Running ‘doRUnit.R’ [16s/13s]
Running the tests in ‘tests/doRUnit.R’ failed.
Complete output:
  >  if(require("RUnit", quietly=TRUE)) {
  + 
  +    library(rJava)
  +    library(fingerprint)
  + 
  +    print(ls())
  +   ## --- 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")
  + }
  character(0)
  
  Running unit tests
  $pkg
  [1] "rcdk"
  
  $getwd
  [1] "/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/rcdk.Rcheck/tests"
  
  $pathToUnitTests
  [1] "/tmp/RtmpRSRkfG/RLIBS_4af75a5c09dc/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.depictiongenerator  ...  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  ... WARNING: An illegal reflective access operation has occurred
  WARNING: Illegal reflective access by RJavaTools to method java.util.Collections$UnmodifiableCollection$1.next()
  WARNING: Please consider reporting this to the maintainers of RJavaTools
  WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
  WARNING: All illegal access operations will be denied in a future release
   done successfully.
  
  
  
  Executing test function test.set.props  ...  done successfully.
  
  
  
  Executing test function test.atom.count  ...  done successfully.
  
  
  
  Executing test function test.desc.calc  ...  done successfully.
  
  
  
  Executing test function test.desc.cats  ... [1] "hybrid"         "constitutional" "topological"    "electronic"    
  [5] "geometrical"   
   done successfully.
  
  
  
  Executing test function test.desc.names  ...  done successfully.
  
  
  
  Executing test function test.formula  ...  done successfully.
  
  
  
  Executing test function test.fp  ...  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 Apr 24 21:51:37 2018 
  *********************************************** 
  Number of test functions: 28 
  Number of errors: 0 
  Number of failures: 0 
  
   
  1 Test Suite : 
  rcdk rcdk Unit Tests - 28 test functions, 0 errors, 0 failures
  Error in file(file, ifelse(append, "a", "w")) : 
    cannot open the connection
  Calls: printTextProtocol -> cat -> file
  In addition: Warning message:
  In file(file, ifelse(append, "a", "w")) :
    cannot open file '/tmp/RtmpRSRkfG/RLIBS_4af75a5c09dc/rcdk/unitTests/reportSummary.txt': Read-only file system
  Execution halted