| Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-09-01 11:43 -0400 (Mon, 01 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4606 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4547 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4579 |
| 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 | ||||
| Package 1766/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Simone Pallotta
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | ... NOT SUPPORTED ... | ||||||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | ... NOT SUPPORTED ... | ||||||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
|
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. |
| Package: RGMQL |
| Version: 1.28.0 |
| Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data RGMQL |
| StartedAt: 2025-08-29 03:52:20 -0000 (Fri, 29 Aug 2025) |
| EndedAt: 2025-08-29 03:53:32 -0000 (Fri, 29 Aug 2025) |
| EllapsedTime: 72.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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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
25/08/29 03:53:25 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
25/08/29 03:53:25 WARN NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
25/08/29 03:53:26 INFO SparkContext: Submitted application: GMQL-R
25/08/29 03:53:26 INFO SecurityManager: Changing view acls to: biocbuild
25/08/29 03:53:26 INFO SecurityManager: Changing modify acls to: biocbuild
25/08/29 03:53:26 INFO SecurityManager: Changing view acls groups to:
25/08/29 03:53:26 INFO SecurityManager: Changing modify acls groups to:
25/08/29 03:53:26 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()
25/08/29 03:53:26 INFO Utils: Successfully started service 'sparkDriver' on port 42505.
25/08/29 03:53:26 INFO SparkEnv: Registering MapOutputTracker
25/08/29 03:53:26 INFO SparkEnv: Registering BlockManagerMaster
25/08/29 03:53:26 INFO BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
25/08/29 03:53:26 INFO BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
25/08/29 03:53:26 INFO DiskBlockManager: Created local directory at /tmp/blockmgr-7b47aac7-4f09-486b-b59e-2cb36a2dda25
25/08/29 03:53:26 INFO MemoryStore: MemoryStore started with capacity 127.2 MB
25/08/29 03:53:26 INFO SparkEnv: Registering OutputCommitCoordinator
25/08/29 03:53:27 INFO Utils: Successfully started service 'SparkUI' on port 4040.
25/08/29 03:53:27 INFO SparkUI: Bound SparkUI to 0.0.0.0, and started at http://192.168.0.231:4040
25/08/29 03:53:27 INFO Executor: Starting executor ID driver on host localhost
25/08/29 03:53:27 INFO Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 38451.
25/08/29 03:53:27 INFO NettyBlockTransferService: Server created on 192.168.0.231:38451
25/08/29 03:53:27 INFO BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
25/08/29 03:53:27 INFO BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 192.168.0.231, 38451, None)
25/08/29 03:53:27 INFO BlockManagerMasterEndpoint: Registering block manager 192.168.0.231:38451 with 127.2 MB RAM, BlockManagerId(driver, 192.168.0.231, 38451, None)
25/08/29 03:53:27 INFO BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 192.168.0.231, 38451, None)
25/08/29 03:53:27 INFO BlockManager: Initialized BlockManager: BlockManagerId(driver, 192.168.0.231, 38451, 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