Last updated on 2023-03-11 08:54:09 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 4.0.6 | 7.54 | 65.56 | 73.10 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 4.0.6 | 4.73 | 49.74 | 54.47 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 4.0.6 | 91.38 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 4.0.6 | 98.24 | ERROR | |||
| r-devel-windows-x86_64 | 4.0.6 | 16.00 | 93.00 | 109.00 | ERROR | |
| r-patched-linux-x86_64 | 4.0.6 | 7.60 | 62.84 | 70.44 | ERROR | |
| r-release-linux-x86_64 | 4.0.6 | 7.46 | 61.70 | 69.16 | ERROR | |
| r-release-macos-arm64 | 4.0.6 | 39.00 | OK | |||
| r-release-macos-x86_64 | 4.0.6 | 55.00 | OK | |||
| r-release-windows-x86_64 | 4.0.6 | 21.00 | 97.00 | 118.00 | ERROR | |
| r-oldrel-macos-arm64 | 4.0.6 | 40.00 | OK | |||
| r-oldrel-macos-x86_64 | 4.0.6 | 50.00 | OK | |||
| r-oldrel-windows-ix86+x86_64 | 4.0.6 | 19.00 | 85.00 | 104.00 | ERROR |
Version: 4.0.6
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-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 4.0.6
Check: tests
Result: ERROR
Running ‘runTests.R’ [3s/7s]
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"
$pathToUnitTests
[1] "/tmp/RtmpHo4vJq/RLIBS_16c31d7ce10bd6/haploR/unitTests"
Executing test function test_queryHaploreg ... Timing stopped at: 0.368 0.048 2.034
Error in tmp.tables[[i]] : subscript out of bounds
In addition: Warning messages:
1: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: Marsaglia-Multicarry has poor statistical properties
2: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
done successfully.
Executing test function test_queryRegulome ... No encoding supplied: defaulting to UTF-8.
done successfully.
RUNIT TEST PROTOCOL -- Fri Mar 10 13:52:49 2023
***********************************************
Number of test functions: 2
Number of errors: 1
Number of failures: 0
1 Test Suite :
haploR unit testing - 2 test functions, 1 error, 0 failures
ERROR in test_queryHaploreg: Error in tmp.tables[[i]] : subscript out of bounds
Error:
Unit testing failed (#test failures: 0,
#R errors: 1)
In addition: Warning messages:
1: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: Marsaglia-Multicarry has poor statistical properties
2: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 4.0.6
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘haplor-vignette.Rmd’ using rmarkdown
Quitting from lines 154-157 (haplor-vignette.Rmd)
Error: processing vignette ‘haplor-vignette.Rmd’ failed with diagnostics:
subscript out of bounds
--- failed re-building ‘haplor-vignette.Rmd’
SUMMARY: processing the following file failed:
‘haplor-vignette.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 4.0.6
Check: tests
Result: ERROR
Running ‘runTests.R’ [2s/6s]
Running the tests in ‘tests/runTests.R’ failed.
Complete output:
> # Adapted from: http://rwiki.sciviews.org/doku.php?id=developers:runit
>
> if( identical( .Platform$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-gcc/Work/PKGS/haploR.Rcheck/tests"
$pathToUnitTests
[1] "/home/hornik/tmp/scratch/Rtmpcb9QaV/RLIBS_c52e041b8fa8f/haploR/unitTests"
Executing test function test_queryHaploreg ... Timing stopped at: 0.319 0.004 1.679
Error in tmp.tables[[i]] : subscript out of bounds
In addition: Warning messages:
1: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: Marsaglia-Multicarry has poor statistical properties
2: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
done successfully.
Executing test function test_queryRegulome ... No encoding supplied: defaulting to UTF-8.
done successfully.
RUNIT TEST PROTOCOL -- Fri Mar 10 22:07:45 2023
***********************************************
Number of test functions: 2
Number of errors: 1
Number of failures: 0
1 Test Suite :
haploR unit testing - 2 test functions, 1 error, 0 failures
ERROR in test_queryHaploreg: Error in tmp.tables[[i]] : subscript out of bounds
Error:
Unit testing failed (#test failures: 0,
#R errors: 1)
In addition: Warning messages:
1: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: Marsaglia-Multicarry has poor statistical properties
2: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 4.0.6
Check: examples
Result: ERROR
Running examples in ‘haploR-Ex.R’ failed
The error most likely occurred in:
> ### Name: getExtendedView
> ### Title: This function queries HaploReg web-based tool in order to
> ### Extended view for SNP of interest
> ### Aliases: getExtendedView
>
> ### ** Examples
>
> tables <- getExtendedView(snp="rs10048158")
Error in tables[[1]] : subscript out of bounds
Calls: getExtendedView
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-release-windows-x86_64, r-oldrel-windows-ix86+x86_64
Version: 4.0.6
Check: tests
Result: ERROR
Running ‘runTests.R’
Running the tests in ‘tests/runTests.R’ failed.
Complete output:
> # Adapted from: http://rwiki.sciviews.org/doku.php?id=developers:runit
>
> if( identical( .Platform$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"
$pathToUnitTests
[1] "/tmp/RtmpnM6Hrr/RLIBS_30762be52353/haploR/unitTests"
Executing test function test_queryHaploreg ... Timing stopped at: 0.479 0.011 1.635
Error in tmp.tables[[i]] : subscript out of bounds
In addition: Warning messages:
1: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: Marsaglia-Multicarry has poor statistical properties
2: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
done successfully.
Executing test function test_queryRegulome ... No encoding supplied: defaulting to UTF-8.
done successfully.
RUNIT TEST PROTOCOL -- Sat Feb 25 08:18:05 2023
***********************************************
Number of test functions: 2
Number of errors: 1
Number of failures: 0
1 Test Suite :
haploR unit testing - 2 test functions, 1 error, 0 failures
ERROR in test_queryHaploreg: Error in tmp.tables[[i]] : subscript out of bounds
Error:
Unit testing failed (#test failures: 0,
#R errors: 1)
In addition: Warning messages:
1: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: Marsaglia-Multicarry has poor statistical properties
2: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 4.0.6
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘haplor-vignette.Rmd’ using rmarkdown
Quitting from lines 154-157 (haplor-vignette.Rmd)
Error: processing vignette 'haplor-vignette.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘haplor-vignette.Rmd’
SUMMARY: processing the following file failed:
‘haplor-vignette.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-release-windows-x86_64
Version: 4.0.6
Check: tests
Result: ERROR
Running ‘runTests.R’
Running the tests in ‘tests/runTests.R’ failed.
Complete output:
> # Adapted from: http://rwiki.sciviews.org/doku.php?id=developers:runit
>
> if( identical( .Platform$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"
$pathToUnitTests
[1] "/data/gannet/ripley/R/packages/tests-devel/haploR.Rcheck/haploR/unitTests"
Executing test function test_queryHaploreg ... Timing stopped at: 0.415 0.01 1.493
Error in tmp.tables[[i]] : subscript out of bounds
In addition: Warning messages:
1: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: Marsaglia-Multicarry has poor statistical properties
2: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
done successfully.
Executing test function test_queryRegulome ... No encoding supplied: defaulting to UTF-8.
done successfully.
RUNIT TEST PROTOCOL -- Sun Mar 5 06:22:17 2023
***********************************************
Number of test functions: 2
Number of errors: 1
Number of failures: 0
1 Test Suite :
haploR unit testing - 2 test functions, 1 error, 0 failures
ERROR in test_queryHaploreg: Error in tmp.tables[[i]] : subscript out of bounds
Error:
Unit testing failed (#test failures: 0,
#R errors: 1)
In addition: Warning messages:
1: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: Marsaglia-Multicarry has poor statistical properties
2: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 4.0.6
Check: tests
Result: ERROR
Running ‘runTests.R’ [3s/7s]
Running the tests in ‘tests/runTests.R’ failed.
Complete output:
> # Adapted from: http://rwiki.sciviews.org/doku.php?id=developers:runit
>
> if( identical( .Platform$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"
$pathToUnitTests
[1] "/tmp/RtmpGPoP07/RLIBS_7bfac7c18fc39/haploR/unitTests"
Executing test function test_queryHaploreg ... Timing stopped at: 0.356 0.059 1.899
Error in tmp.tables[[i]] : subscript out of bounds
In addition: Warning messages:
1: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: Marsaglia-Multicarry has poor statistical properties
2: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
done successfully.
Executing test function test_queryRegulome ... No encoding supplied: defaulting to UTF-8.
done successfully.
RUNIT TEST PROTOCOL -- Wed Mar 8 05:43:12 2023
***********************************************
Number of test functions: 2
Number of errors: 1
Number of failures: 0
1 Test Suite :
haploR unit testing - 2 test functions, 1 error, 0 failures
ERROR in test_queryHaploreg: Error in tmp.tables[[i]] : subscript out of bounds
Error:
Unit testing failed (#test failures: 0,
#R errors: 1)
In addition: Warning messages:
1: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: Marsaglia-Multicarry has poor statistical properties
2: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
Execution halted
Flavor: r-patched-linux-x86_64
Version: 4.0.6
Check: tests
Result: ERROR
Running ‘runTests.R’ [3s/6s]
Running the tests in ‘tests/runTests.R’ failed.
Complete output:
> # Adapted from: http://rwiki.sciviews.org/doku.php?id=developers:runit
>
> if( identical( .Platform$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"
$pathToUnitTests
[1] "/tmp/RtmpWxtyMD/RLIBS_2ba7c54ee49b37/haploR/unitTests"
Executing test function test_queryHaploreg ... Timing stopped at: 0.384 0.176 1.901
Error in tmp.tables[[i]] : subscript out of bounds
In addition: Warning messages:
1: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: Marsaglia-Multicarry has poor statistical properties
2: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
done successfully.
Executing test function test_queryRegulome ... No encoding supplied: defaulting to UTF-8.
done successfully.
RUNIT TEST PROTOCOL -- Thu Mar 9 09:24:43 2023
***********************************************
Number of test functions: 2
Number of errors: 1
Number of failures: 0
1 Test Suite :
haploR unit testing - 2 test functions, 1 error, 0 failures
ERROR in test_queryHaploreg: Error in tmp.tables[[i]] : subscript out of bounds
Error:
Unit testing failed (#test failures: 0,
#R errors: 1)
In addition: Warning messages:
1: In RNGkind(kind = testSuite$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
Version: 4.0.6
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building 'haplor-vignette.Rmd' using rmarkdown
Quitting from lines 154-157 (haplor-vignette.Rmd)
Error: processing vignette 'haplor-vignette.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building 'haplor-vignette.Rmd'
SUMMARY: processing the following file failed:
'haplor-vignette.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-oldrel-windows-ix86+x86_64