Last updated on 2025-05-09 01:50:37 CEST.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| di | 13 | ||
| haploR | 3 | 10 | |
| stpm | 4 | 9 |
Current CRAN status: OK: 13
Current CRAN status: ERROR: 3, OK: 10
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-gcc, r-release-linux-x86_64
Version: 4.0.7
Check: tests
Result: ERROR
Running ‘runTests.R’ [1s/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-devel-gcc/Work/PKGS/haploR.Rcheck/tests"
$pathToUnitTests
[1] "/tmp/RtmpXpTHNC/RLIBS_3cd7d230dad192/haploR/unitTests"
Executing test function test_queryHaploreg ... Timing stopped at: 0.072 0.002 121.6
Error in if (sp[[1]][i] != "") { : missing value where TRUE/FALSE needed
In addition: Warning messages:
1: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: Marsaglia-Multicarry has poor statistical properties
2: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
done successfully.
Executing test function test_queryRegulome ... No encoding supplied: defaulting to UTF-8.
done successfully.
RUNIT TEST PROTOCOL -- Thu May 8 16:12:07 2025
***********************************************
Number of test functions: 2
Number of errors: 1
Number of failures: 0
1 Test Suite :
haploR unit testing - 2 test functions, 1 error, 0 failures
ERROR in test_queryHaploreg: Error in if (sp[[1]][i] != "") { : missing value where TRUE/FALSE needed
Error:
Unit testing failed (#test failures: 0,
#R errors: 1)
In addition: Warning messages:
1: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: Marsaglia-Multicarry has poor statistical properties
2: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 4.0.7
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘haplor-vignette.Rmd’ using rmarkdown
Quitting from haplor-vignette.Rmd:153-157 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `if (sp[[1]][i] != "") ...`:
! missing value where TRUE/FALSE needed
---
Backtrace:
▆
1. └─haploR::queryHaploreg(query = c("rs10048158", "rs4791078"))
2. └─haploR:::simpleQuery(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'haplor-vignette.Rmd' failed with diagnostics:
missing value where TRUE/FALSE needed
--- failed re-building ‘haplor-vignette.Rmd’
SUMMARY: processing the following file failed:
‘haplor-vignette.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-debian-gcc, r-release-linux-x86_64
Version: 4.0.7
Check: tests
Result: ERROR
Running ‘runTests.R’ [2s/126s]
Running the tests in ‘tests/runTests.R’ failed.
Complete output:
> # Adapted from: http://rwiki.sciviews.org/doku.php?id=developers:runit
>
> if( identical( .Platform$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-release-gcc/Work/PKGS/haploR.Rcheck/tests"
$pathToUnitTests
[1] "/home/hornik/tmp/scratch/RtmpR5oxNC/RLIBS_3c2094331a3bb/haploR/unitTests"
Executing test function test_queryHaploreg ... Timing stopped at: 0.196 0.021 120.8
Error in if (sp[[1]][i] != "") { : missing value where TRUE/FALSE needed
In addition: Warning messages:
1: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: Marsaglia-Multicarry has poor statistical properties
2: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
done successfully.
Executing test function test_queryRegulome ... No encoding supplied: defaulting to UTF-8.
done successfully.
RUNIT TEST PROTOCOL -- Thu May 8 00:52:38 2025
***********************************************
Number of test functions: 2
Number of errors: 1
Number of failures: 0
1 Test Suite :
haploR unit testing - 2 test functions, 1 error, 0 failures
ERROR in test_queryHaploreg: Error in if (sp[[1]][i] != "") { : missing value where TRUE/FALSE needed
Error:
Unit testing failed (#test failures: 0,
#R errors: 1)
In addition: Warning messages:
1: In RNGkind(kind = testSuite$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
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
Flavor: r-release-windows-x86_64
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
Flavor: r-release-windows-x86_64
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