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###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RGMQL.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings RGMQL_1.16.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/RGMQL.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'RGMQL/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RGMQL' version '1.16.0'
* 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 files with non-portable file names:
  Example of workflows/use_case_1 - GITHUB.Rmd
  Example of workflows/use_case_1 - GITHUB.html
  Example of workflows/use_case_3 - GITHUB.Rmd
  Example of workflows/use_case_3 - GITHUB.html
  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 89.9Mb
  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 R 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 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()
22/10/19 03:33:29 INFO SparkContext: Running Spark version 2.2.0
22/10/19 03:33:29 INFO SparkContext: Submitted application: GMQL-R
22/10/19 03:33:29 INFO SecurityManager: Changing view acls to: biocbuild
22/10/19 03:33:29 INFO SecurityManager: Changing modify acls to: biocbuild
22/10/19 03:33:29 INFO SecurityManager: Changing view acls groups to: 
22/10/19 03:33:29 INFO SecurityManager: Changing modify acls groups to: 
22/10/19 03:33:29 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()
22/10/19 03:33:29 INFO Utils: Successfully started service 'sparkDriver' on port 53514.
22/10/19 03:33:29 INFO SparkEnv: Registering MapOutputTracker
22/10/19 03:33:29 INFO SparkEnv: Registering BlockManagerMaster
22/10/19 03:33:29 INFO BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
22/10/19 03:33:29 INFO BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
22/10/19 03:33:29 INFO DiskBlockManager: Created local directory at F:\biocbuild\bbs-3.15-bioc\tmp\blockmgr-a918726a-7b7e-416b-9f76-436346578b72
22/10/19 03:33:29 INFO MemoryStore: MemoryStore started with capacity 127.2 MB
22/10/19 03:33:29 INFO SparkEnv: Registering OutputCommitCoordinator
22/10/19 03:33:29 INFO Utils: Successfully started service 'SparkUI' on port 4040.
22/10/19 03:33:29 INFO SparkUI: Bound SparkUI to 0.0.0.0, and started at http://10.0.0.11:4040
22/10/19 03:33:29 INFO Executor: Starting executor ID driver on host localhost
22/10/19 03:33:29 INFO Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 53515.
22/10/19 03:33:29 INFO NettyBlockTransferService: Server created on 10.0.0.11:53515
22/10/19 03:33:29 INFO BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
22/10/19 03:33:29 INFO BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 10.0.0.11, 53515, None)
22/10/19 03:33:29 INFO BlockManagerMasterEndpoint: Registering block manager 10.0.0.11:53515 with 127.2 MB RAM, BlockManagerId(driver, 10.0.0.11, 53515, None)
22/10/19 03:33:29 INFO BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 10.0.0.11, 53515, None)
22/10/19 03:33:29 INFO BlockManager: Initialized BlockManager: BlockManagerId(driver, 10.0.0.11, 53515, 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
22/10/19 03:33:29 INFO MergeMD$: ----------------MergeMD executing..
22/10/19 03:33:29 INFO ReadMD$: ----------------ReadMD executing..
22/10/19 03:33:30 INFO deprecation: mapred.input.dir is deprecated. Instead, use mapreduce.input.fileinputformat.inputdir
22/10/19 03:33:30 INFO deprecation: mapred.max.split.size is deprecated. Instead, use mapreduce.input.fileinputformat.split.maxsize
22/10/19 03:33:39 WARN BlockManager: Putting block broadcast_0 failed due to an exception
22/10/19 03:33:39 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 @5136d012
Calls: take ... gmql_take -> <Anonymous> -> .jrcall -> .jcall -> .jcheck
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... 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-3.15-bioc/meat/RGMQL.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL RGMQL
###
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* installing to library 'F:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'RGMQL' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RGMQL)