############################################################################## ############################################################################## ### ### Running command: ### ### chmod a+r RGMQL -R && F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data RGMQL ### ############################################################################## ############################################################################## * checking for file 'RGMQL/DESCRIPTION' ... OK * preparing 'RGMQL': * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building 'RGMQL-vignette.Rmd' using rmarkdown Using Spark's default log4j profile: org/apache/spark/log4j-defaults.properties 25/01/02 21:31:07 INFO SparkContext: Running Spark version 2.2.0 25/01/02 21:31:07 WARN NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable 25/01/02 21:31:07 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:378) at org.apache.hadoop.util.Shell.getWinUtilsPath(Shell.java:393) at org.apache.hadoop.util.Shell.(Shell.java:386) at org.apache.hadoop.util.StringUtils.(StringUtils.java:79) at org.apache.hadoop.security.Groups.parseStaticMapping(Groups.java:116) at org.apache.hadoop.security.Groups.(Groups.java:93) at org.apache.hadoop.security.Groups.(Groups.java:73) at org.apache.hadoop.security.Groups.getUserToGroupsMappingService(Groups.java:293) at org.apache.hadoop.security.UserGroupInformation.initialize(UserGroupInformation.java:283) at org.apache.hadoop.security.UserGroupInformation.ensureInitialized(UserGroupInformation.java:260) at org.apache.hadoop.security.UserGroupInformation.loginUserFromSubject(UserGroupInformation.java:789) at org.apache.hadoop.security.UserGroupInformation.getLoginUser(UserGroupInformation.java:774) at org.apache.hadoop.security.UserGroupInformation.getCurrentUser(UserGroupInformation.java:647) at org.apache.spark.util.Utils$$anonfun$getCurrentUserName$1.apply(Utils.scala:2430) at org.apache.spark.util.Utils$$anonfun$getCurrentUserName$1.apply(Utils.scala:2430) at scala.Option.getOrElse(Option.scala:121) at org.apache.spark.util.Utils$.getCurrentUserName(Utils.scala:2430) at org.apache.spark.SparkContext.(SparkContext.scala:295) at org.apache.spark.SparkContext$.getOrCreate(SparkContext.scala:2509) at it.polimi.genomics.r.GMQLManager$.initGMQL(GMQLManager.scala:81) at it.polimi.genomics.r.Wrapper$.initGMQL(Wrapper.scala:59) at it.polimi.genomics.r.Wrapper.initGMQL(Wrapper.scala) at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) at java.base/java.lang.reflect.Method.invoke(Method.java:580) at RJavaTools.invokeMethod(RJavaTools.java:399) 25/01/02 21:31:08 INFO SparkContext: Submitted application: GMQL-R 25/01/02 21:31:08 INFO SecurityManager: Changing view acls to: biocbuild 25/01/02 21:31:08 INFO SecurityManager: Changing modify acls to: biocbuild 25/01/02 21:31:08 INFO SecurityManager: Changing view acls groups to: 25/01/02 21:31:08 INFO SecurityManager: Changing modify acls groups to: 25/01/02 21:31:08 INFO SecurityManager: SecurityManager: authentication disabled; ui acls disabled; users with view permissions: Set(biocbuild); groups with view permissions: Set(); users with modify permissions: Set(biocbuild); groups with modify permissions: Set() 25/01/02 21:31:08 INFO PlatformDependent: Your platform does not provide complete low-level API for accessing direct buffers reliably. Unless explicitly requested, heap buffer will always be preferred to avoid potential system unstability. 25/01/02 21:31:08 INFO Utils: Successfully started service 'sparkDriver' on port 50757. 25/01/02 21:31:08 INFO SparkEnv: Registering MapOutputTracker 25/01/02 21:31:08 INFO SparkEnv: Registering BlockManagerMaster 25/01/02 21:31:08 INFO BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information 25/01/02 21:31:08 INFO BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up 25/01/02 21:31:08 INFO DiskBlockManager: Created local directory at F:\biocbuild\bbs-3.20-bioc\tmp\blockmgr-6c2cd9c2-a144-4a52-8554-ed7469f4519f 25/01/02 21:31:08 INFO MemoryStore: MemoryStore started with capacity 127.2 MB 25/01/02 21:31:09 INFO SparkEnv: Registering OutputCommitCoordinator 25/01/02 21:31:09 INFO Utils: Successfully started service 'SparkUI' on port 4040. 25/01/02 21:31:09 INFO SparkUI: Bound SparkUI to 0.0.0.0, and started at http://10.0.0.5:4040 25/01/02 21:31:09 INFO Executor: Starting executor ID driver on host localhost 25/01/02 21:31:09 INFO Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 50759. 25/01/02 21:31:09 INFO NettyBlockTransferService: Server created on 10.0.0.5:50759 25/01/02 21:31:09 INFO BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy 25/01/02 21:31:09 INFO BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 10.0.0.5, 50759, None) 25/01/02 21:31:09 INFO BlockManagerMasterEndpoint: Registering block manager 10.0.0.5:50759 with 127.2 MB RAM, BlockManagerId(driver, 10.0.0.5, 50759, None) 25/01/02 21:31:09 INFO BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 10.0.0.5, 50759, None) 25/01/02 21:31:09 INFO BlockManager: Initialized BlockManager: BlockManagerId(driver, 10.0.0.5, 50759, None) GMQL Server is up Quitting from lines 471-473 [init with guest login] (RGMQL-vignette.Rmd) Error: processing vignette 'RGMQL-vignette.Rmd' failed with diagnostics: --- failed re-building 'RGMQL-vignette.Rmd' SUMMARY: processing the following file failed: 'RGMQL-vignette.Rmd' Error: Vignette re-building failed. Execution halted