CRAN Package Check Results for Package rcdk

Last updated on 2018-04-23 22:47:46 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 3.4.5 5.50 107.37 112.87 ERROR
r-devel-linux-x86_64-debian-gcc 3.4.5 3.83 90.08 93.91 ERROR
r-devel-linux-x86_64-fedora-clang 3.4.5 120.78 OK
r-devel-linux-x86_64-fedora-gcc 3.4.5 118.58 OK
r-devel-windows-ix86+x86_64 3.4.5 11.00 94.00 105.00 OK
r-devel-osx-x86_64 3.4.5 OK
r-patched-linux-x86_64 3.4.5 5.76 118.06 123.82 ERROR
r-patched-solaris-x86 3.4.5 106.90 ERROR
r-release-linux-x86_64 3.4.5 4.14 125.30 129.44 ERROR
r-release-windows-ix86+x86_64 3.4.5 9.00 121.00 130.00 OK
r-release-osx-x86_64 3.4.5 OK
r-oldrel-windows-ix86+x86_64 3.4.5 7.00 92.00 99.00 OK

Check Details

Version: 3.4.5
Check: tests
Result: ERROR
     Running ‘doRUnit.R’ [15s/6s]
    Running R code in ‘doRUnit.R’ had CPU time 2.5 times elapsed time
    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-devel-clang/Work/PKGS/rcdk.Rcheck/tests"
    
     $pathToUnitTests
     [1] "/tmp/RtmpWleSdq/RLIBS_7301265fd2c/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 -- Sun Apr 22 22:12:14 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/RtmpWleSdq/RLIBS_7301265fd2c/rcdk/unitTests/reportSummary.txt': Read-only file system
     Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 3.4.5
Check: tests
Result: ERROR
     Running ‘doRUnit.R’ [12s/10s]
    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-devel-gcc/Work/PKGS/rcdk.Rcheck/tests"
    
     $pathToUnitTests
     [1] "/home/hornik/tmp/scratch/RtmpfMEUGb/RLIBS_591626f800eb/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 -- Mon Apr 23 20:10:37 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 '/home/hornik/tmp/scratch/RtmpfMEUGb/RLIBS_591626f800eb/rcdk/unitTests/reportSummary.txt': Read-only file system
     Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 3.4.5
Check: tests
Result: ERROR
     Running ‘doRUnit.R’ [16s/12s]
    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/RtmpNgBRpn/RLIBS_4e1742ea35c7/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 -- Mon Apr 23 09:51:37 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/RtmpNgBRpn/RLIBS_4e1742ea35c7/rcdk/unitTests/reportSummary.txt': Read-only file system
     Execution halted
Flavor: r-patched-linux-x86_64

Version: 3.4.5
Check: examples
Result: ERROR
    Running examples in ‘rcdk-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: eval.desc
    > ### Title: Evaluate a Molecular Descriptor
    > ### Aliases: eval.desc
    > ### Keywords: programming
    >
    > ### ** Examples
    >
    > smiles <- c('CCC', 'c1ccccc1', 'CC(=O)C')
    > mols <- sapply(smiles, parse.smiles)
    >
    > dnames <- get.desc.names('constitutional')
    Error in .jcall("org/guha/rcdk/descriptors/DescriptorUtilities", "[Ljava/lang/String;", :
     RcallMethod: cannot determine object class
    Calls: get.desc.names -> .jcall
    Execution halted
Flavor: r-patched-solaris-x86

Version: 3.4.5
Check: tests
Result: ERROR
     Running ‘doRUnit.R’
    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/ripley/R/packages/tests32/rcdk.Rcheck/tests"
    
     $pathToUnitTests
     [1] "/tmp/Rtmp4zaaDU/RLIBS_5ce828d14dc7/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 ... Timing stopped at: 0.01 0 0.008
     Error in .jcall("org.guha.rcdk.util.Misc", "Lorg/openscience/cdk/interfaces/IAtomContainer;", :
     RcallMethod: cannot determine object class
     done successfully.
    
    
    
     Executing test function test.mcs2 ... Timing stopped at: 0.001 0 0.001
     Error in .jcall("org/openscience/cdk/DefaultChemObjectBuilder", "Lorg/openscience/cdk/interfaces/IChemObjectBuilder;", :
     java.lang.UnsupportedClassVersionError: org/guha/rcdk/util/Misc : Unsupported major.minor version 52.0
     done successfully.
    
    
    
     Executing test function test.mcs3 ... Timing stopped at: 0.02 0.001 0.028
     Error in .jcall("org.guha.rcdk.util.Misc", "Lorg/openscience/cdk/interfaces/IAtomContainer;", :
     RcallMethod: cannot determine object class
     done successfully.
    
    
    
     Executing test function test.get.properties ... Timing stopped at: 0.001 0 0.001
     Error in .jcall("org/openscience/cdk/DefaultChemObjectBuilder", "Lorg/openscience/cdk/interfaces/IChemObjectBuilder;", :
     java.lang.UnsupportedClassVersionError: org/guha/rcdk/util/Misc : Unsupported major.minor version 52.0
     done successfully.
    
    
    
     Executing test function test.set.props ... Timing stopped at: 0.005 0.001 0.007
     Error in .jcall("org/guha/rcdk/util/Misc", "V", "setProperty", molecule, :
     RcallMethod: cannot determine object class
     done successfully.
    
    
    
     Executing test function test.atom.count ... Timing stopped at: 0.001 0 0.001
     Error in .jcall("org/openscience/cdk/DefaultChemObjectBuilder", "Lorg/openscience/cdk/interfaces/IChemObjectBuilder;", :
     java.lang.UnsupportedClassVersionError: org/guha/rcdk/util/Misc : Unsupported major.minor version 52.0
     done successfully.
    
    
    
     Executing test function test.desc.calc ... Timing stopped at: 0.002 0 0.002
     Error in .jcall("org/guha/rcdk/descriptors/DescriptorUtilities", "[Ljava/lang/String;", :
     RcallMethod: cannot determine object class
     done successfully.
    
    
    
     Executing test function test.desc.cats ... Timing stopped at: 0.001 0 0.001
     Error in .jcall("org/guha/rcdk/descriptors/DescriptorUtilities", "[Ljava/lang/String;", :
     java.lang.UnsupportedClassVersionError: org/guha/rcdk/descriptors/DescriptorUtilities : Unsupported major.minor version 52.0
     done successfully.
    
    
    
     Executing test function test.desc.names ... Timing stopped at: 0.001 0 0.001
     Error in .jcall("org/guha/rcdk/descriptors/DescriptorUtilities", "[Ljava/lang/String;", :
     RcallMethod: cannot determine object class
     done successfully.
    
    
    
     Executing test function test.formula ... done successfully.
    
    
    
     Executing test function test.fp ... Timing stopped at: 0.001 0 0.001
     Error in .jcall("org/openscience/cdk/DefaultChemObjectBuilder", "Lorg/openscience/cdk/interfaces/IChemObjectBuilder;", :
     java.lang.UnsupportedClassVersionError: org/guha/rcdk/descriptors/DescriptorUtilities : Unsupported major.minor version 52.0
     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 ... Timing stopped at: 0.005 0.001 0.006
     Error in .jcall("org.guha.rcdk.util.Misc", "Lorg/openscience/cdk/interfaces/IAtomContainer;", :
     RcallMethod: cannot determine object class
     done successfully.
    
     ------------------- UNIT TEST SUMMARY ---------------------
    
     RUNIT TEST PROTOCOL -- Mon Apr 16 21:08:11 2018
     ***********************************************
     Number of test functions: 28
     Number of errors: 11
     Number of failures: 0
    
    
     1 Test Suite :
     rcdk rcdk Unit Tests - 28 test functions, 11 errors, 0 failures
     ERROR in test.mcs1: Error in .jcall("org.guha.rcdk.util.Misc", "Lorg/openscience/cdk/interfaces/IAtomContainer;", :
     RcallMethod: cannot determine object class
     ERROR in test.mcs2: Error in .jcall("org/openscience/cdk/DefaultChemObjectBuilder", "Lorg/openscience/cdk/interfaces/IChemObjectBuilder;", :
     java.lang.UnsupportedClassVersionError: org/guha/rcdk/util/Misc : Unsupported major.minor version 52.0
     ERROR in test.mcs3: Error in .jcall("org.guha.rcdk.util.Misc", "Lorg/openscience/cdk/interfaces/IAtomContainer;", :
     RcallMethod: cannot determine object class
     ERROR in test.get.properties: Error in .jcall("org/openscience/cdk/DefaultChemObjectBuilder", "Lorg/openscience/cdk/interfaces/IChemObjectBuilder;", :
     java.lang.UnsupportedClassVersionError: org/guha/rcdk/util/Misc : Unsupported major.minor version 52.0
     ERROR in test.set.props: Error in .jcall("org/guha/rcdk/util/Misc", "V", "setProperty", molecule, :
     RcallMethod: cannot determine object class
     ERROR in test.atom.count: Error in .jcall("org/openscience/cdk/DefaultChemObjectBuilder", "Lorg/openscience/cdk/interfaces/IChemObjectBuilder;", :
     java.lang.UnsupportedClassVersionError: org/guha/rcdk/util/Misc : Unsupported major.minor version 52.0
     ERROR in test.desc.calc: Error in .jcall("org/guha/rcdk/descriptors/DescriptorUtilities", "[Ljava/lang/String;", :
     RcallMethod: cannot determine object class
     ERROR in test.desc.cats: Error in .jcall("org/guha/rcdk/descriptors/DescriptorUtilities", "[Ljava/lang/String;", :
     java.lang.UnsupportedClassVersionError: org/guha/rcdk/descriptors/DescriptorUtilities : Unsupported major.minor version 52.0
     ERROR in test.desc.names: Error in .jcall("org/guha/rcdk/descriptors/DescriptorUtilities", "[Ljava/lang/String;", :
     RcallMethod: cannot determine object class
     ERROR in test.fp: Error in .jcall("org/openscience/cdk/DefaultChemObjectBuilder", "Lorg/openscience/cdk/interfaces/IChemObjectBuilder;", :
     java.lang.UnsupportedClassVersionError: org/guha/rcdk/descriptors/DescriptorUtilities : Unsupported major.minor version 52.0
     ERROR in test.get.smiles2: Error in .jcall("org.guha.rcdk.util.Misc", "Lorg/openscience/cdk/interfaces/IAtomContainer;", :
     RcallMethod: cannot determine object class
     Error:
    
     unit testing failed (#test failures: 0, #R errors: 11)
    
     Execution halted
Flavor: r-patched-solaris-x86

Version: 3.4.5
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    Loading required package: rcdklibs
    Loading required package: rJava
    
    Error: processing vignette 'rcdk.Rnw' failed with diagnostics:
     chunk 14
    Error in .jcall("org/guha/rcdk/util/Misc", "V", "setProperty", molecule, :
     RcallMethod: cannot determine object class
    Execution halted
Flavor: r-patched-solaris-x86

Version: 3.4.5
Check: tests
Result: ERROR
     Running ‘doRUnit.R’ [17s/14s]
    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-release-gcc/Work/PKGS/rcdk.Rcheck/tests"
    
     $pathToUnitTests
     [1] "/tmp/RtmpsG2ZN8/RLIBS_5b596a7e0900/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 -- Sat Apr 21 09:55:24 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/RtmpsG2ZN8/RLIBS_5b596a7e0900/rcdk/unitTests/reportSummary.txt': Read-only file system
     Execution halted
Flavor: r-release-linux-x86_64