CRAN Package Check Results for Package rcdk

Last updated on 2021-09-20 04:58:33 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 3.5.0 7.27 103.42 110.69 OK
r-devel-linux-x86_64-debian-gcc 3.5.0 6.43 77.21 83.64 OK
r-devel-linux-x86_64-fedora-clang 3.5.0 139.05 OK
r-devel-linux-x86_64-fedora-gcc 3.5.0 129.61 OK
r-devel-windows-x86_64 3.5.0 10.00 84.00 94.00 OK
r-devel-windows-x86_64-gcc10-UCRT 3.5.0 ERROR
r-patched-linux-x86_64 3.5.0 11.24 102.64 113.88 OK
r-release-linux-x86_64 3.5.0 6.08 101.74 107.82 OK
r-release-macos-arm64 3.5.0 OK
r-release-macos-x86_64 3.5.0 OK
r-release-windows-ix86+x86_64 3.5.0 20.00 82.00 102.00 OK
r-oldrel-macos-x86_64 3.5.0 OK
r-oldrel-windows-ix86+x86_64 3.5.0 19.00 81.00 100.00 OK

Additional issues

M1mac

Check Details

Version: 3.5.0
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     WARNING: installation-time patches will not be applied, could not get the patches index
Flavor: r-devel-windows-x86_64-gcc10-UCRT

Version: 3.5.0
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)
     +
     + ## --- 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] "C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/rcdk/rcdk.Rcheck/tests"
    
     $pathToUnitTests
     [1] "C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/rcdk/rcdk.Rcheck/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 ... Timing stopped at: 0.02 0.02 0.03
     Error in func() :
     java.lang.UnsatisfiedLinkError: C:\Program Files\AdoptOpenJDK\jdk-11.0.11.9-hotspot\bin\awt.dll: Can't find dependent libraries
     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
     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 ... 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.exact.natural.mass ... done successfully.
    
    
    
     Executing test function test.formula ... 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 Sep 18 22:51:40 2021
     ***********************************************
     Number of test functions: 31
     Number of errors: 1
     Number of failures: 0
    
    
     1 Test Suite :
     rcdk rcdk Unit Tests - 31 test functions, 1 error, 0 failures
     ERROR in test.depictiongenerator: Error in func() :
     java.lang.UnsatisfiedLinkError: C:\Program Files\AdoptOpenJDK\jdk-11.0.11.9-hotspot\bin\awt.dll: Can't find dependent libraries
     Error:
    
     unit testing failed (#test failures: 0, #R errors: 1)
    
     In addition: There were 14 warnings (use warnings() to see them)
     Execution halted
Flavor: r-devel-windows-x86_64-gcc10-UCRT

Version: 3.5.0
Check: PDF version of manual
Result: WARN
    LaTeX errors when creating PDF version.
    This typically indicates Rd problems.
Flavor: r-devel-windows-x86_64-gcc10-UCRT

Version: 3.5.0
Check: PDF version of manual without hyperrefs or index
Result: ERROR
    Re-running with no redirection of stdout/stderr.
Flavor: r-devel-windows-x86_64-gcc10-UCRT