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

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 taishan

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results

Summary

Package: RGMQL

Version: 1.26.0

Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data RGMQL

StartedAt: 2025-01-21 02:27:38 -0000 (Tue, 21 Jan 2025)

EndedAt: 2025-01-21 02:28:43 -0000 (Tue, 21 Jan 2025)

EllapsedTime: 65.0 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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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
25/01/21 02:28:34 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-4.4.2/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
25/01/21 02:28:34 WARN NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
25/01/21 02:28:34 INFO SparkContext: Submitted application: GMQL-R
25/01/21 02:28:34 INFO SecurityManager: Changing view acls to: biocbuild
25/01/21 02:28:34 INFO SecurityManager: Changing modify acls to: biocbuild
25/01/21 02:28:34 INFO SecurityManager: Changing view acls groups to: 
25/01/21 02:28:34 INFO SecurityManager: Changing modify acls groups to: 
25/01/21 02:28:34 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()
25/01/21 02:28:35 INFO Utils: Successfully started service 'sparkDriver' on port 43835.
25/01/21 02:28:35 INFO SparkEnv: Registering MapOutputTracker
25/01/21 02:28:35 INFO SparkEnv: Registering BlockManagerMaster
25/01/21 02:28:35 INFO BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
25/01/21 02:28:35 INFO BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
25/01/21 02:28:35 INFO DiskBlockManager: Created local directory at /tmp/blockmgr-e8030751-3578-4b31-890c-8be84b62b385
25/01/21 02:28:35 INFO MemoryStore: MemoryStore started with capacity 127.2 MB
25/01/21 02:28:35 INFO SparkEnv: Registering OutputCommitCoordinator
25/01/21 02:28:35 INFO Utils: Successfully started service 'SparkUI' on port 4040.
25/01/21 02:28:35 INFO SparkUI: Bound SparkUI to 0.0.0.0, and started at http://192.168.1.35:4040
25/01/21 02:28:35 INFO Executor: Starting executor ID driver on host localhost
25/01/21 02:28:35 INFO Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 36573.
25/01/21 02:28:35 INFO NettyBlockTransferService: Server created on 192.168.1.35:36573
25/01/21 02:28:35 INFO BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
25/01/21 02:28:35 INFO BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 192.168.1.35, 36573, None)
25/01/21 02:28:35 INFO BlockManagerMasterEndpoint: Registering block manager 192.168.1.35:36573 with 127.2 MB RAM, BlockManagerId(driver, 192.168.1.35, 36573, None)
25/01/21 02:28:35 INFO BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 192.168.1.35, 36573, None)
25/01/21 02:28:35 INFO BlockManager: Initialized BlockManager: BlockManagerId(driver, 192.168.1.35, 36573, 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