CRAN Package Check Results for Maintainer ‘Ilya Y. Zhbannikov <ilya.zhbannikov at duke.edu>’

Last updated on 2025-05-15 09:53:01 CEST.

Package ERROR NOTE OK
di 13
haploR 7 6
stpm 4 9

Package di

Current CRAN status: OK: 13

Package haploR

Current CRAN status: ERROR: 7, OK: 6

Version: 4.0.7
Check: examples
Result: ERROR Running examples in ‘haploR-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: getExtendedView > ### Title: This function queries HaploReg web-based tool in order to > ### Extended view for SNP of interest > ### Aliases: getExtendedView > > ### ** Examples > > tables <- getExtendedView(snp="rs10048158") Error in tables[[1]] : subscript out of bounds Calls: getExtendedView Execution halted Flavors: r-devel-linux-x86_64-debian-clang, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 4.0.7
Check: tests
Result: ERROR Running ‘runTests.R’ [2s/126s] Running the tests in ‘tests/runTests.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)) { + require("RCurl", quietly = TRUE) + pkg <- "haploR" + if(Sys.getenv("RCMDCHECK") == "FALSE") { + path <- file.path(getwd(), "..", "inst", "unitTests") + } else { + 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) + + # Define tests + testSuite <- defineTestSuite(name=paste(pkg, "unit testing"), + dirs=path, + testFuncRegexp = "^test_+", + testFileRegexp = "^test_+") + + # Run + tests <- runTestSuite(testSuite) + + # Default report name + pathReport <- file.path(path, "report") + + # Report to stdout + printTextProtocol(tests, showDetails=FALSE) + + # 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] "haploR" $getwd [1] "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/haploR.Rcheck/tests" $pathToUnitTests [1] "/home/hornik/tmp/scratch/RtmpMY0PUd/RLIBS_287bfb592bb3d7/haploR/unitTests" Executing test function test_queryHaploreg ... Timing stopped at: 0.183 0.028 120.9 Error in if (sp[[1]][i] != "") { : missing value where TRUE/FALSE needed In addition: Warning messages: 1: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: Marsaglia-Multicarry has poor statistical properties 2: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry done successfully. Executing test function test_queryRegulome ... No encoding supplied: defaulting to UTF-8. done successfully. RUNIT TEST PROTOCOL -- Tue May 13 01:18:24 2025 *********************************************** Number of test functions: 2 Number of errors: 1 Number of failures: 0 1 Test Suite : haploR unit testing - 2 test functions, 1 error, 0 failures ERROR in test_queryHaploreg: Error in if (sp[[1]][i] != "") { : missing value where TRUE/FALSE needed Error: Unit testing failed (#test failures: 0, #R errors: 1) In addition: Warning messages: 1: In RNGkind(kind = testSuite$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 Execution halted Flavor: r-devel-linux-x86_64-debian-clang

Version: 4.0.7
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘haplor-vignette.Rmd’ using rmarkdown Quitting from haplor-vignette.Rmd:153-157 [unnamed-chunk-3] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `if (sp[[1]][i] != "") ...`: ! missing value where TRUE/FALSE needed --- Backtrace: ▆ 1. └─haploR::queryHaploreg(query = c("rs10048158", "rs4791078")) 2. └─haploR:::simpleQuery(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'haplor-vignette.Rmd' failed with diagnostics: missing value where TRUE/FALSE needed --- failed re-building ‘haplor-vignette.Rmd’ SUMMARY: processing the following file failed: ‘haplor-vignette.Rmd’ Error: Vignette re-building failed. Execution halted Flavors: r-devel-linux-x86_64-debian-clang, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 4.0.7
Check: examples
Result: ERROR Running examples in ‘haploR-Ex.R’ failed The error most likely occurred in: > ### Name: getExtendedView > ### Title: This function queries HaploReg web-based tool in order to > ### Extended view for SNP of interest > ### Aliases: getExtendedView > > ### ** Examples > > tables <- getExtendedView(snp="rs10048158") Error in tables[[1]] : subscript out of bounds Calls: getExtendedView Execution halted Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-release-windows-x86_64

Version: 4.0.7
Check: tests
Result: ERROR Running ‘runTests.R’ [3s/129s] Running the tests in ‘tests/runTests.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)) { + require("RCurl", quietly = TRUE) + pkg <- "haploR" + if(Sys.getenv("RCMDCHECK") == "FALSE") { + path <- file.path(getwd(), "..", "inst", "unitTests") + } else { + 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) + + # Define tests + testSuite <- defineTestSuite(name=paste(pkg, "unit testing"), + dirs=path, + testFuncRegexp = "^test_+", + testFileRegexp = "^test_+") + + # Run + tests <- runTestSuite(testSuite) + + # Default report name + pathReport <- file.path(path, "report") + + # Report to stdout + printTextProtocol(tests, showDetails=FALSE) + + # 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] "haploR" $getwd [1] "/data/gannet/ripley/R/packages/tests-clang/haploR.Rcheck/tests" $pathToUnitTests [1] "/tmp/RtmpiOn0Pz/RLIBS_160ed220132c1b/haploR/unitTests" Executing test function test_queryHaploreg ... Timing stopped at: 0.123 0.008 121.6 Error in if (sp[[1]][i] != "") { : missing value where TRUE/FALSE needed In addition: Warning messages: 1: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: Marsaglia-Multicarry has poor statistical properties 2: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry done successfully. Executing test function test_queryRegulome ... No encoding supplied: defaulting to UTF-8. done successfully. RUNIT TEST PROTOCOL -- Sun May 11 05:00:14 2025 *********************************************** Number of test functions: 2 Number of errors: 1 Number of failures: 0 1 Test Suite : haploR unit testing - 2 test functions, 1 error, 0 failures ERROR in test_queryHaploreg: Error in if (sp[[1]][i] != "") { : missing value where TRUE/FALSE needed Error: Unit testing failed (#test failures: 0, #R errors: 1) In addition: Warning messages: 1: In RNGkind(kind = testSuite$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 Execution halted Flavor: r-devel-linux-x86_64-fedora-clang

Version: 4.0.7
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: --- re-building ‘haplor-vignette.Rmd’ using rmarkdown Quitting from haplor-vignette.Rmd:153-157 [unnamed-chunk-3] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `if (sp[[1]][i] != "") ...`: ! missing value where TRUE/FALSE needed --- Backtrace: ▆ 1. └─haploR::queryHaploreg(query = c("rs10048158", "rs4791078")) 2. └─haploR:::simpleQuery(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'haplor-vignette.Rmd' failed with diagnostics: missing value where TRUE/FALSE needed --- failed re-building ‘haplor-vignette.Rmd’ SUMMARY: processing the following file failed: ‘haplor-vignette.Rmd’ Error: Vignette re-building failed. Execution halted Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-release-windows-x86_64

Version: 4.0.7
Check: tests
Result: ERROR Running ‘runTests.R’ [3s/125s] Running the tests in ‘tests/runTests.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)) { + require("RCurl", quietly = TRUE) + pkg <- "haploR" + if(Sys.getenv("RCMDCHECK") == "FALSE") { + path <- file.path(getwd(), "..", "inst", "unitTests") + } else { + 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) + + # Define tests + testSuite <- defineTestSuite(name=paste(pkg, "unit testing"), + dirs=path, + testFuncRegexp = "^test_+", + testFileRegexp = "^test_+") + + # Run + tests <- runTestSuite(testSuite) + + # Default report name + pathReport <- file.path(path, "report") + + # Report to stdout + printTextProtocol(tests, showDetails=FALSE) + + # 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] "haploR" $getwd [1] "/data/gannet/ripley/R/packages/tests-devel/haploR.Rcheck/tests" $pathToUnitTests [1] "/data/gannet/ripley/R/packages/tests-devel/haploR.Rcheck/haploR/unitTests" Executing test function test_queryHaploreg ... Timing stopped at: 0.114 0.011 120.8 Error in if (sp[[1]][i] != "") { : missing value where TRUE/FALSE needed In addition: Warning messages: 1: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: Marsaglia-Multicarry has poor statistical properties 2: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry done successfully. Executing test function test_queryRegulome ... No encoding supplied: defaulting to UTF-8. done successfully. RUNIT TEST PROTOCOL -- Sun May 11 08:12:22 2025 *********************************************** Number of test functions: 2 Number of errors: 1 Number of failures: 0 1 Test Suite : haploR unit testing - 2 test functions, 1 error, 0 failures ERROR in test_queryHaploreg: Error in if (sp[[1]][i] != "") { : missing value where TRUE/FALSE needed Error: Unit testing failed (#test failures: 0, #R errors: 1) In addition: Warning messages: 1: In RNGkind(kind = testSuite$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 Execution halted Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 4.0.7
Check: tests
Result: ERROR Running ‘runTests.R’ [2s/125s] Running the tests in ‘tests/runTests.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)) { + require("RCurl", quietly = TRUE) + pkg <- "haploR" + if(Sys.getenv("RCMDCHECK") == "FALSE") { + path <- file.path(getwd(), "..", "inst", "unitTests") + } else { + 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) + + # Define tests + testSuite <- defineTestSuite(name=paste(pkg, "unit testing"), + dirs=path, + testFuncRegexp = "^test_+", + testFileRegexp = "^test_+") + + # Run + tests <- runTestSuite(testSuite) + + # Default report name + pathReport <- file.path(path, "report") + + # Report to stdout + printTextProtocol(tests, showDetails=FALSE) + + # 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] "haploR" $getwd [1] "/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/haploR.Rcheck/tests" $pathToUnitTests [1] "/home/hornik/tmp/scratch/RtmpsvtWA7/RLIBS_30af315f384d41/haploR/unitTests" Executing test function test_queryHaploreg ... Timing stopped at: 0.195 0.013 120.9 Error in if (sp[[1]][i] != "") { : missing value where TRUE/FALSE needed In addition: Warning messages: 1: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: Marsaglia-Multicarry has poor statistical properties 2: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry done successfully. Executing test function test_queryRegulome ... No encoding supplied: defaulting to UTF-8. done successfully. RUNIT TEST PROTOCOL -- Wed May 14 01:04:49 2025 *********************************************** Number of test functions: 2 Number of errors: 1 Number of failures: 0 1 Test Suite : haploR unit testing - 2 test functions, 1 error, 0 failures ERROR in test_queryHaploreg: Error in if (sp[[1]][i] != "") { : missing value where TRUE/FALSE needed Error: Unit testing failed (#test failures: 0, #R errors: 1) In addition: Warning messages: 1: In RNGkind(kind = testSuite$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 Execution halted Flavor: r-patched-linux-x86_64

Version: 4.0.7
Check: tests
Result: ERROR Running ‘runTests.R’ [2s/125s] Running the tests in ‘tests/runTests.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)) { + require("RCurl", quietly = TRUE) + pkg <- "haploR" + if(Sys.getenv("RCMDCHECK") == "FALSE") { + path <- file.path(getwd(), "..", "inst", "unitTests") + } else { + 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) + + # Define tests + testSuite <- defineTestSuite(name=paste(pkg, "unit testing"), + dirs=path, + testFuncRegexp = "^test_+", + testFileRegexp = "^test_+") + + # Run + tests <- runTestSuite(testSuite) + + # Default report name + pathReport <- file.path(path, "report") + + # Report to stdout + printTextProtocol(tests, showDetails=FALSE) + + # 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] "haploR" $getwd [1] "/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/haploR.Rcheck/tests" $pathToUnitTests [1] "/home/hornik/tmp/scratch/Rtmpv6nabE/RLIBS_1d6bf031dc501/haploR/unitTests" Executing test function test_queryHaploreg ... Timing stopped at: 0.18 0.036 120.8 Error in if (sp[[1]][i] != "") { : missing value where TRUE/FALSE needed In addition: Warning messages: 1: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: Marsaglia-Multicarry has poor statistical properties 2: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry done successfully. Executing test function test_queryRegulome ... No encoding supplied: defaulting to UTF-8. done successfully. RUNIT TEST PROTOCOL -- Sun May 11 00:58:10 2025 *********************************************** Number of test functions: 2 Number of errors: 1 Number of failures: 0 1 Test Suite : haploR unit testing - 2 test functions, 1 error, 0 failures ERROR in test_queryHaploreg: Error in if (sp[[1]][i] != "") { : missing value where TRUE/FALSE needed Error: Unit testing failed (#test failures: 0, #R errors: 1) In addition: Warning messages: 1: In RNGkind(kind = testSuite$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 Execution halted Flavor: r-release-linux-x86_64

Package stpm

Current CRAN status: NOTE: 4, OK: 9

Version: 1.7.12
Check: CRAN incoming feasibility
Result: NOTE Maintainer: ‘Ilya Y. Zhbannikov <ilya.zhbannikov@duke.edu>’ No Authors@R field in DESCRIPTION. Please add one, modifying Authors@R: c(person(given = "I.", family = "Zhbannikov", role = "aut"), person(given = "Liang", family = "He", role = "aut"), person(given = "K.", family = "Arbeev", role = "aut"), person(given = "I.", family = "Akushevich", role = "aut"), person(given = "A.", family = "Yashin.", role = "aut"), person(given = c("Ilya", "Y."), family = "Zhbannikov", role = "cre", email = "ilya.zhbannikov@duke.edu")) as necessary. Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 1.7.12
Check: installed package size
Result: NOTE installed size is 9.0Mb sub-directories of 1Mb or more: libs 6.7Mb Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.