Multiple platform build/check report for BioC 3.20 - BUILD results for RGMQL on palomino8

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4746
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4493
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4517
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4469
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4394
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

BUILD results for RGMQL on palomino8

To the developers/maintainers of the RGMQL package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RGMQL.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: RGMQL

Version: 1.26.0

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

StartedAt: 2025-01-20 21:24:59 -0500 (Mon, 20 Jan 2025)

EndedAt: 2025-01-20 21:26:47 -0500 (Mon, 20 Jan 2025)

EllapsedTime: 108.9 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
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###
### 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
25/01/20 21:26:40 INFO SparkContext: Running Spark version 2.2.0
25/01/20 21:26:40 WARN NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
25/01/20 21:26:40 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.<clinit>(Shell.java:386)
	at org.apache.hadoop.util.StringUtils.<clinit>(StringUtils.java:79)
	at org.apache.hadoop.security.Groups.parseStaticMapping(Groups.java:116)
	at org.apache.hadoop.security.Groups.<init>(Groups.java:93)
	at org.apache.hadoop.security.Groups.<init>(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.<init>(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)
25/01/20 21:26:40 INFO SparkContext: Submitted application: GMQL-R
25/01/20 21:26:41 INFO SecurityManager: Changing view acls to: biocbuild
25/01/20 21:26:41 INFO SecurityManager: Changing modify acls to: biocbuild
25/01/20 21:26:41 INFO SecurityManager: Changing view acls groups to: 
25/01/20 21:26:41 INFO SecurityManager: Changing modify acls groups to: 
25/01/20 21:26:41 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()
25/01/20 21:26:41 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.
25/01/20 21:26:41 INFO Utils: Successfully started service 'sparkDriver' on port 49999.
25/01/20 21:26:41 INFO SparkEnv: Registering MapOutputTracker
25/01/20 21:26:41 INFO SparkEnv: Registering BlockManagerMaster
25/01/20 21:26:41 INFO BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
25/01/20 21:26:41 INFO BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
25/01/20 21:26:41 INFO DiskBlockManager: Created local directory at F:\biocbuild\bbs-3.20-bioc\tmp\blockmgr-428dd953-3e59-42f5-9fd5-c621ba6d4822
25/01/20 21:26:41 INFO MemoryStore: MemoryStore started with capacity 127.2 MB
25/01/20 21:26:41 INFO SparkEnv: Registering OutputCommitCoordinator
25/01/20 21:26:42 INFO Utils: Successfully started service 'SparkUI' on port 4040.
25/01/20 21:26:42 INFO SparkUI: Bound SparkUI to 0.0.0.0, and started at http://10.0.0.5:4040
25/01/20 21:26:42 INFO Executor: Starting executor ID driver on host localhost
25/01/20 21:26:42 INFO Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 50000.
25/01/20 21:26:42 INFO NettyBlockTransferService: Server created on 10.0.0.5:50000
25/01/20 21:26:42 INFO BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
25/01/20 21:26:42 INFO BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 10.0.0.5, 50000, None)
25/01/20 21:26:42 INFO BlockManagerMasterEndpoint: Registering block manager 10.0.0.5:50000 with 127.2 MB RAM, BlockManagerId(driver, 10.0.0.5, 50000, None)
25/01/20 21:26:42 INFO BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 10.0.0.5, 50000, None)
25/01/20 21:26:42 INFO BlockManager: Initialized BlockManager: BlockManagerId(driver, 10.0.0.5, 50000, 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