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### Running command:
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###   /home/biocbuild/R/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
25/05/23 03:36:50 INFO SparkContext: Running Spark version 2.2.0
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by org.apache.hadoop.security.authentication.util.KerberosUtil (file:/home/biocbuild/R/R-devel_2025-02-19/site-library/RGMQLlib/extdata/java/GMQL.jar) to method sun.security.krb5.Config.getInstance()
WARNING: Please consider reporting this to the maintainers of org.apache.hadoop.security.authentication.util.KerberosUtil
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
25/05/23 03:36:51 WARN NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
25/05/23 03:36:51 INFO SparkContext: Submitted application: GMQL-R
25/05/23 03:36:51 INFO SecurityManager: Changing view acls to: biocbuild
25/05/23 03:36:51 INFO SecurityManager: Changing modify acls to: biocbuild
25/05/23 03:36:51 INFO SecurityManager: Changing view acls groups to: 
25/05/23 03:36:51 INFO SecurityManager: Changing modify acls groups to: 
25/05/23 03:36:51 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()
25/05/23 03:36:51 INFO Utils: Successfully started service 'sparkDriver' on port 36741.
25/05/23 03:36:51 INFO SparkEnv: Registering MapOutputTracker
25/05/23 03:36:51 INFO SparkEnv: Registering BlockManagerMaster
25/05/23 03:36:51 INFO BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
25/05/23 03:36:51 INFO BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
25/05/23 03:36:52 INFO DiskBlockManager: Created local directory at /tmp/blockmgr-22f99acc-ff3c-4c67-920d-94f967d8482b
25/05/23 03:36:52 INFO MemoryStore: MemoryStore started with capacity 127.2 MB
25/05/23 03:36:52 INFO SparkEnv: Registering OutputCommitCoordinator
25/05/23 03:36:52 INFO Utils: Successfully started service 'SparkUI' on port 4040.
25/05/23 03:36:52 INFO SparkUI: Bound SparkUI to 0.0.0.0, and started at http://192.168.0.231:4040
25/05/23 03:36:52 INFO Executor: Starting executor ID driver on host localhost
25/05/23 03:36:52 INFO Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 36267.
25/05/23 03:36:52 INFO NettyBlockTransferService: Server created on 192.168.0.231:36267
25/05/23 03:36:52 INFO BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
25/05/23 03:36:52 INFO BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 192.168.0.231, 36267, None)
25/05/23 03:36:52 INFO BlockManagerMasterEndpoint: Registering block manager 192.168.0.231:36267 with 127.2 MB RAM, BlockManagerId(driver, 192.168.0.231, 36267, None)
25/05/23 03:36:52 INFO BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 192.168.0.231, 36267, None)
25/05/23 03:36:52 INFO BlockManager: Initialized BlockManager: BlockManagerId(driver, 192.168.0.231, 36267, None)
GMQL Server is up

Quitting from RGMQL-vignette.Rmd:470-473 [init with guest login]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `login_gmql()`:
---
Backtrace:
    ▆
 1. └─RGMQL::login_gmql(test_url)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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