Multiple platform build/check report for BioC 3.22 - BUILD results for RGMQL on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.5.0 beta (2025-04-02 r88102) -- "How About a Twenty-Six"	4737
palomino8	Windows Server 2022 Datacenter	x64	4.5.0 RC (2025-04-03 r88103 ucrt) -- "How About a Twenty-Six"	4524
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: 1.27.1

Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 RGMQL

StartedAt: 2025-04-08 18:57:37 -0400 (Tue, 08 Apr 2025)

EndedAt: 2025-04-08 18:58:27 -0400 (Tue, 08 Apr 2025)

EllapsedTime: 50.1 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 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
25/04/08 18:58:24 INFO SparkContext: Running Spark version 2.2.0
25/04/08 18:58:25 WARN NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
25/04/08 18:58:25 WARN Utils: Your hostname, nebbiolo2 resolves to a loopback address: 127.0.1.1; using 155.52.47.146 instead (on interface enp175s0f1np1)
25/04/08 18:58:25 WARN Utils: Set SPARK_LOCAL_IP if you need to bind to another address
25/04/08 18:58:25 INFO SparkContext: Submitted application: GMQL-R
25/04/08 18:58:25 INFO SecurityManager: Changing view acls to: biocbuild
25/04/08 18:58:25 INFO SecurityManager: Changing modify acls to: biocbuild
25/04/08 18:58:25 INFO SecurityManager: Changing view acls groups to: 
25/04/08 18:58:25 INFO SecurityManager: Changing modify acls groups to: 
25/04/08 18:58:25 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()
25/04/08 18:58:25 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.
25/04/08 18:58:25 INFO Utils: Successfully started service 'sparkDriver' on port 45077.
25/04/08 18:58:25 INFO SparkEnv: Registering MapOutputTracker
25/04/08 18:58:25 INFO SparkEnv: Registering BlockManagerMaster
25/04/08 18:58:25 INFO BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
25/04/08 18:58:25 INFO BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
25/04/08 18:58:25 INFO DiskBlockManager: Created local directory at /tmp/blockmgr-39451fd4-f318-41eb-8c93-b350f466a7eb
25/04/08 18:58:25 INFO MemoryStore: MemoryStore started with capacity 127.2 MB
25/04/08 18:58:25 INFO SparkEnv: Registering OutputCommitCoordinator
25/04/08 18:58:25 INFO Utils: Successfully started service 'SparkUI' on port 4040.
25/04/08 18:58:25 INFO SparkUI: Bound SparkUI to 0.0.0.0, and started at http://155.52.47.146:4040
25/04/08 18:58:25 INFO Executor: Starting executor ID driver on host localhost
25/04/08 18:58:25 INFO Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 43443.
25/04/08 18:58:25 INFO NettyBlockTransferService: Server created on 155.52.47.146:43443
25/04/08 18:58:25 INFO BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
25/04/08 18:58:25 INFO BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 155.52.47.146, 43443, None)
25/04/08 18:58:25 INFO BlockManagerMasterEndpoint: Registering block manager 155.52.47.146:43443 with 127.2 MB RAM, BlockManagerId(driver, 155.52.47.146, 43443, None)
25/04/08 18:58:25 INFO BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 155.52.47.146, 43443, None)
25/04/08 18:58:25 INFO BlockManager: Initialized BlockManager: BlockManagerId(driver, 155.52.47.146, 43443, 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