CRAN Package Check Results for Package CompGLM

Last updated on 2018-01-20 22:46:53 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0 11.94 35.17 47.11 ERROR
r-devel-linux-x86_64-debian-gcc 1.0 10.12 27.49 37.61 ERROR
r-devel-linux-x86_64-fedora-clang 1.0 62.51 NOTE
r-devel-linux-x86_64-fedora-gcc 1.0 62.64 NOTE
r-devel-windows-ix86+x86_64 1.0 47.00 114.00 161.00 NOTE
r-patched-linux-x86_64 1.0 13.13 34.12 47.25 ERROR
r-patched-solaris-x86 1.0 78.50 NOTE
r-release-linux-x86_64 1.0 11.79 34.12 45.91 ERROR
r-release-windows-ix86+x86_64 1.0 38.00 111.00 149.00 NOTE
r-release-osx-x86_64 1.0 NOTE
r-oldrel-windows-ix86+x86_64 1.0 37.00 103.00 140.00 NOTE
r-oldrel-osx-x86_64 1.0 NOTE

Check Details

Version: 1.0
Check: R code for possible problems
Result: NOTE
    glm.comp: no visible global function definition for ‘model.frame’
    glm.comp: no visible global function definition for ‘model.response’
    glm.comp: no visible global function definition for ‘model.matrix’
    glm.comp: no visible global function definition for ‘model.offset’
    glm.comp: no visible global function definition for ‘glm.fit’
    glm.comp: no visible global function definition for ‘poisson’
    glm.comp: no visible global function definition for ‘optim’
    predict.Comp: no visible global function definition for
     ‘delete.response’
    predict.Comp: no visible global function definition for ‘model.frame’
    predict.Comp: no visible global function definition for ‘model.matrix’
    print.Comp: no visible global function definition for ‘AIC’
    print.summary.Comp: no visible global function definition for
     ‘printCoefmat’
    summary.Comp: no visible global function definition for ‘pt’
    summary.Comp: no visible global function definition for ‘AIC’
    Undefined global functions or variables:
     AIC delete.response glm.fit model.frame model.matrix model.offset
     model.response optim poisson printCoefmat pt
    Consider adding
     importFrom("stats", "AIC", "delete.response", "glm.fit", "model.frame",
     "model.matrix", "model.offset", "model.response", "optim",
     "poisson", "printCoefmat", "pt")
    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: 1.0
Check: compiled code
Result: NOTE
    File ‘CompGLM/libs/CompGLM.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: 1.0
Check: tests
Result: ERROR
     Running ‘doRUnit.R’ [7s/9s]
    Running the tests in ‘tests/doRUnit.R’ failed.
    Complete output:
     > ## unit tests will not be done if RUnit is not available
     > if(require("RUnit", quietly=TRUE)) {
     +
     + ## --- Setup ---
     +
     + pkg <- "CompGLM"
     + 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, "unit testing"),
     + 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] "CompGLM"
    
     $getwd
     [1] "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/CompGLM.Rcheck/tests"
    
     $pathToUnitTests
     [1] "/tmp/RtmpDbHVCN/RLIBS_68b86ea00f3b/CompGLM/unitTests"
    
    
    
     Executing test function test.dcomp ... done successfully.
    
    
    
     Executing test function test.glm.comp ... done successfully.
    
    
    
     Executing test function test.pcomp ... done successfully.
    
     ------------------- UNIT TEST SUMMARY ---------------------
    
     RUNIT TEST PROTOCOL -- Fri Jan 19 04:28:13 2018
     ***********************************************
     Number of test functions: 3
     Number of errors: 0
     Number of failures: 0
    
    
     1 Test Suite :
     CompGLM unit testing - 3 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/RtmpDbHVCN/RLIBS_68b86ea00f3b/CompGLM/unitTests/reportSummary.txt': Read-only file system
     Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.0
Check: tests
Result: ERROR
     Running ‘doRUnit.R’ [5s/8s]
    Running the tests in ‘tests/doRUnit.R’ failed.
    Complete output:
     > ## unit tests will not be done if RUnit is not available
     > if(require("RUnit", quietly=TRUE)) {
     +
     + ## --- Setup ---
     +
     + pkg <- "CompGLM"
     + 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, "unit testing"),
     + 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] "CompGLM"
    
     $getwd
     [1] "/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/CompGLM.Rcheck/tests"
    
     $pathToUnitTests
     [1] "/tmp/Rtmpsz091T/RLIBS_5224fa6a654/CompGLM/unitTests"
    
    
    
     Executing test function test.dcomp ... done successfully.
    
    
    
     Executing test function test.glm.comp ... done successfully.
    
    
    
     Executing test function test.pcomp ... done successfully.
    
     ------------------- UNIT TEST SUMMARY ---------------------
    
     RUNIT TEST PROTOCOL -- Sat Jan 20 15:58:33 2018
     ***********************************************
     Number of test functions: 3
     Number of errors: 0
     Number of failures: 0
    
    
     1 Test Suite :
     CompGLM unit testing - 3 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/Rtmpsz091T/RLIBS_5224fa6a654/CompGLM/unitTests/reportSummary.txt': Read-only file system
     Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.0
Check: tests
Result: ERROR
     Running ‘doRUnit.R’ [7s/8s]
    Running the tests in ‘tests/doRUnit.R’ failed.
    Complete output:
     > ## unit tests will not be done if RUnit is not available
     > if(require("RUnit", quietly=TRUE)) {
     +
     + ## --- Setup ---
     +
     + pkg <- "CompGLM"
     + 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, "unit testing"),
     + 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] "CompGLM"
    
     $getwd
     [1] "/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/CompGLM.Rcheck/tests"
    
     $pathToUnitTests
     [1] "/tmp/RtmpgR2A0T/RLIBS_1f4f76b06d86/CompGLM/unitTests"
    
    
    
     Executing test function test.dcomp ... done successfully.
    
    
    
     Executing test function test.glm.comp ... done successfully.
    
    
    
     Executing test function test.pcomp ... done successfully.
    
     ------------------- UNIT TEST SUMMARY ---------------------
    
     RUNIT TEST PROTOCOL -- Fri Jan 19 16:31:49 2018
     ***********************************************
     Number of test functions: 3
     Number of errors: 0
     Number of failures: 0
    
    
     1 Test Suite :
     CompGLM unit testing - 3 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/RtmpgR2A0T/RLIBS_1f4f76b06d86/CompGLM/unitTests/reportSummary.txt': Read-only file system
     Execution halted
Flavor: r-patched-linux-x86_64

Version: 1.0
Check: tests
Result: ERROR
     Running ‘doRUnit.R’ [7s/8s]
    Running the tests in ‘tests/doRUnit.R’ failed.
    Complete output:
     > ## unit tests will not be done if RUnit is not available
     > if(require("RUnit", quietly=TRUE)) {
     +
     + ## --- Setup ---
     +
     + pkg <- "CompGLM"
     + 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, "unit testing"),
     + 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] "CompGLM"
    
     $getwd
     [1] "/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/CompGLM.Rcheck/tests"
    
     $pathToUnitTests
     [1] "/tmp/RtmpVhyYKz/RLIBS_722c40e2f705/CompGLM/unitTests"
    
    
    
     Executing test function test.dcomp ... done successfully.
    
    
    
     Executing test function test.glm.comp ... done successfully.
    
    
    
     Executing test function test.pcomp ... done successfully.
    
     ------------------- UNIT TEST SUMMARY ---------------------
    
     RUNIT TEST PROTOCOL -- Sat Jan 20 04:31:33 2018
     ***********************************************
     Number of test functions: 3
     Number of errors: 0
     Number of failures: 0
    
    
     1 Test Suite :
     CompGLM unit testing - 3 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/RtmpVhyYKz/RLIBS_722c40e2f705/CompGLM/unitTests/reportSummary.txt': Read-only file system
     Execution halted
Flavor: r-release-linux-x86_64