CRAN Package Check Results for Package Rclusterpp

Last updated on 2018-05-09 22:48:47 CEST.

Check Details

Version: 0.2.3
Check: dependencies in R code
Result: NOTE
    Packages in Depends field not imported from:
     ‘Rcpp’ ‘RcppEigen’
     These packages need to be imported from (in the NAMESPACE file)
     for when this namespace is loaded but not attached.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 0.2.3
Check: foreign function calls
Result: NOTE
    Calls with DUP:
     .Call("hclust_from_distance", data = as.double(x), size = as.integer(attributes(x)$Size),
     link = as.integer(method), DUP = FALSE, NAOK = FALSE, PACKAGE = "Rclusterpp")
     .Call("hclust_from_data", data = x, link = as.integer(method),
     dist = as.integer(distance), p = as.numeric(p), DUP = FALSE,
     NAOK = FALSE, PACKAGE = "Rclusterpp")
    DUP is no longer supported and will be ignored.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 0.2.3
Check: R code for possible problems
Result: NOTE
    Rclusterpp.package.skeleton: no visible global function definition for
     ‘packageDescription’
    Undefined global functions or variables:
     packageDescription
    Consider adding
     importFrom("utils", "packageDescription")
    to your NAMESPACE file.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 0.2.3
Check: compiled code
Result: NOTE
    File ‘Rclusterpp/libs/Rclusterpp.so’:
     Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’
    
    It is good practice to register native routines and to disable symbol
    search.
    
    See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 0.2.3
Check: tests
Result: ERROR
     Running ‘doRUnit.R’ [9s/8s]
    Running the tests in ‘tests/doRUnit.R’ failed.
    Complete output:
     > # Adapted from: http://rwiki.sciviews.org/doku.php?id=developers:runit
     >
     > if( identical( .Platform$OS.type, "windows" ) && identical( .Platform$r_arch, "x64" ) ){
     + print( "unit tests not run on windows 64 (workaround alert)" )
     + } else {
     + if(require("RUnit", quietly = TRUE)) {
     + pkg <- "Rclusterpp"
     + if(Sys.getenv("RCMDCHECK") == "FALSE") {
     + path <- file.path(getwd(), "..", "inst", "unit_tests")
     + } else {
     + path <- system.file(package=pkg, "unit_tests")
     + }
     + cat("\nRunning unit tests:\n")
     + print(list(pkg=pkg, getwd=getwd(), pathToUnitTests=path))
     +
     + library(package=pkg, character.only=TRUE)
     +
     + # Define tests
     + testSuite <- defineTestSuite(name=paste(pkg, "unit testing"), dirs=path)
     +
     + # Run
     + tests <- runTestSuite(testSuite)
     +
     + # Default report name
     + pathReport <- file.path(path, "report")
     +
     + # Report to stdout and text files
     + 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 {
     + print( "package RUnit not available, cannot run unit tests" )
     + }
     + }
    
     Running unit tests:
     $pkg
     [1] "Rclusterpp"
    
     $getwd
     [1] "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/Rclusterpp.Rcheck/tests"
    
     $pathToUnitTests
     [1] "/tmp/Rtmpupn9Bu/RLIBS_7d55690dea6f/Rclusterpp/unit_tests"
    
     Loading required package: Rcpp
     Loading required package: RcppEigen
    
    
     Executing test function test.hclust.average.euclidean ... done successfully.
    
    
    
     Executing test function test.hclust.average.manhattan ... done successfully.
    
    
    
     Executing test function test.hclust.average.maximum ... done successfully.
    
    
    
     Executing test function test.hclust.average.minkowski ... done successfully.
    
    
    
     Executing test function test.hclust.complete.euclidean ... done successfully.
    
    
    
     Executing test function test.hclust.single.euclidean ... done successfully.
    
    
    
     Executing test function test.hclust.single.manhattan ... done successfully.
    
    
    
     Executing test function test.hclust.single.maximum ... done successfully.
    
    
    
     Executing test function test.hclust.single.minkowski ... done successfully.
    
    
    
     Executing test function test.hclust.ward ... The "ward" method has been renamed to "ward.D"; note new "ward.D2"
     done successfully.
    
    
    
     Executing test function test.storedistance.average.euclidean ... done successfully.
    
    
    
     Executing test function test.storedistance.average.manhattan ... done successfully.
    
    
    
     Executing test function test.storedistance.complete.euclidean ... done successfully.
    
    
    
     Executing test function test.storedistance.single.euclidean ... done successfully.
    
     RUNIT TEST PROTOCOL -- Tue May 8 06:22:53 2018
     ***********************************************
     Number of test functions: 14
     Number of errors: 0
     Number of failures: 0
    
    
     1 Test Suite :
     Rclusterpp unit testing - 14 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/Rtmpupn9Bu/RLIBS_7d55690dea6f/Rclusterpp/unit_tests/reportSummary.txt': Read-only file system
     Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.2.3
Check: tests
Result: ERROR
     Running ‘doRUnit.R’ [9s/11s]
    Running the tests in ‘tests/doRUnit.R’ failed.
    Complete output:
     > # Adapted from: http://rwiki.sciviews.org/doku.php?id=developers:runit
     >
     > if( identical( .Platform$OS.type, "windows" ) && identical( .Platform$r_arch, "x64" ) ){
     + print( "unit tests not run on windows 64 (workaround alert)" )
     + } else {
     + if(require("RUnit", quietly = TRUE)) {
     + pkg <- "Rclusterpp"
     + if(Sys.getenv("RCMDCHECK") == "FALSE") {
     + path <- file.path(getwd(), "..", "inst", "unit_tests")
     + } else {
     + path <- system.file(package=pkg, "unit_tests")
     + }
     + cat("\nRunning unit tests:\n")
     + print(list(pkg=pkg, getwd=getwd(), pathToUnitTests=path))
     +
     + library(package=pkg, character.only=TRUE)
     +
     + # Define tests
     + testSuite <- defineTestSuite(name=paste(pkg, "unit testing"), dirs=path)
     +
     + # Run
     + tests <- runTestSuite(testSuite)
     +
     + # Default report name
     + pathReport <- file.path(path, "report")
     +
     + # Report to stdout and text files
     + 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 {
     + print( "package RUnit not available, cannot run unit tests" )
     + }
     + }
    
     Running unit tests:
     $pkg
     [1] "Rclusterpp"
    
     $getwd
     [1] "/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Rclusterpp.Rcheck/tests"
    
     $pathToUnitTests
     [1] "/home/hornik/tmp/scratch/Rtmp0nJMkI/RLIBS_760731716b2f/Rclusterpp/unit_tests"
    
     Loading required package: Rcpp
     Loading required package: RcppEigen
    
    
     Executing test function test.hclust.average.euclidean ... done successfully.
    
    
    
     Executing test function test.hclust.average.manhattan ... done successfully.
    
    
    
     Executing test function test.hclust.average.maximum ... done successfully.
    
    
    
     Executing test function test.hclust.average.minkowski ... done successfully.
    
    
    
     Executing test function test.hclust.complete.euclidean ... done successfully.
    
    
    
     Executing test function test.hclust.single.euclidean ... done successfully.
    
    
    
     Executing test function test.hclust.single.manhattan ... done successfully.
    
    
    
     Executing test function test.hclust.single.maximum ... done successfully.
    
    
    
     Executing test function test.hclust.single.minkowski ... done successfully.
    
    
    
     Executing test function test.hclust.ward ... The "ward" method has been renamed to "ward.D"; note new "ward.D2"
     done successfully.
    
    
    
     Executing test function test.storedistance.average.euclidean ... done successfully.
    
    
    
     Executing test function test.storedistance.average.manhattan ... done successfully.
    
    
    
     Executing test function test.storedistance.complete.euclidean ... done successfully.
    
    
    
     Executing test function test.storedistance.single.euclidean ... done successfully.
    
     RUNIT TEST PROTOCOL -- Wed May 9 17:24:14 2018
     ***********************************************
     Number of test functions: 14
     Number of errors: 0
     Number of failures: 0
    
    
     1 Test Suite :
     Rclusterpp unit testing - 14 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/Rtmp0nJMkI/RLIBS_760731716b2f/Rclusterpp/unit_tests/reportSummary.txt': Read-only file system
     Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.2.3
Check: tests
Result: ERROR
     Running ‘doRUnit.R’ [9s/11s]
    Running the tests in ‘tests/doRUnit.R’ failed.
    Complete output:
     > # Adapted from: http://rwiki.sciviews.org/doku.php?id=developers:runit
     >
     > if( identical( .Platform$OS.type, "windows" ) && identical( .Platform$r_arch, "x64" ) ){
     + print( "unit tests not run on windows 64 (workaround alert)" )
     + } else {
     + if(require("RUnit", quietly = TRUE)) {
     + pkg <- "Rclusterpp"
     + if(Sys.getenv("RCMDCHECK") == "FALSE") {
     + path <- file.path(getwd(), "..", "inst", "unit_tests")
     + } else {
     + path <- system.file(package=pkg, "unit_tests")
     + }
     + cat("\nRunning unit tests:\n")
     + print(list(pkg=pkg, getwd=getwd(), pathToUnitTests=path))
     +
     + library(package=pkg, character.only=TRUE)
     +
     + # Define tests
     + testSuite <- defineTestSuite(name=paste(pkg, "unit testing"), dirs=path)
     +
     + # Run
     + tests <- runTestSuite(testSuite)
     +
     + # Default report name
     + pathReport <- file.path(path, "report")
     +
     + # Report to stdout and text files
     + 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 {
     + print( "package RUnit not available, cannot run unit tests" )
     + }
     + }
    
     Running unit tests:
     $pkg
     [1] "Rclusterpp"
    
     $getwd
     [1] "/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Rclusterpp.Rcheck/tests"
    
     $pathToUnitTests
     [1] "/tmp/RtmpS1Ryxs/RLIBS_1ba9585c8f58/Rclusterpp/unit_tests"
    
     Loading required package: Rcpp
     Loading required package: RcppEigen
    
    
     Executing test function test.hclust.average.euclidean ... done successfully.
    
    
    
     Executing test function test.hclust.average.manhattan ... done successfully.
    
    
    
     Executing test function test.hclust.average.maximum ... done successfully.
    
    
    
     Executing test function test.hclust.average.minkowski ... done successfully.
    
    
    
     Executing test function test.hclust.complete.euclidean ... done successfully.
    
    
    
     Executing test function test.hclust.single.euclidean ... done successfully.
    
    
    
     Executing test function test.hclust.single.manhattan ... done successfully.
    
    
    
     Executing test function test.hclust.single.maximum ... done successfully.
    
    
    
     Executing test function test.hclust.single.minkowski ... done successfully.
    
    
    
     Executing test function test.hclust.ward ... The "ward" method has been renamed to "ward.D"; note new "ward.D2"
     done successfully.
    
    
    
     Executing test function test.storedistance.average.euclidean ... done successfully.
    
    
    
     Executing test function test.storedistance.average.manhattan ... done successfully.
    
    
    
     Executing test function test.storedistance.complete.euclidean ... done successfully.
    
    
    
     Executing test function test.storedistance.single.euclidean ... done successfully.
    
     RUNIT TEST PROTOCOL -- Tue May 8 18:13:18 2018
     ***********************************************
     Number of test functions: 14
     Number of errors: 0
     Number of failures: 0
    
    
     1 Test Suite :
     Rclusterpp unit testing - 14 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/RtmpS1Ryxs/RLIBS_1ba9585c8f58/Rclusterpp/unit_tests/reportSummary.txt': Read-only file system
     Execution halted
Flavor: r-patched-linux-x86_64

Version: 0.2.3
Check: tests
Result: ERROR
     Running ‘doRUnit.R’ [12s/13s]
    Running the tests in ‘tests/doRUnit.R’ failed.
    Complete output:
     > # Adapted from: http://rwiki.sciviews.org/doku.php?id=developers:runit
     >
     > if( identical( .Platform$OS.type, "windows" ) && identical( .Platform$r_arch, "x64" ) ){
     + print( "unit tests not run on windows 64 (workaround alert)" )
     + } else {
     + if(require("RUnit", quietly = TRUE)) {
     + pkg <- "Rclusterpp"
     + if(Sys.getenv("RCMDCHECK") == "FALSE") {
     + path <- file.path(getwd(), "..", "inst", "unit_tests")
     + } else {
     + path <- system.file(package=pkg, "unit_tests")
     + }
     + cat("\nRunning unit tests:\n")
     + print(list(pkg=pkg, getwd=getwd(), pathToUnitTests=path))
     +
     + library(package=pkg, character.only=TRUE)
     +
     + # Define tests
     + testSuite <- defineTestSuite(name=paste(pkg, "unit testing"), dirs=path)
     +
     + # Run
     + tests <- runTestSuite(testSuite)
     +
     + # Default report name
     + pathReport <- file.path(path, "report")
     +
     + # Report to stdout and text files
     + 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 {
     + print( "package RUnit not available, cannot run unit tests" )
     + }
     + }
    
     Running unit tests:
     $pkg
     [1] "Rclusterpp"
    
     $getwd
     [1] "/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/Rclusterpp.Rcheck/tests"
    
     $pathToUnitTests
     [1] "/tmp/RtmpqO5qr1/RLIBS_269519b35b14/Rclusterpp/unit_tests"
    
     Loading required package: Rcpp
     Loading required package: RcppEigen
    
    
     Executing test function test.hclust.average.euclidean ... done successfully.
    
    
    
     Executing test function test.hclust.average.manhattan ... done successfully.
    
    
    
     Executing test function test.hclust.average.maximum ... done successfully.
    
    
    
     Executing test function test.hclust.average.minkowski ... done successfully.
    
    
    
     Executing test function test.hclust.complete.euclidean ... done successfully.
    
    
    
     Executing test function test.hclust.single.euclidean ... done successfully.
    
    
    
     Executing test function test.hclust.single.manhattan ... done successfully.
    
    
    
     Executing test function test.hclust.single.maximum ... done successfully.
    
    
    
     Executing test function test.hclust.single.minkowski ... done successfully.
    
    
    
     Executing test function test.hclust.ward ... The "ward" method has been renamed to "ward.D"; note new "ward.D2"
     done successfully.
    
    
    
     Executing test function test.storedistance.average.euclidean ... done successfully.
    
    
    
     Executing test function test.storedistance.average.manhattan ... done successfully.
    
    
    
     Executing test function test.storedistance.complete.euclidean ... done successfully.
    
    
    
     Executing test function test.storedistance.single.euclidean ... done successfully.
    
     RUNIT TEST PROTOCOL -- Wed May 9 06:12:36 2018
     ***********************************************
     Number of test functions: 14
     Number of errors: 0
     Number of failures: 0
    
    
     1 Test Suite :
     Rclusterpp unit testing - 14 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/RtmpqO5qr1/RLIBS_269519b35b14/Rclusterpp/unit_tests/reportSummary.txt': Read-only file system
     Execution halted
Flavor: r-release-linux-x86_64

Version: 0.2.3
Check: re-building of vignette outputs
Result: NOTE
    Error in re-building vignettes:
     ...
    Loading required package: Rclusterpp
    Loading required package: Rcpp
    Loading required package: RcppEigen
    Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, :
     Running 'texi2dvi' on 'Rclusterpp.tex' failed.
    LaTeX errors:
    ! LaTeX Error: File `multirow.sty' not found.
    
    Type X to quit or <RETURN> to proceed,
    or enter new name. (Default extension: sty)
    
    ! Emergency stop.
    <read *>
    
    l.7 \lstset
     {language=C++,basicstyle=\footnotesize\ttfamily}^^M
    ! ==> Fatal error occurred, no output PDF file produced!
    Calls: buildVignettes -> texi2pdf -> texi2dvi
    Execution halted
Flavor: r-oldrel-osx-x86_64