparkR.sparkContext(master, appName, sparkHome, sparkConfigMap, sparkExecutorEnvMap, sparkJars, sparkPackages) 3: file(path, open = "rb") Launching java with spark-submit command C:\Users\ligges\AppData\Local\Apache\Spark\Cache/spark-2.2.2-bin-hadoop2.7/bin/spark-submit2.cmd --driver-java-options "-Djava.io.tmpdir=D:\temp\RtmpABZLQj" sparkr-shell D:\temp\RtmpABZLQj\backend_port16d085df97d88 Picked up _JAVA_OPTIONS: -XX:-UsePerfData Using Spark's default log4j profile: org/apache/spark/log4j-defaults.properties Setting default log level to "WARN". To adjust logging level use sc.setLogLevel(newLevel). For SparkR, use setLogLevel(newLevel). 18/07/09 18:10:43 ERROR Shell: Failed to locate the winutils binary in the hadoop binary path java.io.IOException: Could not locate executable null\bin\winutils.exe in the Hadoop binaries. at org.apache.hadoop.util.Shell.getQualifiedBinPath(Shell.java:379) at org.apache.hadoop.util.Shell.getWinUtilsPath(Shell.java:394) at org.apache.hadoop.util.Shell.<clinit>(Shell.java:387) at org.apache.hadoop.util.StringUtils.<clinit>(StringUtils.java:80) at org.apache.hadoop.security.SecurityUtil.getAuthenticationMethod(SecurityUtil.java:611) at org.apache.hadoop.security.UserGroupInformation.initialize(UserGroupInformation.java:273) at org.apache.hadoop.security.UserGroupInformation.ensureInitialized(UserGroupInformation.java:261) at org.apache.hadoop.security.UserGroupInformation.loginUserFromSubject(UserGroupInformation.java:791) at org.apache.hadoop.security.UserGroupInformation.getLoginUser(UserGroupInformation.java:761) at org.apache.hadoop.security.UserGroupInformation.getCurrentUser(UserGroupInformation.java:634) at org.apache.spark.util.Utils$$anonfun$getCurrentUserName$1.apply(Utils.scala:2427) at org.apache.spark.util.Utils$$anonfun$getCurrentUserName$1.apply(Utils.scala:2427) at scala.Option.getOrElse(Option.scala:121) at org.apache.spark.util.Utils$.getCurrentUserName(Utils.scala:2427) at org.apache.spark.SparkContext.<init>(SparkContext.scala:295) at org.apache.spark.SparkContext$.getOrCreate(SparkContext.scala:2516) at org.apache.spark.api.r.RRDD$.createSparkContext(RRDD.scala:139) at org.apache.spark.api.r.RRDD.createSparkContext(RRDD.scala) 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.apache.spark.api.r.RBackendHandler.handleMethodCall(RBackendHandler.scala:167) at org.apache.spark.api.r.RBackendHandler.channelRead0(RBackendHandler.scala:108) at org.apache.spark.api.r.RBackendHandler.channelRead0(RBackendHandler.scala:40) at io.netty.channel.SimpleChannelInboundHandler.channelRead(SimpleChannelInboundHandler.java:105) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:357) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:343) at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:336) at io.netty.handler.timeout.IdleStateHandler.channelRead(IdleStateHandler.java:287) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:357) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:343) at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:336) at io.netty.handler.codec.MessageToMessageDecoder.channelRead(MessageToMessageDecoder.java:102) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:357) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:343) at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:336) at io.netty.handler.codec.ByteToMessageDecoder.fireChannelRead(ByteToMessageDecoder.java:293) at io.netty.handler.codec.ByteToMessageDecoder.channelRead(ByteToMessageDecoder.java:267) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:357) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:343) at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:336) at io.netty.channel.DefaultChannelPipeline$HeadContext.channelRead(DefaultChannelPipeline.java:1294) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:357) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:343) at io.netty.channel.DefaultChannelPipeline.fireChannelRead(DefaultChannelPipeline.java:911) at io.netty.channel.nio.AbstractNioByteChannel$NioByteUnsafe.read(AbstractNioByteChannel.java:131) at io.netty.channel.nio.NioEventLoop.processSelectedKey(NioEventLoop.java:643) at io.netty.channel.nio.NioEventLoop.processSelectedKeysOptimized(NioEventLoop.java:566) at io.netty.channel.nio.NioEventLoop.processSelectedKeys(NioEventLoop.java:480) at io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:442) at io.netty.util.concurrent.SingleThreadEventExecutor$2.run(SingleThreadEventExecutor.java:131) at io.netty.util.concurrent.DefaultThreadFactory$DefaultRunnableDecorator.run(DefaultThreadFactory.java:144) at java.lang.Thread.run(Thread.java:748) 18/07/09 18:10:43 WARN NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable Picked up _JAVA_OPTIONS: -XX:-UsePerfData 18/07/09 18:10:54 WARN WeightedLeastSquares: regParam is zero, which might cause numerical instability and overfitting. 18/07/09 18:10:55 WARN BLAS: Failed to load implementation from: com.github.fommil.netlib.NativeSystemBLAS 18/07/09 18:10:55 WARN BLAS: Failed to load implementation from: com.github.fommil.netlib.NativeRefBLAS 18/07/09 18:10:55 WARN LAPACK: Failed to load implementation from: com.github.fommil.netlib.NativeSystemLAPACK 18/07/09 18:10:55 WARN LAPACK: Failed to load implementation from: com.github.fommil.netlib.NativeRefLAPACK 18/07/09 18:11:12 WARN WeightedLeastSquares: regParam is zero, which might cause numerical instability and overfitting. 18/07/09 18:11:14 WARN WeightedLeastSquares: regParam is zero, which might cause numerical instability and overfitting. 18/07/09 18:11:15 WARN WeightedLeastSquares: regParam is zero, which might cause numerical instability and overfitting. 18/07/09 18:11:17 WARN WeightedLeastSquares: regParam is zero, which might cause numerical instability and overfitting. 18/07/09 18:11:18 WARN WeightedLeastSquares: regParam is zero, which might cause numerical instability and overfitting. 18/07/09 18:11:19 WARN WeightedLeastSquares: regParam is zero, which might cause numerical instability and overfitting. 18/07/09 18:11:21 WARN WeightedLeastSquares: regParam is zero, which might cause numerical instability and overfitting. 18/07/09 18:11:22 WARN WeightedLeastSquares: regParam is zero, which might cause numerical instability and overfitting. 18/07/09 18:11:23 WARN WeightedLeastSquares: regParam is zero, which might cause numerical instability and overfitting. 18/07/09 18:11:25 WARN WeightedLeastSquares: regParam is zero, which might cause numerical instability and overfitting. 18/07/09 18:11:26 WARN WeightedLeastSquares: regParam is zero, which might cause numerical instability and overfitting. 18/07/09 18:11:28 WARN WeightedLeastSquares: regParam is zero, which might cause numerical instability and overfitting. 18/07/09 18:11:29 WARN WeightedLeastSquares: regParam is zero, which might cause numerical instability and overfitting. 18/07/09 18:11:46 WARN WeightedLeastSquares: regParam is zero, which might cause numerical instability and overfitting. 18/07/09 18:11:47 WARN WeightedLeastSquares: regParam is zero, which might cause numerical instability and overfitting. 18/07/09 18:11:49 WARN WeightedLeastSquares: regParam is zero, which might cause numerical instability and overfitting. 18/07/09 18:11:50 WARN WeightedLeastSquares: regParam is zero, which might cause numerical instability and overfitting. == testthat results =========================================================== OK: 6 SKIPPED: 0 FAILED: 1 1. Error: create DataFrame from list or data.frame (@test_basic.R#21) Error: testthat unit tests failed Execution halted Picked up _JAVA_OPTIONS: -XX:-UsePerfData Flavor: r-devel-linux-x86_64-debian-gcc Check: tests, Result: ERROR Running 'run-all.R' [6s/15s] Running the tests in 'tests/run-all.R' failed. Complete output: > # > # Licensed to the Apache Software Foundation (ASF) under one or more > # contributor license agreements. See the NOTICE file distributed with > # this work for additional information regarding copyright ownership. > # The ASF licenses this file to You under the Apache License, Version 2.0 > # (the "License"); you may not use this file except in compliance with > # the License. You may obtain a copy of the License at > # > # http://www.apache.org/licenses/LICENSE-2.0 > # > # Unless required by applicable law or agreed to in writing, software > # distributed under the License is distributed on an "AS IS" BASIS, > # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. > # See the License for the specific language governing permissions and > # limitations under the License. > # > > library(testthat) > library(SparkR) Attaching package: 'SparkR' The following object is masked from 'package:testthat': describe The following objects are masked from 'package:stats': cov, filter, lag, na.omit, predict, sd, var, window The following objects are masked from 'package:base': as.data.frame, colnames, colnames<-, drop, endsWith, intersect, rank, rbind, sample, startsWith, subset, summary, transform, union > > # Turn all warnings into errors > options("warn" = 2) > > if (.Platform$OS.type == "windows") { + Sys.setenv(TZ = "GMT") + } > > # Setup global test environment > # Install Spark first to set SPARK_HOME > > # NOTE(shivaram): We set overwrite to handle any old tar.gz files or directories left behind on > # CRAN machines. For Jenkins we should already have SPARK_HOME set. > install.spark(overwrite = TRUE) Overwrite = TRUE: download and overwrite the tar fileand Spark package directory if they exist. Spark not found in the cache directory. Installation will start. MirrorUrl not provided. Looking for preferred site from apache website... Preferred mirror site found: http://mirror.klaus-uwe.me/apache/spark Downloading spark-2.2.2 for Hadoop 2.7 from: - http://mirror.klaus-uwe.me/apache/spark/spark-2.2.2/spark-2.2.2-bin-hadoop2.7.tgz trying URL 'http://mirror.klaus-uwe.me/apache/spark/spark-2.2.2/spark-2.2.2-bin-hadoop2.7.tgz' Content type 'application/octet-stream' length 200743115 bytes (191.4 MB) ================================================== downloaded 191.4 MB Installing to /home/hornik/.cache/spark DONE. SPARK_HOME set to /home/hornik/.cache/spark/spark-2.2.2-bin-hadoop2.7 > > sparkRDir <- file.path(Sys.getenv("SPARK_HOME"), "R") > sparkRWhitelistSQLDirs <- c("spark-warehouse", "metastore_db") > invisible(lapply(sparkRWhitelistSQLDirs, + function(x) { unlink(file.path(sparkRDir, x), recursive = TRUE, force = TRUE)})) > sparkRFilesBefore <- list.files(path = sparkRDir, all.files = TRUE) > > sparkRTestMaster <- "local[1]" > sparkRTestConfig <- list() > if (identical(Sys.getenv("NOT_CRAN"), "true")) { + sparkRTestMaster <- "" + } else { + # Disable hsperfdata on CRAN + old_java_opt <- Sys.getenv("_JAVA_OPTIONS") + Sys.setenv("_JAVA_OPTIONS" = paste("-XX:-UsePerfData", old_java_opt)) + tmpDir <- tempdir() + tmpArg <- paste0("-Djava.io.tmpdir=", tmpDir) + sparkRTestConfig <- list(spark.driver.extraJavaOptions = tmpArg, + spark.executor.extraJavaOptions = tmpArg) + } > > test_package("SparkR") Launching java with spark-submit command /home/hornik/.cache/spark/spark-2.2.2-bin-hadoop2.7/bin/spark-submit --driver-java-options "-Djava.io.tmpdir=/tmp/Rtmpkd8Lf6" sparkr-shell /tmp/Rtmpkd8Lf6/backend_port289f65a5f5e0 Picked up _JAVA_OPTIONS: -XX:-UsePerfData Picked up _JAVA_OPTIONS: -XX:-UsePerfData Using Spark's default log4j profile: org/apache/spark/log4j-defaults.properties Setting default log level to "WARN". To adjust logging level use sc.setLogLevel(newLevel). For SparkR, use setLogLevel(newLevel). WARNING: An illegal reflective access operation has occurred WARNING: Illegal reflective access by io.netty.util.internal.PlatformDependent0$1 (file:/home/hornik/.cache/spark/spark-2.2.2-bin-hadoop2.7/jars/netty-all-4.0.43.Final.jar) to field java.nio.Buffer.address WARNING: Please consider reporting this to the maintainers of io.netty.util.internal.PlatformDependent0$1 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations WARNING: All illegal access operations will be denied in a future release 18/07/09 17:58:50 WARN NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable 18/07/09 17:58:54 ERROR RBackendHandler: count on 13 failed java.lang.reflect.InvocationTargetException at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:564) at org.apache.spark.api.r.RBackendHandler.handleMethodCall(RBackendHandler.scala:167) at org.apache.spark.api.r.RBackendHandler.channelRead0(RBackendHandler.scala:108) at org.apache.spark.api.r.RBackendHandler.channelRead0(RBackendHandler.scala:40) at io.netty.channel.SimpleChannelInboundHandler.channelRead(SimpleChannelInboundHandler.java:105) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:357) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:343) at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:336) at io.netty.handler.timeout.IdleStateHandler.channelRead(IdleStateHandler.java:287) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:357) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:343) at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:336) at io.netty.handler.codec.MessageToMessageDecoder.channelRead(MessageToMessageDecoder.java:102) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:357) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:343) at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:336) at io.netty.handler.codec.ByteToMessageDecoder.fireChannelRead(ByteToMessageDecoder.java:293) at io.netty.handler.codec.ByteToMessageDecoder.channelRead(ByteToMessageDecoder.java:267) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:357) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:343) at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:336) at io.netty.channel.DefaultChannelPipeline$HeadContext.channelRead(DefaultChannelPipeline.java:1294) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:357) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:343) at io.netty.channel.DefaultChannelPipeline.fireChannelRead(DefaultChannelPipeline.java:911) at io.netty.channel.nio.AbstractNioByteChannel$NioByteUnsafe.read(AbstractNioByteChannel.java:131) at io.netty.channel.nio.NioEventLoop.processSelectedKey(NioEventLoop.java:643) at io.netty.channel.nio.NioEventLoop.processSelectedKeysOptimized(NioEventLoop.java:566) at io.netty.channel.nio.NioEventLoop.processSelectedKeys(NioEventLoop.java:480) at io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:442) at io.netty.util.concurrent.SingleThreadEventExecutor$2.run(SingleThreadEventExecutor.java:131) at io.netty.util.concurrent.DefaultThreadFactory$DefaultRunnableDecorator.run(DefaultThreadFactory.java:144) at java.base/java.lang.Thread.run(Thread.java:844) Caused by: java.lang.IllegalArgumentException at org.apache.xbean.asm5.ClassReader.<init>(Unknown Source) at org.apache.xbean.asm5.ClassReader.<init>(Unknown Source) at org.apache.xbean.asm5.ClassReader.<init>(Unknown Source) at org.apache.spark.util.ClosureCleaner$.getClassReader(ClosureCleaner.scala:46) at org.apache.spark.util.FieldAccessFinder$$anon$3$$anonfun$visitMethodInsn$2.apply(ClosureCleaner.scala:443) at org.apache.spark.util.FieldAccessFinder$$anon$3$$anonfun$visitMethodInsn$2.apply(ClosureCleaner.scala:426) at scala.collection.TraversableLike$WithFilter$$anonfun$foreach$1.apply(TraversableLike.scala:733) at scala.collection.mutable.HashMap$$anon$1$$anonfun$foreach$2.apply(HashMap.scala:103) at scala.collection.mutable.HashMap$$anon$1$$anonfun$foreach$2.apply(HashMap.scala:103) at scala.collection.mutable.HashTable$class.foreachEntry(HashTable.scala:230) at scala.collection.mutable.HashMap.foreachEntry(HashMap.scala:40) at scala.collection.mutable.HashMap$$anon$1.foreach(HashMap.scala:103) at scala.collection.TraversableLike$WithFilter.foreach(TraversableLike.scala:732) at org.apache.spark.util.FieldAccessFinder$$anon$3.visitMethodInsn(ClosureCleaner.scala:426) at org.apache.xbean.asm5.ClassReader.a(Unknown Source) at org.apache.xbean.asm5.ClassReader.b(Unknown Source) at org.apache.xbean.asm5.ClassReader.accept(Unknown Source) at org.apache.xbean.asm5.ClassReader.accept(Unknown Source) at org.apache.spark.util.ClosureCleaner$$anonfun$org$apache$spark$util$ClosureCleaner$$clean$14.apply(ClosureCleaner.scala:257) at org.apache.spark.util.ClosureCleaner$$anonfun$org$apache$spark$util$ClosureCleaner$$clean$14.apply(ClosureCleaner.scala:256) at scala.collection.immutable.List.foreach(List.scala:381) at org.apache.spark.util.ClosureCleaner$.org$apache$spark$util$ClosureCleaner$$clean(ClosureCleaner.scala:256) at org.apache.spark.util.ClosureCleaner$.clean(ClosureCleaner.scala:156) at org.apache.spark.SparkContext.clean(SparkContext.scala:2294) at org.apache.spark.SparkContext.runJob(SparkContext.scala:2068) at org.apache.spark.SparkContext.runJob(SparkContext.scala:2094) at org.apache.spark.rdd.RDD$$anonfun$collect$1.apply(RDD.scala:936) at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151) at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112) at org.apache.spark.rdd.RDD.withScope(RDD.scala:362) at org.apache.spark.rdd.RDD.collect(RDD.scala:935) at org.apache.spark.sql.execution.SparkPlan.executeCollect(SparkPlan.scala:278) at org.apache.spark.sql.Dataset$$anonfun$count$1.apply(Dataset.scala:2439) at org.apache.spark.sql.Dataset$$anonfun$count$1.apply(Dataset.scala:2438) at org.apache.spark.sql.Dataset$$anonfun$55.apply(Dataset.scala:2846) at org.apache.spark.sql.execution.SQLExecution$.withNewExecutionId(SQLExecution.scala:65) at org.apache.spark.sql.Dataset.withAction(Dataset.scala:2845) at org.apache.spark.sql.Dataset.count(Dataset.scala:2438) ... 36 more ── 1. Error: create DataFrame from list or data.frame (@test_basic.R#26) ────── java.lang.IllegalArgumentException at org.apache.xbean.asm5.ClassReader.<init>(Unknown Source) at org.apache.xbean.asm5.ClassReader.<init>(Unknown Source) at org.apache.xbean.asm5.ClassReader.<init>(Unknown Source) at org.apache.spark.util.ClosureCleaner$.getClassReader(ClosureCleaner.scala:46) at org.apache.spark.util.FieldAccessFinder$$anon$3$$anonfun$visitMethodInsn$2.apply(ClosureCleaner.scala:443) at org.apache.spark.util.FieldAccessFinder$$anon$3$$anonfun$visitMethodInsn$2.apply(ClosureCleaner.scala:426) at scala.collection.TraversableLike$WithFilter$$anonfun$foreach$1.apply(TraversableLike.scala:733) at scala.collection.mutable.HashMap$$anon$1$$anonfun$foreach$2.apply(HashMap.scala:103) at scala.collection.mutable.HashMap$$anon$1$$anonfun$foreach$2.apply(HashMap.scala:103) at scala.collection.mutable.HashTable$class.foreachEntry(HashTable.scala:230) at scala.collection.mutable.HashMap.foreachEntry(HashMap.scala:40) at scala.collection.mutable.HashMap$$anon$1.foreach(HashMap.scala:103) at scala.collection.TraversableLike$WithFilter.foreach(TraversableLike.scala:732) at org.apache.spark.util.FieldAccessFinder$$anon$3.visitMethodInsn(ClosureCleaner.scala:426) at org.apache.xbean.asm5.ClassReader.a(Unknown Source) at org.apache.xbean.asm5.ClassReader.b(Unknown Source) at org.apache.xbean.asm5.ClassReader.accept(Unknown Source) at org.apache.xbean.asm5.ClassReader.accept(Unknown Source) at org.apache.spark.util.ClosureCleaner$$anonfun$org$apache$spark$util$ClosureCleaner$$clean$14.apply(ClosureCleaner.scala:257) at org.apache.spark.util.ClosureCleaner$$anonfun$org$apache$spark$util$ClosureCleaner$$clean$14.apply(ClosureCleaner.scala:256) at scala.collection.immutable.List.foreach(List.scala:381) at org.apache.spark.util.ClosureCleaner$.org$apache$spark$util$ClosureCleaner$$clean(ClosureCleaner.scala:256) at org.apache.spark.util.ClosureCleaner$.clean(ClosureCleaner.scala:156) at org.apache.spark.SparkContext.clean(SparkContext.scala:2294) at org.apache.spark.SparkContext.runJob(SparkContext.scala:2068) at org.apache.spark.SparkContext.runJob(SparkContext.scala:2094) at org.apache.spark.rdd.RDD$$anonfun$collect$1.apply(RDD.scala:936) at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151) at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112) at org.apache.spark.rdd.RDD.withScope(RDD.scala:362) at org.apache.spark.rdd.RDD.collect(RDD.scala:935) at org.apache.spark.sql.execution.SparkPlan.executeCollect(SparkPlan.scala:278) at org.apache.spark.sql.Dataset$$anonfun$count$1.apply(Dataset.scala:2439) at org.apache.spark.sql.Dataset$$anonfun$count$1.apply(Dataset.scala:2438) at org.apache.spark.sql.Dataset$$anonfun$55.apply(Dataset.scala:2846) at org.apache.spark.sql.execution.SQLExecution$.withNewExecutionId(SQLExecution.scala:65) at org.apache.spark.sql.Dataset.withAction(Dataset.scala:2845) at org.apache.spark.sql.Dataset.count(Dataset.scala:2438) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:564) at org.apache.spark.api.r.RBackendHandler.handleMethodCall(RBackendHandler.scala:167) at org.apache.spark.api.r.RBackendHandler.channelRead0(RBackendHandler.scala:108) at org.apache.spark.api.r.RBackendHandler.channelRead0(RBackendHandler.scala:40) at io.netty.channel.SimpleChannelInboundHandler.channelRead(SimpleChannelInboundHandler.java:105) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:357) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:343) at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:336) at io.netty.handler.timeout.IdleStateHandler.channelRead(IdleStateHandler.java:287) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:357) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:343) at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:336) at io.netty.handler.codec.MessageToMessageDecoder.channelRead(MessageToMessageDecoder.java:102) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:357) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:343) at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:336) at io.netty.handler.codec.ByteToMessageDecoder.fireChannelRead(ByteToMessageDecoder.java:293) at io.netty.handler.codec.ByteToMessageDecoder.channelRead(ByteToMessageDecoder.java:267) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:357) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:343) at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:336) at io.netty.channel.DefaultChannelPipeline$HeadContext.channelRead(DefaultChannelPipeline.java:1294) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:357) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:343) at io.netty.channel.DefaultChannelPipeline.fireChannelRead(DefaultChannelPipeline.java:911) at io.netty.channel.nio.AbstractNioByteChannel$NioByteUnsafe.read(AbstractNioByteChannel.java:131) at io.netty.channel.nio.NioEventLoop.processSelectedKey(NioEventLoop.java:643) at io.netty.channel.nio.NioEventLoop.processSelectedKeysOptimized(NioEventLoop.java:566) at io.netty.channel.nio.NioEventLoop.processSelectedKeys(NioEventLoop.java:480) at io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:442) at io.netty.util.concurrent.SingleThreadEventExecutor$2.run(SingleThreadEventExecutor.java:131) at io.netty.util.concurrent.DefaultThreadFactory$DefaultRunnableDecorator.run(DefaultThreadFactory.java:144) at java.base/java.lang.Thread.run(Thread.java:844) 1: expect_equal(count(df), i) at /srv/hornik/tmp/CRAN/SparkR.Rcheck/SparkR/tests/testthat/test_basic.R:26 2: quasi_label(enquo(object), label) 3: eval_bare(get_expr(quo), get_env(quo)) 4: count(df) 5: count(df) 6: callJMethod(x@sdf, "count") 7: invokeJava(isStatic = FALSE, objId$id, methodName, ...) 8: handleErrors(returnStatus, conn) 9: stop(readString(conn)) 18/07/09 17:58:54 ERROR RBackendHandler: fit on org.apache.spark.ml.r.GeneralizedLinearRegressionWrapper failed java.lang.reflect.InvocationTargetException at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:564) at org.apache.spark.api.r.RBackendHandler.handleMethodCall(RBackendHandler.scala:167) at org.apache.spark.api.r.RBackendHandler.channelRead0(RBackendHandler.scala:108) at org.apache.spark.api.r.RBackendHandler.channelRead0(RBackendHandler.scala:40) at io.netty.channel.SimpleChannelInboundHandler.channelRead(SimpleChannelInboundHandler.java:105) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:357) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:343) at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:336) at io.netty.handler.timeout.IdleStateHandler.channelRead(IdleStateHandler.java:287) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:357) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:343) at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:336) at io.netty.handler.codec.MessageToMessageDecoder.channelRead(MessageToMessageDecoder.java:102) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:357) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:343) at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:336) at io.netty.handler.codec.ByteToMessageDecoder.fireChannelRead(ByteToMessageDecoder.java:293) at io.netty.handler.codec.ByteToMessageDecoder.channelRead(ByteToMessageDecoder.java:267) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:357) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:343) at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:336) at io.netty.channel.DefaultChannelPipeline$HeadContext.channelRead(DefaultChannelPipeline.java:1294) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:357) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:343) at io.netty.channel.DefaultChannelPipeline.fireChannelRead(DefaultChannelPipeline.java:911) at io.netty.channel.nio.AbstractNioByteChannel$NioByteUnsafe.read(AbstractNioByteChannel.java:131) at io.netty.channel.nio.NioEventLoop.processSelectedKey(NioEventLoop.java:643) at io.netty.channel.nio.NioEventLoop.processSelectedKeysOptimized(NioEventLoop.java:566) at io.netty.channel.nio.NioEventLoop.processSelectedKeys(NioEventLoop.java:480) at io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:442) at io.netty.util.concurrent.SingleThreadEventExecutor$2.run(SingleThreadEventExecutor.java:131) at io.netty.util.concurrent.DefaultThreadFactory$DefaultRunnableDecorator.run(DefaultThreadFactory.java:144) at java.base/java.lang.Thread.run(Thread.java:844) Caused by: java.lang.IllegalArgumentException at org.apache.xbean.asm5.ClassReader.<init>(Unknown Source) at org.apache.xbean.asm5.ClassReader.<init>(Unknown Source) at org.apache.xbean.asm5.ClassReader.<init>(Unknown Source) at org.apache.spark.util.ClosureCleaner$.getClassReader(ClosureCleaner.scala:46) at org.apache.spark.util.FieldAccessFinder$$anon$3$$anonfun$visitMethodInsn$2.apply(ClosureCleaner.scala:443) at org.apache.spark.util.FieldAccessFinder$$anon$3$$anonfun$visitMethodInsn$2.apply(ClosureCleaner.scala:426) at scala.collection.TraversableLike$WithFilter$$anonfun$foreach$1.apply(TraversableLike.scala:733) at scala.collection.mutable.HashMap$$anon$1$$anonfun$foreach$2.apply(HashMap.scala:103) at scala.collection.mutable.HashMap$$anon$1$$anonfun$foreach$2.apply(HashMap.scala:103) at scala.collection.mutable.HashTable$class.foreachEntry(HashTable.scala:230) at scala.collection.mutable.HashMap.foreachEntry(HashMap.scala:40) at scala.collection.mutable.HashMap$$anon$1.foreach(HashMap.scala:103) at scala.collection.TraversableLike$WithFilter.foreach(TraversableLike.scala:732) at org.apache.spark.util.FieldAccessFinder$$anon$3.visitMethodInsn(ClosureCleaner.scala:426) at org.apache.xbean.asm5.ClassReader.a(Unknown Source) at org.apache.xbean.asm5.ClassReader.b(Unknown Source) at org.apache.xbean.asm5.ClassReader.accept(Unknown Source) at org.apache.xbean.asm5.ClassReader.accept(Unknown Source) at org.apache.spark.util.ClosureCleaner$$anonfun$org$apache$spark$util$ClosureCleaner$$clean$14.apply(ClosureCleaner.scala:257) at org.apache.spark.util.ClosureCleaner$$anonfun$org$apache$spark$util$ClosureCleaner$$clean$14.apply(ClosureCleaner.scala:256) at scala.collection.immutable.List.foreach(List.scala:381) at org.apache.spark.util.ClosureCleaner$.org$apache$spark$util$ClosureCleaner$$clean(ClosureCleaner.scala:256) at org.apache.spark.util.ClosureCleaner$.clean(ClosureCleaner.scala:156) at org.apache.spark.SparkContext.clean(SparkContext.scala:2294) at org.apache.spark.SparkContext.runJob(SparkContext.scala:2068) at org.apache.spark.SparkContext.runJob(SparkContext.scala:2094) at org.apache.spark.rdd.RDD$$anonfun$collect$1.apply(RDD.scala:936) at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151) at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112) at org.apache.spark.rdd.RDD.withScope(RDD.scala:362) at org.apache.spark.rdd.RDD.collect(RDD.scala:935) at org.apache.spark.rdd.PairRDDFunctions$$anonfun$countByKey$1.apply(PairRDDFunctions.scala:373) at org.apache.spark.rdd.PairRDDFunctions$$anonfun$countByKey$1.apply(PairRDDFunctions.scala:373) at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151) at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112) at org.apache.spark.rdd.RDD.withScope(RDD.scala:362) at org.apache.spark.rdd.PairRDDFunctions.countByKey(PairRDDFunctions.scala:372) at org.apache.spark.rdd.RDD$$anonfun$countByValue$1.apply(RDD.scala:1204) at org.apache.spark.rdd.RDD$$anonfun$countByValue$1.apply(RDD.scala:1204) at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151) at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112) at org.apache.spark.rdd.RDD.withScope(RDD.scala:362) at org.apache.spark.rdd.RDD.countByValue(RDD.scala:1203) at org.apache.spark.ml.feature.StringIndexer.fit(StringIndexer.scala:113) at org.apache.spark.ml.feature.StringIndexer.fit(StringIndexer.scala:88) at org.apache.spark.ml.Pipeline$$anonfun$fit$2.apply(Pipeline.scala:153) at org.apache.spark.ml.Pipeline$$anonfun$fit$2.apply(Pipeline.scala:149) at scala.collection.Iterator$class.foreach(Iterator.scala:893) at scala.collection.AbstractIterator.foreach(Iterator.scala:1336) at scala.collection.IterableViewLike$Transformed$class.foreach(IterableViewLike.scala:44) at scala.collection.SeqViewLike$AbstractTransformed.foreach(SeqViewLike.scala:37) at org.apache.spark.ml.Pipeline.fit(Pipeline.scala:149) at org.apache.spark.ml.feature.RFormula.fit(RFormula.scala:198) at org.apache.spark.ml.r.GeneralizedLinearRegressionWrapper$.fit(GeneralizedLinearRegressionWrapper.scala:81) at org.apache.spark.ml.r.GeneralizedLinearRegressionWrapper.fit(GeneralizedLinearRegressionWrapper.scala) ... 36 more ── 2. Error: spark.glm and predict (@test_basic.R#58) ───────────────────────── java.lang.IllegalArgumentException at org.apache.xbean.asm5.ClassReader.<init>(Unknown Source) at org.apache.xbean.asm5.ClassReader.<init>(Unknown Source) at org.apache.xbean.asm5.ClassReader.<init>(Unknown Source) at org.apache.spark.util.ClosureCleaner$.getClassReader(ClosureCleaner.scala:46) at org.apache.spark.util.FieldAccessFinder$$anon$3$$anonfun$visitMethodInsn$2.apply(ClosureCleaner.scala:443) at org.apache.spark.util.FieldAccessFinder$$anon$3$$anonfun$visitMethodInsn$2.apply(ClosureCleaner.scala:426) at scala.collection.TraversableLike$WithFilter$$anonfun$foreach$1.apply(TraversableLike.scala:733) at scala.collection.mutable.HashMap$$anon$1$$anonfun$foreach$2.apply(HashMap.scala:103) at scala.collection.mutable.HashMap$$anon$1$$anonfun$foreach$2.apply(HashMap.scala:103) at scala.collection.mutable.HashTable$class.foreachEntry(HashTable.scala:230) at scala.collection.mutable.HashMap.foreachEntry(HashMap.scala:40) at scala.collection.mutable.HashMap$$anon$1.foreach(HashMap.scala:103) at scala.collection.TraversableLike$WithFilter.foreach(TraversableLike.scala:732) at org.apache.spark.util.FieldAccessFinder$$anon$3.visitMethodInsn(ClosureCleaner.scala:426) at org.apache.xbean.asm5.ClassReader.a(Unknown Source) at org.apache.xbean.asm5.ClassReader.b(Unknown Source) at org.apache.xbean.asm5.ClassReader.accept(Unknown Source) at org.apache.xbean.asm5.ClassReader.accept(Unknown Source) at org.apache.spark.util.ClosureCleaner$$anonfun$org$apache$spark$util$ClosureCleaner$$clean$14.apply(ClosureCleaner.scala:257) at org.apache.spark.util.ClosureCleaner$$anonfun$org$apache$spark$util$ClosureCleaner$$clean$14.apply(ClosureCleaner.scala:256) at scala.collection.immutable.List.foreach(List.scala:381) at org.apache.spark.util.ClosureCleaner$.org$apache$spark$util$ClosureCleaner$$clean(ClosureCleaner.scala:256) at org.apache.spark.util.ClosureCleaner$.clean(ClosureCleaner.scala:156) at org.apache.spark.SparkContext.clean(SparkContext.scala:2294) at org.apache.spark.SparkContext.runJob(SparkContext.scala:2068) at org.apache.spark.SparkContext.runJob(SparkContext.scala:2094) at org.apache.spark.rdd.RDD$$anonfun$collect$1.apply(RDD.scala:936) at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151) at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112) at org.apache.spark.rdd.RDD.withScope(RDD.scala:362) at org.apache.spark.rdd.RDD.collect(RDD.scala:935) at org.apache.spark.rdd.PairRDDFunctions$$anonfun$countByKey$1.apply(PairRDDFunctions.scala:373) at org.apache.spark.rdd.PairRDDFunctions$$anonfun$countByKey$1.apply(PairRDDFunctions.scala:373) at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151) at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112) at org.apache.spark.rdd.RDD.withScope(RDD.scala:362) at org.apache.spark.rdd.PairRDDFunctions.countByKey(PairRDDFunctions.scala:372) at org.apache.spark.rdd.RDD$$anonfun$countByValue$1.apply(RDD.scala:1204) at org.apache.spark.rdd.RDD$$anonfun$countByValue$1.apply(RDD.scala:1204) at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151) at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112) at org.apache.spark.rdd.RDD.withScope(RDD.scala:362) at org.apache.spark.rdd.RDD.countByValue(RDD.scala:1203) at org.apache.spark.ml.feature.StringIndexer.fit(StringIndexer.scala:113) at org.apache.spark.ml.feature.StringIndexer.fit(StringIndexer.scala:88) at org.apache.spark.ml.Pipeline$$anonfun$fit$2.apply(Pipeline.scala:153) at org.apache.spark.ml.Pipeline$$anonfun$fit$2.apply(Pipeline.scala:149) at scala.collection.Iterator$class.foreach(Iterator.scala:893) at scala.collection.AbstractIterator.foreach(Iterator.scala:1336) at scala.collection.IterableViewLike$Transformed$class.foreach(IterableViewLike.scala:44) at scala.collection.SeqViewLike$AbstractTransformed.foreach(SeqViewLike.scala:37) at org.apache.spark.ml.Pipeline.fit(Pipeline.scala:149) at org.apache.spark.ml.feature.RFormula.fit(RFormula.scala:198) at org.apache.spark.ml.r.GeneralizedLinearRegressionWrapper$.fit(GeneralizedLinearRegressionWrapper.scala:81) at org.apache.spark.ml.r.GeneralizedLinearRegressionWrapper.fit(GeneralizedLinearRegressionWrapper.scala) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:564) at org.apache.spark.api.r.RBackendHandler.handleMethodCall(RBackendHandler.scala:167) at org.apache.spark.api.r.RBackendHandler.channelRead0(RBackendHandler.scala:108) at org.apache.spark.api.r.RBackendHandler.channelRead0(RBackendHandler.scala:40) at io.netty.channel.SimpleChannelInboundHandler.channelRead(SimpleChannelInboundHandler.java:105) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:357) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:343) at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:336) at io.netty.handler.timeout.IdleStateHandler.channelRead(IdleStateHandler.java:287) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:357) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:343) at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:336) at io.netty.handler.codec.MessageToMessageDecoder.channelRead(MessageToMessageDecoder.java:102) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:357) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:343) at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:336) at io.netty.handler.codec.ByteToMessageDecoder.fireChannelRead(ByteToMessageDecoder.java:293) at io.netty.handler.codec.ByteToMessageDecoder.channelRead(ByteToMessageDecoder.java:267) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:357) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:343) at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:336) at io.netty.channel.DefaultChannelPipeline$HeadContext.channelRead(DefaultChannelPipeline.java:1294) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:357) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:343) at io.netty.channel.DefaultChannelPipeline.fireChannelRead(DefaultChannelPipeline.java:911) at io.netty.channel.nio.AbstractNioByteChannel$NioByteUnsafe.read(AbstractNioByteChannel.java:131) at io.netty.channel.nio.NioEventLoop.processSelectedKey(NioEventLoop.java:643) at io.netty.channel.nio.NioEventLoop.processSelectedKeysOptimized(NioEventLoop.java:566) at io.netty.channel.nio.NioEventLoop.processSelectedKeys(NioEventLoop.java:480) at io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:442) at io.netty.util.concurrent.SingleThreadEventExecutor$2.run(SingleThreadEventExecutor.java:131) at io.netty.util.concurrent.DefaultThreadFactory$DefaultRunnableDecorator.run(DefaultThreadFactory.java:144) at java.base/java.lang.Thread.run(Thread.java:844) 1: spark.glm(training, Sepal_Width ~ Sepal_Length + Species) at /srv/hornik/tmp/CRAN/SparkR.Rcheck/SparkR/tests/testthat/test_basic.R:58 2: spark.glm(training, Sepal_Width ~ Sepal_Length + Species) 3: .local(data, formula, ...) 4: callJStatic("org.apache.spark.ml.r.GeneralizedLinearRegressionWrapper", "fit", formula, data@sdf, tolower(family$family), family$link, tol, as.integer(maxIter), weightCol, regParam, as.double(var.power), as.double(link.power)) 5: invokeJava(isStatic = TRUE, className, methodName, ...) 6: handleErrors(returnStatus, conn) 7: stop(readString(conn)) ══ testthat results ═══════════════════════════════════════════════════════════ OK: 0 SKIPPED: 0 FAILED: 2 1. Error: create DataFrame from list or data.frame (@test_basic.R#26) 2. Error: spark.glm and predict (@test_basic.R#58) Error: testthat unit tests failed Execution halted Flavor: r-devel-linux-x86_64-debian-gcc Check: re-building of vignette outputs, Result: WARNING Error in re-building vignettes: ... Attaching package: 'SparkR' The following objects are masked from 'package:stats': cov, filter, lag, na.omit, predict, sd, var, window The following objects are masked from 'package:base': as.data.frame, colnames, colnames<-, drop, endsWith, intersect, rank, rbind, sample, startsWith, subset, summary, transform, union Picked up _JAVA_OPTIONS: -XX:-UsePerfData Picked up _JAVA_OPTIONS: -XX:-UsePerfData Using Spark's default log4j profile: org/apache/spark/log4j-defaults.properties Setting default log level to "WARN". To adjust logging level use sc.setLogLevel(newLevel). For SparkR, use setLogLevel(newLevel). WARNING: An illegal reflective access operation has occurred WARNING: Illegal reflective access by io.netty.util.internal.PlatformDependent0$1 (file:/home/hornik/.cache/spark/spark-2.2.2-bin-hadoop2.7/jars/netty-all-4.0.43.Final.jar) to field java.nio.Buffer.address WARNING: Please consider reporting this to the maintainers of io.netty.util.internal.PlatformDependent0$1 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations WARNING: All illegal access operations will be denied in a future release 18/07/09 17:58:59 WARN NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable 18/07/09 17:59:07 ERROR RBackendHandler: dfToCols on org.apache.spark.sql.api.r.SQLUtils failed java.lang.reflect.InvocationTargetException at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:564) at org.apache.spark.api.r.RBackendHandler.handleMethodCall(RBackendHandler.scala:167) at org.apache.spark.api.r.RBackendHandler.channelRead0(RBackendHandler.scala:108) at org.apache.spark.api.r.RBackendHandler.channelRead0(RBackendHandler.scala:40) at io.netty.channel.SimpleChannelInboundHandler.channelRead(SimpleChannelInboundHandler.java:105) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:357) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:343) at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:336) at io.netty.handler.timeout.IdleStateHandler.channelRead(IdleStateHandler.java:287) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:357) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:343) at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:336) at io.netty.handler.codec.MessageToMessageDecoder.channelRead(MessageToMessageDecoder.java:102) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:357) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:343) at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:336) at io.netty.handler.codec.ByteToMessageDecoder.fireChannelRead(ByteToMessageDecoder.java:293) at io.netty.handler.codec.ByteToMessageDecoder.channelRead(ByteToMessageDecoder.java:267) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:357) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:343) at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:336) at io.netty.channel.DefaultChannelPipeline$HeadContext.channelRead(DefaultChannelPipeline.java:1294) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:357) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:343) at io.netty.channel.DefaultChannelPipeline.fireChannelRead(DefaultChannelPipeline.java:911) at io.netty.channel.nio.AbstractNioByteChannel$NioByteUnsafe.read(AbstractNioByteChannel.java:131) at io.netty.channel.nio.NioEventLoop.processSelectedKey(NioEventLoop.java:643) at io.netty.channel.nio.NioEventLoop.processSelectedKeysOptimized(NioEventLoop.java:566) at io.netty.channel.nio.NioEventLoop.processSelectedKeys(NioEventLoop.java:480) at io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:442) at io.netty.util.concurrent.SingleThreadEventExecutor$2.run(SingleThreadEventExecutor.java:131) at io.netty.util.concurrent.DefaultThreadFactory$DefaultRunnableDecorator.run(DefaultThreadFactory.java:144) at java.base/java.lang.Thread.run(Thread.java:844) Caused by: java.lang.IllegalArgumentException at org.apache.xbean.asm5.ClassReader.<init>(Unknown Source) at org.apache.xbean.asm5.ClassReader.<init>(Unknown Source) at org.apache.xbean.asm5.ClassReader.<init>(Unknown Source) at org.apache.spark.util.ClosureCleaner$.getClassReader(ClosureCleaner.scala:46) at org.apache.spark.util.FieldAccessFinder$$anon$3$$anonfun$visitMethodInsn$2.apply(ClosureCleaner.scala:443) at org.apache.spark.util.FieldAccessFinder$$anon$3$$anonfun$visitMethodInsn$2.apply(ClosureCleaner.scala:426) at scala.collection.TraversableLike$WithFilter$$anonfun$foreach$1.apply(TraversableLike.scala:733) at scala.collection.mutable.HashMap$$anon$1$$anonfun$foreach$2.apply(HashMap.scala:103) at scala.collection.mutable.HashMap$$anon$1$$anonfun$foreach$2.apply(HashMap.scala:103) at scala.collection.mutable.HashTable$class.foreachEntry(HashTable.scala:230) at scala.collection.mutable.HashMap.foreachEntry(HashMap.scala:40) at scala.collection.mutable.HashMap$$anon$1.foreach(HashMap.scala:103) at scala.collection.TraversableLike$WithFilter.foreach(TraversableLike.scala:732) at org.apache.spark.util.FieldAccessFinder$$anon$3.visitMethodInsn(ClosureCleaner.scala:426) at org.apache.xbean.asm5.ClassReader.a(Unknown Source) at org.apache.xbean.asm5.ClassReader.b(Unknown Source) at org.apache.xbean.asm5.ClassReader.accept(Unknown Source) at org.apache.xbean.asm5.ClassReader.accept(Unknown Source) at org.apache.spark.util.ClosureCleaner$$anonfun$org$apache$spark$util$ClosureCleaner$$clean$14.apply(ClosureCleaner.scala:257) at org.apache.spark.util.ClosureCleaner$$anonfun$org$apache$spark$util$ClosureCleaner$$clean$14.apply(ClosureCleaner.scala:256) at scala.collection.immutable.List.foreach(List.scala:381) at org.apache.spark.util.ClosureCleaner$.org$apache$spark$util$ClosureCleaner$$clean(ClosureCleaner.scala:256) at org.apache.spark.util.ClosureCleaner$.clean(ClosureCleaner.scala:156) at org.apache.spark.SparkContext.clean(SparkContext.scala:2294) at org.apache.spark.SparkContext.runJob(SparkContext.scala:2068) at org.apache.spark.SparkContext.runJob(SparkContext.scala:2094) at org.apache.spark.rdd.RDD$$anonfun$collect$1.apply(RDD.scala:936) at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151) at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112) at org.apache.spark.rdd.RDD.withScope(RDD.scala:362) at org.apache.spark.rdd.RDD.collect(RDD.scala:935) at org.apache.spark.sql.execution.SparkPlan.executeCollect(SparkPlan.scala:278) at org.apache.spark.sql.Dataset.org$apache$spark$sql$Dataset$$collectFromPlan(Dataset.scala:2865) at org.apache.spark.sql.Dataset$$anonfun$collect$1.apply(Dataset.scala:2391) at org.apache.spark.sql.Dataset$$anonfun$collect$1.apply(Dataset.scala:2391) at org.apache.spark.sql.Dataset$$anonfun$55.apply(Dataset.scala:2846) at org.apache.spark.sql.execution.SQLExecution$.withNewExecutionId(SQLExecution.scala:65) at org.apache.spark.sql.Dataset.withAction(Dataset.scala:2845) at org.apache.spark.sql.Dataset.collect(Dataset.scala:2391) at org.apache.spark.sql.api.r.SQLUtils$.dfToCols(SQLUtils.scala:212) at org.apache.spark.sql.api.r.SQLUtils.dfToCols(SQLUtils.scala) ... 36 more Quitting from lines 102-104 (sparkr-vignettes.Rmd) Error: processing vignette 'sparkr-vignettes.Rmd' failed with diagnostics: java.lang.IllegalArgumentException at org.apache.xbean.asm5.ClassReader.<init>(Unknown Source) at org.apache.xbean.asm5.ClassReader.<init>(Unknown Source) at org.apache.xbean.asm5.ClassReader.<init>(Unknown Source) at org.apache.spark.util.ClosureCleaner$.getClassReader(ClosureCleaner.scala:46) at org.apache.spark.util.FieldAccessFinder$$anon$3$$anonfun$visitMethodInsn$2.apply(ClosureCleaner.scala:443) at org.apache.spark.util.FieldAccessFinder$$anon$3$$anonfun$visitMethodInsn$2.apply(ClosureCleaner.scala:426) at scala.collection.TraversableLike$WithFilter$$anonfun$foreach$1.apply(TraversableLike.scala:733) at scala.collection.mutable.HashMap$$anon$1$$anonfun$foreach$2.apply(HashMap.scala:103) at scala.collection.mutable.HashMap$$anon$1$$anonfun$foreach$2.apply(HashMap.scala:103) at scala.collection.mutable.HashTable$class.foreachEntry(HashTable.scala:230) at scala.collection.mutable.HashMap.fore Execution halted --------------------------------------------------------------------- To unsubscribe e-mail: 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