| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-04-09 11:56 -0400 (Wed, 09 Apr 2025).
| 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 | ||||
| Package 1761/2335 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Simone Pallotta
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | 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: 1.27.1 |
| Command: chmod a+r RGMQL -R && F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data RGMQL |
| StartedAt: 2025-04-08 21:51:32 -0400 (Tue, 08 Apr 2025) |
| EndedAt: 2025-04-08 21:53:58 -0400 (Tue, 08 Apr 2025) |
| EllapsedTime: 146.7 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### chmod a+r RGMQL -R && F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data 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
25/04/08 21:53:26 INFO SparkContext: Running Spark version 2.2.0
25/04/08 21:53:26 WARN NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
25/04/08 21:53:26 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)
25/04/08 21:53:27 INFO SparkContext: Submitted application: GMQL-R
25/04/08 21:53:27 INFO SecurityManager: Changing view acls to: biocbuild
25/04/08 21:53:27 INFO SecurityManager: Changing modify acls to: biocbuild
25/04/08 21:53:27 INFO SecurityManager: Changing view acls groups to:
25/04/08 21:53:27 INFO SecurityManager: Changing modify acls groups to:
25/04/08 21:53:27 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 21:53:27 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 21:53:52 INFO Utils: Successfully started service 'sparkDriver' on port 53658.
25/04/08 21:53:52 INFO SparkEnv: Registering MapOutputTracker
25/04/08 21:53:52 INFO SparkEnv: Registering BlockManagerMaster
25/04/08 21:53:52 INFO BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
25/04/08 21:53:52 INFO BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
25/04/08 21:53:52 INFO DiskBlockManager: Created local directory at F:\biocbuild\bbs-3.22-bioc\tmp\blockmgr-9391f639-ffec-4733-8d92-a50f281e1979
25/04/08 21:53:52 INFO MemoryStore: MemoryStore started with capacity 127.2 MB
25/04/08 21:53:53 INFO SparkEnv: Registering OutputCommitCoordinator
25/04/08 21:53:53 INFO Utils: Successfully started service 'SparkUI' on port 4040.
25/04/08 21:53:53 INFO SparkUI: Bound SparkUI to 0.0.0.0, and started at http://10.0.0.5:4040
25/04/08 21:53:53 INFO Executor: Starting executor ID driver on host localhost
25/04/08 21:53:53 INFO Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 53659.
25/04/08 21:53:53 INFO NettyBlockTransferService: Server created on 10.0.0.5:53659
25/04/08 21:53:53 INFO BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
25/04/08 21:53:53 INFO BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 10.0.0.5, 53659, None)
25/04/08 21:53:53 INFO BlockManagerMasterEndpoint: Registering block manager 10.0.0.5:53659 with 127.2 MB RAM, BlockManagerId(driver, 10.0.0.5, 53659, None)
25/04/08 21:53:53 INFO BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 10.0.0.5, 53659, None)
25/04/08 21:53:53 INFO BlockManager: Initialized BlockManager: BlockManagerId(driver, 10.0.0.5, 53659, 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