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### Running command:
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###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RGMQL.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings RGMQL_1.25.0.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/RGMQL.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'RGMQL/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RGMQL' version '1.25.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... WARNING
Found the following file with a non-portable file name:
  Example of workflows
These are not fully portable file names.
See section 'Package structure' in the 'Writing R Extensions' manual.
* checking whether package 'RGMQL' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 90.0Mb
  sub-directories of 1Mb or more:
    example  89.3Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'RGMQL-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: take
> ### Title: Method take
> ### Aliases: take take,GMQLDataset-method take-method
> 
> ### ** Examples
> 
> ## This statement initializes and runs the GMQL server for local execution 
> ## and creation of results on disk. Then, with system.file() it defines 
> ## the path to the folder "DATASET" in the subdirectory "example"
> ## of the package "RGMQL" and opens such folder as a GMQL dataset 
> ## named "rd" using CustomParser
> 
> init_gmql()
24/06/10 08:24:35 INFO SparkContext: Running Spark version 2.2.0
24/06/10 08:24:35 INFO SparkContext: Submitted application: GMQL-R
24/06/10 08:24:35 INFO SecurityManager: Changing view acls to: biocbuild
24/06/10 08:24:35 INFO SecurityManager: Changing modify acls to: biocbuild
24/06/10 08:24:35 INFO SecurityManager: Changing view acls groups to: 
24/06/10 08:24:35 INFO SecurityManager: Changing modify acls groups to: 
24/06/10 08:24:35 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()
24/06/10 08:24:35 INFO Utils: Successfully started service 'sparkDriver' on port 50907.
24/06/10 08:24:35 INFO SparkEnv: Registering MapOutputTracker
24/06/10 08:24:35 INFO SparkEnv: Registering BlockManagerMaster
24/06/10 08:24:35 INFO BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
24/06/10 08:24:35 INFO BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
24/06/10 08:24:35 INFO DiskBlockManager: Created local directory at F:\biocbuild\bbs-3.20-bioc\tmp\blockmgr-7d986ba7-a8ff-4453-a05a-3bc647ec20d4
24/06/10 08:24:35 INFO MemoryStore: MemoryStore started with capacity 127.2 MB
24/06/10 08:24:35 INFO SparkEnv: Registering OutputCommitCoordinator
24/06/10 08:24:35 INFO Utils: Successfully started service 'SparkUI' on port 4040.
24/06/10 08:24:35 INFO SparkUI: Bound SparkUI to 0.0.0.0, and started at http://10.0.0.5:4040
24/06/10 08:24:35 INFO Executor: Starting executor ID driver on host localhost
24/06/10 08:24:35 INFO Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 50908.
24/06/10 08:24:35 INFO NettyBlockTransferService: Server created on 10.0.0.5:50908
24/06/10 08:24:35 INFO BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
24/06/10 08:24:35 INFO BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 10.0.0.5, 50908, None)
24/06/10 08:24:35 INFO BlockManagerMasterEndpoint: Registering block manager 10.0.0.5:50908 with 127.2 MB RAM, BlockManagerId(driver, 10.0.0.5, 50908, None)
24/06/10 08:24:35 INFO BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 10.0.0.5, 50908, None)
24/06/10 08:24:35 INFO BlockManager: Initialized BlockManager: BlockManagerId(driver, 10.0.0.5, 50908, None)
GMQL Server is up
> test_path <- system.file("example", "DATASET", package = "RGMQL")
> rd = read_gmql(test_path)
> 
> ## This statement creates a dataset called 'aggr' which contains one 
> ## sample for each antibody_target and cell value found within the metadata 
> ## of the 'rd' dataset sample; each created sample contains all regions 
> ## from all 'rd' samples with a specific value for their 
> ## antibody_target and cell metadata attributes.
>  
> aggr = aggregate(rd, conds(c("antibody_target", "cell")))
> 
> ## This statement performs the query and returns the resulted dataset as 
> ## GRangesList named 'taken'. It returns only the first 45 regions of 
> ## each sample present into GRangesList and all the medatata associated 
> ## with each sample
> 
> taken <- take(aggr, rows = 45)
[OPTIM] variabili da materializzare: 0
24/06/10 08:24:35 INFO MergeMD$: ----------------MergeMD executing..
24/06/10 08:24:35 INFO ReadMD$: ----------------ReadMD executing..
24/06/10 08:24:35 INFO deprecation: mapred.input.dir is deprecated. Instead, use mapreduce.input.fileinputformat.inputdir
24/06/10 08:24:35 INFO deprecation: mapred.max.split.size is deprecated. Instead, use mapreduce.input.fileinputformat.split.maxsize
24/06/10 08:24:49 WARN BlockManager: Putting block broadcast_0 failed due to an exception
24/06/10 08:24:49 WARN BlockManager: Block broadcast_0 could not be removed as it was not found on disk or in memory
Error in .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl,  : 
  java.lang.reflect.InaccessibleObjectException: Unable to make field transient java.lang.Object[] java.util.ArrayList.elementData accessible: module java.base does not "opens java.util" to unnamed module @693fe6c9
Calls: take ... gmql_take -> <Anonymous> -> .jrcall -> .jcall -> .jcheck
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 2 NOTEs
See
  'F:/biocbuild/bbs-3.20-bioc/meat/RGMQL.Rcheck/00check.log'
for details.