Running 'doRUnit.R' [20s/12s]
Running the tests in 'tests/doRUnit.R' failed.
Complete output:
  >  if(require("RUnit", quietly=TRUE)) {
  + 
  +    library(rJava)
  +    library(fingerprint)
  + 
  +   ## --- Setup ---
  +  
  +   pkg <- "rcdk" # <-- Change to package name!
  +   if(Sys.getenv("RCMDCHECK") == "FALSE") {
  +     ## Path to unit tests for standalone running under Makefile (not R CMD check)
  +     ## PKG/tests/../inst/unitTests
  +     path <- file.path(getwd(), "..", "inst", "unitTests")
  +   } else {
  +     ## Path to unit tests for R CMD check
  +     ## PKG.Rcheck/tests/../PKG/unitTests
  +     path <- system.file(package=pkg, "unitTests")
  +   }
  +   cat("\nRunning unit tests\n")
  +   print(list(pkg=pkg, getwd=getwd(), pathToUnitTests=path))
  +  
  +   library(package=pkg, character.only=TRUE)
  +  
  +   ## If desired, load the name space to allow testing of private functions
  +   ## if (is.element(pkg, loadedNamespaces()))
  +   ##     attach(loadNamespace(pkg), name=paste("namespace", pkg, sep=":"), pos=3)
  +   ##
  +   ## or simply call PKG:::myPrivateFunction() in tests
  +  
  +   ## --- Testing ---
  +  
  +   ## Define tests
  +   testSuite <- defineTestSuite(name=paste(pkg, "rcdk Unit Tests"),
  +                                           dirs=path)
  +   ## Run
  +   tests <- runTestSuite(testSuite)
  +  
  +   ## Default report name
  +   #pathReport <- file.path(path, "report")
  +  
  +   ## Report to stdout and text files
  +   cat("------------------- UNIT TEST SUMMARY ---------------------\n\n")
  +   printTextProtocol(tests, showDetails=FALSE)
  +   #printTextProtocol(tests, showDetails=FALSE,
  +   #                  fileName=paste(pathReport, "Summary.txt", sep=""))
  +   #printTextProtocol(tests, showDetails=TRUE,
  +   #                  fileName=paste(pathReport, ".txt", sep=""))
  +  
  +   ## Report to HTML file
  +   #printHTMLProtocol(tests, fileName=paste(pathReport, ".html", sep=""))
  +  
  +   ## Return stop() to cause R CMD check stop in case of
  +   ##  - failures i.e. FALSE to unit tests or
  +   ##  - errors i.e. R errors
  +   tmp <- getErrors(tests)
  +   if(tmp$nFail > 0 | tmp$nErr > 0) {
  +     stop(paste("\n\nunit testing failed (#test failures: ", tmp$nFail,
  +                ", #R errors: ",  tmp$nErr, ")\n\n", sep=""))
  +   }
  + } else {
  +   warning("cannot run unit tests -- package RUnit is not available")
  + }
  
  Running unit tests
  $pkg
  [1] "rcdk"
  
  $getwd
  [1] "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/rcdk.Rcheck/tests"
  
  $pathToUnitTests
  [1] "/tmp/RtmpLvLYun/RLIBS_2942d95cdcd1f0/rcdk/unitTests"
  
  Loading required package: rcdklibs
  
  
  Executing test function test.charges  ...  done successfully.
  
  
  
  Executing test function test.get.hcount  ...  done successfully.
  
  
  
  Executing test function test.is.aromatic  ...  done successfully.
  
  
  
  Executing test function test.bond.order  ...  done successfully.
  
  
  
  Executing test function test.depictiongenerator  ...  done successfully.
  
  
  
  Executing test function test.atom.descriptor.conjugated.pi.system  ... Processing  IsProtonInConjugatedPiSystemDescriptor 
  	 computed 1 descriptor values
  Processing  VdWRadiusDescriptor 
  	 computed 1 descriptor values
  Processing  IsProtonInConjugatedPiSystemDescriptor 
  	 computed 1 descriptor values
  Processing  VdWRadiusDescriptor 
  	 computed 1 descriptor values
   done successfully.
  
  
  
  Executing test function test.atom.descriptors.alanine  ... Processing  VdWRadiusDescriptor 
  	 computed 1 descriptor values
  Processing  RDFProtonDescriptor_GHR 
  	 computed 15 descriptor values
   done successfully.
  
  
  
  Executing test function test.atom.descriptors.rdf.glutamine  ... Processing  RDFProtonDescriptor_GSR 
  	 computed 7 descriptor values
  Processing  RDFProtonDescriptor_GHR_topol 
  	 computed 15 descriptor values
  Processing  RDFProtonDescriptor_GHR 
  	 computed 15 descriptor values
  Processing  RDFProtonDescriptor_GDR 
  	 computed 7 descriptor values
  Processing  RDFProtonDescriptor_G3R 
  	 computed 13 descriptor values
   done successfully.
  
  
  
  Executing test function test.fp  ...  done successfully.
  
  
  
  Executing test function test.fp.substructures.binary  ...  done successfully.
  
  
  
  Executing test function test.fp.substructures.count  ...  done successfully.
  
  
  
  Executing test function test.frag1  ...  done successfully.
  
  
  
  Executing test function test.frag2  ...  done successfully.
  
  
  
  Executing test function test.frag3  ...  done successfully.
  
  
  
  Executing test function test.aromaticity.match  ...  done successfully.
  
  
  
  Executing test function test.match1  ...  done successfully.
  
  
  
  Executing test function test.match2  ...  done successfully.
  
  
  
  Executing test function test.match3  ...  done successfully.
  
  
  
  Executing test function test.match4  ...  done successfully.
  
  
  
  Executing test function test.mcs1  ...  done successfully.
  
  
  
  Executing test function test.mcs2  ...  done successfully.
  
  
  
  Executing test function test.mcs3  ...  done successfully.
  
  
  
  Executing test function test.get.properties  ...  done successfully.
  
  
  
  Executing test function test.set.props  ...  done successfully.
  
  
  
  Executing test function test.atom.count  ...  done successfully.
  
  
  
  Executing test function test.desc.calc  ... org.openscience.cdk.io.cml.CMLHandler WARN: Detected unknown convention: cdk:substructureList
   done successfully.
  
  
  
  Executing test function test.desc.cats  ... [1] "protein"        "hybrid"         "constitutional" "topological"   
  [5] "electronic"     "geometrical"   
  Timing stopped at: 0.064 0 0.023
  Error in checkEquals(5, length(cats)) : Mean relative difference: 0.2
  
  In addition: There were 50 or more warnings (use warnings() to see the first 50)
   done successfully.
  
  
  
  Executing test function test.desc.names  ...  done successfully.
  
  
  
  Executing test function test.exact.natural.mass  ...  done successfully.
  
  
  
  Executing test function test.formula  ... org.openscience.cdk.stereo.StereoElementFactory WARN: Inverse wedge bond used for stereo at atom index 44
   done successfully.
  
  
  
  Executing test function test.get.largest  ...  done successfully.
  
  
  
  Executing test function test.is.connected  ...  done successfully.
  
  
  
  Executing test function test.is.neutral  ...  done successfully.
  
  
  
  Executing test function test.get.smiles  ...  done successfully.
  
  
  
  Executing test function test.get.smiles2  ...  done successfully.
  
  ------------------- UNIT TEST SUMMARY ---------------------
  
  RUNIT TEST PROTOCOL -- Tue Sep 27 05:38:42 2022 
  *********************************************** 
  Number of test functions: 35 
  Number of errors: 0 
  Number of failures: 1 
  
   
  1 Test Suite : 
  rcdk rcdk Unit Tests - 35 test functions, 0 errors, 1 failure
  FAILURE in test.desc.cats: Error in checkEquals(5, length(cats)) : Mean relative difference: 0.2
  
  Error: 
  
  unit testing failed (#test failures: 1, #R errors: 0)
  
  In addition: Warning messages:
  1: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
    RNGkind: Marsaglia-Multicarry has poor statistical properties
  2: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
    RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
  3: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
    RNGkind: Marsaglia-Multicarry has poor statistical properties
  4: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
    RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
  Execution halted