CRAN Package Check Results for Package krm

Last updated on 2018-01-21 08:48:27 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2016.7-9 6.01 36.89 42.90 ERROR
r-devel-linux-x86_64-debian-gcc 2016.7-9 5.01 28.82 33.83 ERROR
r-devel-linux-x86_64-fedora-clang 2016.7-9 56.87 NOTE
r-devel-linux-x86_64-fedora-gcc 2016.7-9 51.96 NOTE
r-devel-windows-ix86+x86_64 2016.7-9 32.00 77.00 109.00 OK
r-patched-linux-x86_64 2016.7-9 5.78 36.84 42.62 ERROR
r-patched-solaris-x86 2016.7-9 77.30 OK
r-release-linux-x86_64 2016.7-9 5.75 36.35 42.10 ERROR
r-release-windows-ix86+x86_64 2016.7-9 24.00 73.00 97.00 OK
r-release-osx-x86_64 2016.7-9 OK
r-oldrel-windows-ix86+x86_64 2016.7-9 26.00 70.00 96.00 OK
r-oldrel-osx-x86_64 2016.7-9 OK

Check Details

Version: 2016.7-9
Check: compiled code
Result: NOTE
    File ‘krm/libs/krm.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: 2016.7-9
Check: tests
Result: ERROR
     Running ‘doRUnit.R’ [12s/16s]
    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 <- "krm" # <-- 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(), "unitTests")
     + } else {
     + ## Path to unit tests for R CMD check
     + ## PKG.Rcheck/tests/../PKG/unitTests
     + path <- system.file("unitTests", package=pkg)
     + }
     + 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] "krm"
    
     $getwd
     [1] "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/krm.Rcheck/tests"
    
     $pathToUnitTests
     [1] "/tmp/RtmpQqig7h/RLIBS_20ea18cf8925/krm/unitTests"
    
     Loading required package: kyotil
    
    
     Executing test function test.getSeqKernel ... done successfully.
    
    
    
     Executing test function test.krm.mos.test ... Loading required namespace: MASS
     formula.kern: ~z.1 + z.2 + z.3 + z.4 + z.5
     <environment: 0x3c52980>
     summary(c(l2dist)) = 0.211 5.4 8.88 10.3 13.5 67.9 100
     summary(c(rhos)) = 1.29 11.5 21.7 21.7 31.9 42.1
     rhos defined. time passed: Time difference of 0.07693362 secs
     dim(X) = 100 2
     beta.h = 0.347 0.761
     Total time passed: Time difference of 4.819507 secs
     formula.kern: ~z.1 + z.2 + z.3 + z.4 + z.5
     <environment: 0x3c52980>
     summary(c(l2dist)) = 0.211 5.4 8.88 10.3 13.5 67.9 100
     summary(c(rhos)) = 1.29 11.5 21.7 21.7 31.9 42.1
     rhos defined. time passed: Time difference of 0.1125717 secs
     dim(X) = 100 2
     beta.h = 0.347 0.761
     num [1:100, 1:100] 1 0.01383 0.03779 0.00277 0.00143 ...
     - attr(*, "dimnames")=List of 2
     ..$ : chr [1:100] "1" "2" "3" "4" ...
     ..$ : chr [1:100] "1" "2" "3" "4" ...
     num [1:100, 1:100] 0.97747 -0.02172 0.0023 -0.00945 -0.01565 ...
     num [1:100, 1:100] 1 0.996 0.997 0.994 0.994 ...
     - attr(*, "dimnames")=List of 2
     ..$ : chr [1:100] "1" "2" "3" "4" ...
     ..$ : chr [1:100] "1" "2" "3" "4" ...
     num [1:100, 1:100] 0.97747 -0.02172 0.0023 -0.00945 -0.01565 ...
     Total time passed: Time difference of 1.84239 secs
     formula.kern: ~z.1 + z.2 + z.3 + z.4 + z.5
     <environment: 0x3c52980>
     summary(c(l2dist)) = 0.504 5 7.95 9.31 12.7 43.8 50
     summary(c(rhos)) = 0.224 10.5 14.8 13.9 18.1 20.9
     rhos defined. time passed: Time difference of 0.004705667 secs
     dim(X) = 50 2
     beta.h = -0.214 0.984
     Total time passed: Time difference of 0.3670862 secs
     seq.file.name = /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/krm/misc/sim1.fasta
     summary(c(l2dist)) = 78.6 104 114 121 138 185 20
     summary(c(rhos)) = 4.64 41.2 77.8 77.8 114 151
     rhos defined. time passed: Time difference of 1.071886 secs
     dim(X) = 20 1
     beta.h = -0.847
     Total time passed: Time difference of 1.627902 secs
     formula.kern: ~seq
     <environment: 0x3c52980>
     summary(c(l2dist)) = 78.6 104 114 121 138 185 20
     summary(c(rhos)) = 4.64 41.2 77.8 77.8 114 151
     rhos defined. time passed: Time difference of 1.174671 secs
     dim(X) = 20 1
     beta.h = -0.847
     Total time passed: Time difference of 2.043262 secs
     formula.kern: ~seq
     <environment: 0x3c52980>
     summary(c(l2dist)) = 6.29 12.5 15.3 15.4 18.1 23.9 20
     summary(c(rhos)) = 1.7 15.1 28.5 28.5 41.9 55.2
     rhos defined. time passed: Time difference of 0.255465 secs
     dim(X) = 20 1
     beta.h = -0.847
     Total time passed: Time difference of 0.9075532 secs
     done successfully.
    
    
    
     Executing test function test.krm.score.test ... done successfully.
    
     ------------------- UNIT TEST SUMMARY ---------------------
    
     RUNIT TEST PROTOCOL -- Fri Jan 19 08:18:34 2018
     ***********************************************
     Number of test functions: 3
     Number of errors: 0
     Number of failures: 0
    
    
     1 Test Suite :
     krm 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/RtmpQqig7h/RLIBS_20ea18cf8925/krm/unitTests/reportSummary.txt': Read-only file system
     Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 2016.7-9
Check: tests
Result: ERROR
     Running ‘doRUnit.R’ [9s/13s]
    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 <- "krm" # <-- 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(), "unitTests")
     + } else {
     + ## Path to unit tests for R CMD check
     + ## PKG.Rcheck/tests/../PKG/unitTests
     + path <- system.file("unitTests", package=pkg)
     + }
     + 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] "krm"
    
     $getwd
     [1] "/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/krm.Rcheck/tests"
    
     $pathToUnitTests
     [1] "/tmp/RtmpaQTcKP/RLIBS_239977ec8fd7/krm/unitTests"
    
     Loading required package: kyotil
    
    
     Executing test function test.getSeqKernel ... done successfully.
    
    
    
     Executing test function test.krm.mos.test ... Loading required namespace: MASS
     formula.kern: ~z.1 + z.2 + z.3 + z.4 + z.5
     <environment: 0x55c1dc5cc600>
     summary(c(l2dist)) = 0.211 5.4 8.88 10.3 13.5 67.9 100
     summary(c(rhos)) = 1.29 11.5 21.7 21.7 31.9 42.1
     rhos defined. time passed: Time difference of 0.09218144 secs
     dim(X) = 100 2
     beta.h = 0.347 0.761
     Total time passed: Time difference of 3.135522 secs
     formula.kern: ~z.1 + z.2 + z.3 + z.4 + z.5
     <environment: 0x55c1dc5cc600>
     summary(c(l2dist)) = 0.211 5.4 8.88 10.3 13.5 67.9 100
     summary(c(rhos)) = 1.29 11.5 21.7 21.7 31.9 42.1
     rhos defined. time passed: Time difference of 0.04410553 secs
     dim(X) = 100 2
     beta.h = 0.347 0.761
     num [1:100, 1:100] 1 0.01383 0.03779 0.00277 0.00143 ...
     - attr(*, "dimnames")=List of 2
     ..$ : chr [1:100] "1" "2" "3" "4" ...
     ..$ : chr [1:100] "1" "2" "3" "4" ...
     num [1:100, 1:100] 0.97747 -0.02172 0.0023 -0.00945 -0.01565 ...
     num [1:100, 1:100] 1 0.996 0.997 0.994 0.994 ...
     - attr(*, "dimnames")=List of 2
     ..$ : chr [1:100] "1" "2" "3" "4" ...
     ..$ : chr [1:100] "1" "2" "3" "4" ...
     num [1:100, 1:100] 0.97747 -0.02172 0.0023 -0.00945 -0.01565 ...
     Total time passed: Time difference of 1.2622 secs
     formula.kern: ~z.1 + z.2 + z.3 + z.4 + z.5
     <environment: 0x55c1dc5cc600>
     summary(c(l2dist)) = 0.504 5 7.95 9.31 12.7 43.8 50
     summary(c(rhos)) = 0.224 10.5 14.8 13.9 18.1 20.9
     rhos defined. time passed: Time difference of 0.01371241 secs
     dim(X) = 50 2
     beta.h = -0.214 0.984
     Total time passed: Time difference of 0.462142 secs
     seq.file.name = /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/krm/misc/sim1.fasta
     summary(c(l2dist)) = 78.6 104 114 121 138 185 20
     summary(c(rhos)) = 4.64 41.2 77.8 77.8 114 151
     rhos defined. time passed: Time difference of 0.7946863 secs
     dim(X) = 20 1
     beta.h = -0.847
     Total time passed: Time difference of 1.458995 secs
     formula.kern: ~seq
     <environment: 0x55c1dc5cc600>
     summary(c(l2dist)) = 78.6 104 114 121 138 185 20
     summary(c(rhos)) = 4.64 41.2 77.8 77.8 114 151
     rhos defined. time passed: Time difference of 1.143505 secs
     dim(X) = 20 1
     beta.h = -0.847
     Total time passed: Time difference of 1.635276 secs
     formula.kern: ~seq
     <environment: 0x55c1dc5cc600>
     summary(c(l2dist)) = 6.29 12.5 15.3 15.4 18.1 23.9 20
     summary(c(rhos)) = 1.7 15.1 28.5 28.5 41.9 55.2
     rhos defined. time passed: Time difference of 0.178056 secs
     dim(X) = 20 1
     beta.h = -0.847
     Total time passed: Time difference of 1.029869 secs
     done successfully.
    
    
    
     Executing test function test.krm.score.test ... done successfully.
    
     ------------------- UNIT TEST SUMMARY ---------------------
    
     RUNIT TEST PROTOCOL -- Sat Jan 20 18:53:41 2018
     ***********************************************
     Number of test functions: 3
     Number of errors: 0
     Number of failures: 0
    
    
     1 Test Suite :
     krm 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/RtmpaQTcKP/RLIBS_239977ec8fd7/krm/unitTests/reportSummary.txt': Read-only file system
     Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 2016.7-9
Check: tests
Result: ERROR
     Running ‘doRUnit.R’ [13s/15s]
    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 <- "krm" # <-- 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(), "unitTests")
     + } else {
     + ## Path to unit tests for R CMD check
     + ## PKG.Rcheck/tests/../PKG/unitTests
     + path <- system.file("unitTests", package=pkg)
     + }
     + 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] "krm"
    
     $getwd
     [1] "/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/krm.Rcheck/tests"
    
     $pathToUnitTests
     [1] "/tmp/RtmpKr9Qze/RLIBS_4df11432489/krm/unitTests"
    
     Loading required package: kyotil
    
    
     Executing test function test.getSeqKernel ... done successfully.
    
    
    
     Executing test function test.krm.mos.test ... Loading required namespace: MASS
     formula.kern: ~z.1 + z.2 + z.3 + z.4 + z.5
     <environment: 0x55acbb1f1c48>
     summary(c(l2dist)) = 0.211 5.4 8.88 10.3 13.5 67.9 100
     summary(c(rhos)) = 1.29 11.5 21.7 21.7 31.9 42.1
     rhos defined. time passed: Time difference of 0.1118257 secs
     dim(X) = 100 2
     beta.h = 0.347 0.761
     Total time passed: Time difference of 4.820995 secs
     formula.kern: ~z.1 + z.2 + z.3 + z.4 + z.5
     <environment: 0x55acbb1f1c48>
     summary(c(l2dist)) = 0.211 5.4 8.88 10.3 13.5 67.9 100
     summary(c(rhos)) = 1.29 11.5 21.7 21.7 31.9 42.1
     rhos defined. time passed: Time difference of 0.06379747 secs
     dim(X) = 100 2
     beta.h = 0.347 0.761
     num [1:100, 1:100] 1 0.01383 0.03779 0.00277 0.00143 ...
     - attr(*, "dimnames")=List of 2
     ..$ : chr [1:100] "1" "2" "3" "4" ...
     ..$ : chr [1:100] "1" "2" "3" "4" ...
     num [1:100, 1:100] 0.97747 -0.02172 0.0023 -0.00945 -0.01565 ...
     num [1:100, 1:100] 1 0.996 0.997 0.994 0.994 ...
     - attr(*, "dimnames")=List of 2
     ..$ : chr [1:100] "1" "2" "3" "4" ...
     ..$ : chr [1:100] "1" "2" "3" "4" ...
     num [1:100, 1:100] 0.97747 -0.02172 0.0023 -0.00945 -0.01565 ...
     Total time passed: Time difference of 1.647518 secs
     formula.kern: ~z.1 + z.2 + z.3 + z.4 + z.5
     <environment: 0x55acbb1f1c48>
     summary(c(l2dist)) = 0.504 5 7.95 9.31 12.7 43.8 50
     summary(c(rhos)) = 0.224 10.5 14.8 13.9 18.1 20.9
     rhos defined. time passed: Time difference of 0.004720926 secs
     dim(X) = 50 2
     beta.h = -0.214 0.984
     Total time passed: Time difference of 0.5458667 secs
     seq.file.name = /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/krm/misc/sim1.fasta
     summary(c(l2dist)) = 78.6 104 114 121 138 185 20
     summary(c(rhos)) = 4.64 41.2 77.8 77.8 114 151
     rhos defined. time passed: Time difference of 0.9755752 secs
     dim(X) = 20 1
     beta.h = -0.847
     Total time passed: Time difference of 1.598082 secs
     formula.kern: ~seq
     <environment: 0x55acbb1f1c48>
     summary(c(l2dist)) = 78.6 104 114 121 138 185 20
     summary(c(rhos)) = 4.64 41.2 77.8 77.8 114 151
     rhos defined. time passed: Time difference of 1.132735 secs
     dim(X) = 20 1
     beta.h = -0.847
     Total time passed: Time difference of 1.811226 secs
     formula.kern: ~seq
     <environment: 0x55acbb1f1c48>
     summary(c(l2dist)) = 6.29 12.5 15.3 15.4 18.1 23.9 20
     summary(c(rhos)) = 1.7 15.1 28.5 28.5 41.9 55.2
     rhos defined. time passed: Time difference of 0.1291304 secs
     dim(X) = 20 1
     beta.h = -0.847
     Total time passed: Time difference of 0.7603676 secs
     done successfully.
    
    
    
     Executing test function test.krm.score.test ... done successfully.
    
     ------------------- UNIT TEST SUMMARY ---------------------
    
     RUNIT TEST PROTOCOL -- Fri Jan 19 20:20:19 2018
     ***********************************************
     Number of test functions: 3
     Number of errors: 0
     Number of failures: 0
    
    
     1 Test Suite :
     krm 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/RtmpKr9Qze/RLIBS_4df11432489/krm/unitTests/reportSummary.txt': Read-only file system
     Execution halted
Flavor: r-patched-linux-x86_64

Version: 2016.7-9
Check: tests
Result: ERROR
     Running ‘doRUnit.R’ [12s/15s]
    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 <- "krm" # <-- 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(), "unitTests")
     + } else {
     + ## Path to unit tests for R CMD check
     + ## PKG.Rcheck/tests/../PKG/unitTests
     + path <- system.file("unitTests", package=pkg)
     + }
     + 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] "krm"
    
     $getwd
     [1] "/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/krm.Rcheck/tests"
    
     $pathToUnitTests
     [1] "/tmp/Rtmp0w8as8/RLIBS_7f52115b6932/krm/unitTests"
    
     Loading required package: kyotil
    
    
     Executing test function test.getSeqKernel ... done successfully.
    
    
    
     Executing test function test.krm.mos.test ... Loading required namespace: MASS
     formula.kern: ~z.1 + z.2 + z.3 + z.4 + z.5
     <environment: 0x561a8cdf67a8>
     summary(c(l2dist)) = 0.211 5.4 8.88 10.3 13.5 67.9 100
     summary(c(rhos)) = 1.29 11.5 21.7 21.7 31.9 42.1
     rhos defined. time passed: Time difference of 0.09044552 secs
     dim(X) = 100 2
     beta.h = 0.347 0.761
     Total time passed: Time difference of 4.995609 secs
     formula.kern: ~z.1 + z.2 + z.3 + z.4 + z.5
     <environment: 0x561a8cdf67a8>
     summary(c(l2dist)) = 0.211 5.4 8.88 10.3 13.5 67.9 100
     summary(c(rhos)) = 1.29 11.5 21.7 21.7 31.9 42.1
     rhos defined. time passed: Time difference of 0.05507994 secs
     dim(X) = 100 2
     beta.h = 0.347 0.761
     num [1:100, 1:100] 1 0.01383 0.03779 0.00277 0.00143 ...
     - attr(*, "dimnames")=List of 2
     ..$ : chr [1:100] "1" "2" "3" "4" ...
     ..$ : chr [1:100] "1" "2" "3" "4" ...
     num [1:100, 1:100] 0.97747 -0.02172 0.0023 -0.00945 -0.01565 ...
     num [1:100, 1:100] 1 0.996 0.997 0.994 0.994 ...
     - attr(*, "dimnames")=List of 2
     ..$ : chr [1:100] "1" "2" "3" "4" ...
     ..$ : chr [1:100] "1" "2" "3" "4" ...
     num [1:100, 1:100] 0.97747 -0.02172 0.0023 -0.00945 -0.01565 ...
     Total time passed: Time difference of 1.82287 secs
     formula.kern: ~z.1 + z.2 + z.3 + z.4 + z.5
     <environment: 0x561a8cdf67a8>
     summary(c(l2dist)) = 0.504 5 7.95 9.31 12.7 43.8 50
     summary(c(rhos)) = 0.224 10.5 14.8 13.9 18.1 20.9
     rhos defined. time passed: Time difference of 0.005116701 secs
     dim(X) = 50 2
     beta.h = -0.214 0.984
     Total time passed: Time difference of 0.4804842 secs
     seq.file.name = /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/krm/misc/sim1.fasta
     summary(c(l2dist)) = 78.6 104 114 121 138 185 20
     summary(c(rhos)) = 4.64 41.2 77.8 77.8 114 151
     rhos defined. time passed: Time difference of 1.300852 secs
     dim(X) = 20 1
     beta.h = -0.847
     Total time passed: Time difference of 2.000584 secs
     formula.kern: ~seq
     <environment: 0x561a8cdf67a8>
     summary(c(l2dist)) = 78.6 104 114 121 138 185 20
     summary(c(rhos)) = 4.64 41.2 77.8 77.8 114 151
     rhos defined. time passed: Time difference of 0.8899593 secs
     dim(X) = 20 1
     beta.h = -0.847
     Total time passed: Time difference of 1.531859 secs
     formula.kern: ~seq
     <environment: 0x561a8cdf67a8>
     summary(c(l2dist)) = 6.29 12.5 15.3 15.4 18.1 23.9 20
     summary(c(rhos)) = 1.7 15.1 28.5 28.5 41.9 55.2
     rhos defined. time passed: Time difference of 0.1232872 secs
     dim(X) = 20 1
     beta.h = -0.847
     Total time passed: Time difference of 0.6957598 secs
     done successfully.
    
    
    
     Executing test function test.krm.score.test ... done successfully.
    
     ------------------- UNIT TEST SUMMARY ---------------------
    
     RUNIT TEST PROTOCOL -- Sat Jan 20 08:19:41 2018
     ***********************************************
     Number of test functions: 3
     Number of errors: 0
     Number of failures: 0
    
    
     1 Test Suite :
     krm 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/Rtmp0w8as8/RLIBS_7f52115b6932/krm/unitTests/reportSummary.txt': Read-only file system
     Execution halted
Flavor: r-release-linux-x86_64