Multiple platform build/check report for BioC 3.20 - BUILD results for RGMQL on nebbiolo2

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"	4744
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4487
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4515
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4467
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 nebbiolo2

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: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 RGMQL

StartedAt: 2024-12-19 18:40:32 -0500 (Thu, 19 Dec 2024)

EndedAt: 2024-12-19 18:41:20 -0500 (Thu, 19 Dec 2024)

EllapsedTime: 48.1 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 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
24/12/19 18:41:17 INFO SparkContext: Running Spark version 2.2.0
24/12/19 18:41:17 WARN NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
24/12/19 18:41:17 WARN Utils: Your hostname, nebbiolo2 resolves to a loopback address: 127.0.1.1; using 155.52.47.146 instead (on interface enp175s0f1np1)
24/12/19 18:41:17 WARN Utils: Set SPARK_LOCAL_IP if you need to bind to another address
24/12/19 18:41:17 INFO SparkContext: Submitted application: GMQL-R
24/12/19 18:41:17 INFO SecurityManager: Changing view acls to: biocbuild
24/12/19 18:41:17 INFO SecurityManager: Changing modify acls to: biocbuild
24/12/19 18:41:17 INFO SecurityManager: Changing view acls groups to: 
24/12/19 18:41:17 INFO SecurityManager: Changing modify acls groups to: 
24/12/19 18:41:17 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()
24/12/19 18:41:18 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.
24/12/19 18:41:18 INFO Utils: Successfully started service 'sparkDriver' on port 34015.
24/12/19 18:41:18 INFO SparkEnv: Registering MapOutputTracker
24/12/19 18:41:18 INFO SparkEnv: Registering BlockManagerMaster
24/12/19 18:41:18 INFO BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
24/12/19 18:41:18 INFO BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
24/12/19 18:41:18 INFO DiskBlockManager: Created local directory at /tmp/blockmgr-5276c3fb-160c-4451-aca8-4b700cc20fd6
24/12/19 18:41:18 INFO MemoryStore: MemoryStore started with capacity 127.2 MB
24/12/19 18:41:18 INFO SparkEnv: Registering OutputCommitCoordinator
24/12/19 18:41:18 INFO Utils: Successfully started service 'SparkUI' on port 4040.
24/12/19 18:41:18 INFO SparkUI: Bound SparkUI to 0.0.0.0, and started at http://155.52.47.146:4040
24/12/19 18:41:18 INFO Executor: Starting executor ID driver on host localhost
24/12/19 18:41:18 INFO Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 38667.
24/12/19 18:41:18 INFO NettyBlockTransferService: Server created on 155.52.47.146:38667
24/12/19 18:41:18 INFO BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
24/12/19 18:41:18 INFO BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 155.52.47.146, 38667, None)
24/12/19 18:41:18 INFO BlockManagerMasterEndpoint: Registering block manager 155.52.47.146:38667 with 127.2 MB RAM, BlockManagerId(driver, 155.52.47.146, 38667, None)
24/12/19 18:41:18 INFO BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 155.52.47.146, 38667, None)
24/12/19 18:41:18 INFO BlockManager: Initialized BlockManager: BlockManagerId(driver, 155.52.47.146, 38667, 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