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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data RGMQL
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* 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
25/02/10 19:04:37 INFO SparkContext: Running Spark version 2.2.0
25/02/10 19:04:37 WARN NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
25/02/10 19:04:37 WARN Utils: Your hostname, nebbiolo1 resolves to a loopback address: 127.0.1.1; using 155.52.47.135 instead (on interface enp175s0f1np1)
25/02/10 19:04:37 WARN Utils: Set SPARK_LOCAL_IP if you need to bind to another address
25/02/10 19:04:37 INFO SparkContext: Submitted application: GMQL-R
25/02/10 19:04:37 INFO SecurityManager: Changing view acls to: biocbuild
25/02/10 19:04:37 INFO SecurityManager: Changing modify acls to: biocbuild
25/02/10 19:04:37 INFO SecurityManager: Changing view acls groups to: 
25/02/10 19:04:37 INFO SecurityManager: Changing modify acls groups to: 
25/02/10 19:04:37 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()
25/02/10 19:04:37 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.
25/02/10 19:04:37 INFO Utils: Successfully started service 'sparkDriver' on port 46391.
25/02/10 19:04:37 INFO SparkEnv: Registering MapOutputTracker
25/02/10 19:04:37 INFO SparkEnv: Registering BlockManagerMaster
25/02/10 19:04:37 INFO BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
25/02/10 19:04:37 INFO BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
25/02/10 19:04:37 INFO DiskBlockManager: Created local directory at /tmp/blockmgr-fa28fa3f-db81-483f-a138-bbb33cba22da
25/02/10 19:04:38 INFO MemoryStore: MemoryStore started with capacity 127.2 MB
25/02/10 19:04:38 INFO SparkEnv: Registering OutputCommitCoordinator
25/02/10 19:04:38 INFO Utils: Successfully started service 'SparkUI' on port 4040.
25/02/10 19:04:38 INFO SparkUI: Bound SparkUI to 0.0.0.0, and started at http://155.52.47.135:4040
25/02/10 19:04:38 INFO Executor: Starting executor ID driver on host localhost
25/02/10 19:04:38 INFO Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 45411.
25/02/10 19:04:38 INFO NettyBlockTransferService: Server created on 155.52.47.135:45411
25/02/10 19:04:38 INFO BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
25/02/10 19:04:38 INFO BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 155.52.47.135, 45411, None)
25/02/10 19:04:38 INFO BlockManagerMasterEndpoint: Registering block manager 155.52.47.135:45411 with 127.2 MB RAM, BlockManagerId(driver, 155.52.47.135, 45411, None)
25/02/10 19:04:38 INFO BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 155.52.47.135, 45411, None)
25/02/10 19:04:38 INFO BlockManager: Initialized BlockManager: BlockManagerId(driver, 155.52.47.135, 45411, 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