############################################################################## ############################################################################## ### ### Running command: ### ### 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 ### ############################################################################## ############################################################################## * 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 -> -> .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.