| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-08-18 11:42 -0400 (Mon, 18 Aug 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 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4566 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4604 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4545 |
| 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 | |||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | 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. |
| Package: RGMQL |
| Version: 1.28.0 |
| Command: chmod a+r RGMQL -R && E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data RGMQL |
| StartedAt: 2025-08-14 21:43:35 -0400 (Thu, 14 Aug 2025) |
| EndedAt: 2025-08-14 21:45:51 -0400 (Thu, 14 Aug 2025) |
| EllapsedTime: 136.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
###
### chmod a+r RGMQL -R && E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe 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
25/08/14 21:45:21 INFO SparkContext: Running Spark version 2.2.0
25/08/14 21:45:22 WARN NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
25/08/14 21:45:22 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)
25/08/14 21:45:22 INFO SparkContext: Submitted application: GMQL-R
25/08/14 21:45:23 INFO SecurityManager: Changing view acls to: biocbuild
25/08/14 21:45:23 INFO SecurityManager: Changing modify acls to: biocbuild
25/08/14 21:45:23 INFO SecurityManager: Changing view acls groups to:
25/08/14 21:45:23 INFO SecurityManager: Changing modify acls groups to:
25/08/14 21:45:23 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()
25/08/14 21:45:23 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.
25/08/14 21:45:46 INFO Utils: Successfully started service 'sparkDriver' on port 49586.
25/08/14 21:45:46 INFO SparkEnv: Registering MapOutputTracker
25/08/14 21:45:46 INFO SparkEnv: Registering BlockManagerMaster
25/08/14 21:45:46 INFO BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
25/08/14 21:45:46 INFO BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
25/08/14 21:45:46 INFO DiskBlockManager: Created local directory at E:\biocbuild\bbs-3.21-bioc\tmp\blockmgr-b9bbb965-3f99-4385-a3b8-8dd28ed9855a
25/08/14 21:45:46 INFO MemoryStore: MemoryStore started with capacity 127.2 MB
25/08/14 21:45:46 INFO SparkEnv: Registering OutputCommitCoordinator
25/08/14 21:45:46 INFO Utils: Successfully started service 'SparkUI' on port 4040.
25/08/14 21:45:46 INFO SparkUI: Bound SparkUI to 0.0.0.0, and started at http://10.0.0.4:4040
25/08/14 21:45:47 INFO Executor: Starting executor ID driver on host localhost
25/08/14 21:45:47 INFO Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 49599.
25/08/14 21:45:47 INFO NettyBlockTransferService: Server created on 10.0.0.4:49599
25/08/14 21:45:47 INFO BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
25/08/14 21:45:47 INFO BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 10.0.0.4, 49599, None)
25/08/14 21:45:47 INFO BlockManagerMasterEndpoint: Registering block manager 10.0.0.4:49599 with 127.2 MB RAM, BlockManagerId(driver, 10.0.0.4, 49599, None)
25/08/14 21:45:47 INFO BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 10.0.0.4, 49599, None)
25/08/14 21:45:47 INFO BlockManager: Initialized BlockManager: BlockManagerId(driver, 10.0.0.4, 49599, 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