Last updated on 2025-02-24 19:50:35 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 4.0.7 | 6.25 | 56.83 | 63.08 | OK | |
| r-devel-linux-x86_64-debian-gcc | 4.0.7 | 4.16 | 41.72 | 45.88 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 4.0.7 | 100.09 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 4.0.7 | 108.49 | OK | |||
| r-devel-macos-arm64 | 4.0.7 | 65.00 | OK | |||
| r-devel-macos-x86_64 | 4.0.7 | 98.00 | OK | |||
| r-devel-windows-x86_64 | 4.0.7 | 9.00 | 82.00 | 91.00 | OK | |
| r-patched-linux-x86_64 | 4.0.7 | 6.14 | 52.66 | 58.80 | OK | |
| r-release-linux-x86_64 | 4.0.7 | 5.54 | 53.30 | 58.84 | ERROR | |
| r-release-macos-arm64 | 4.0.7 | 59.00 | OK | |||
| r-release-macos-x86_64 | 4.0.7 | 88.00 | OK | |||
| r-release-windows-x86_64 | 4.0.7 | 7.00 | 93.00 | 100.00 | OK | |
| r-oldrel-macos-arm64 | 4.0.7 | 53.00 | OK | |||
| r-oldrel-macos-x86_64 | 4.0.7 | 86.00 | OK | |||
| r-oldrel-windows-x86_64 | 4.0.7 | 10.00 | 86.00 | 96.00 | OK |
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: queryRegulome
> ### Title: This function queries RegulomeDB web-based tool and returns
> ### results in a data frame.
> ### Aliases: queryRegulome
>
> ### ** Examples
>
> data <- queryRegulome(c("rs4791078","rs10048158"))
<simpleError in file(con, "r"): cannot open the connection>
Error in regulomeSummary(query = query, genomeAssembly = genomeAssembly, :
object 'out' not found
Calls: queryRegulome -> regulomeSummary -> as_tibble
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/9s]
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"
$pathToUnitTests
[1] "/tmp/RtmpXp2Iiq/RLIBS_390dcf682cf5cb/haploR/unitTests"
Executing test function test_queryHaploreg ... done successfully.
Executing test function test_queryRegulome ... <simpleError in file(con, "r"): cannot open the connection>
Timing stopped at: 0.035 0.005 1.58
Error in regulomeSummary(c("rs4791078", "rs10048158"), timeout = 1e+05) :
object 'out' not found
In addition: Warning messages:
1: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: Marsaglia-Multicarry has poor statistical properties
2: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
3: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: Marsaglia-Multicarry has poor statistical properties
4: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
done successfully.
RUNIT TEST PROTOCOL -- Mon Feb 24 15:54:03 2025
***********************************************
Number of test functions: 2
Number of errors: 1
Number of failures: 0
1 Test Suite :
haploR unit testing - 2 test functions, 1 error, 0 failures
ERROR in test_queryRegulome: Error in regulomeSummary(c("rs4791078", "rs10048158"), timeout = 1e+05) :
object 'out' not found
Error:
Unit testing failed (#test failures: 0,
#R errors: 1)
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 4.0.7
Check: tests
Result: ERROR
Running ‘runTests.R’ [3s/9s]
Running the tests in ‘tests/runTests.R’ failed.
Complete output:
> # Adapted from: http://rwiki.sciviews.org/doku.php?id=developers:runit
>
> if( identical( .Platform$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"
$pathToUnitTests
[1] "/home/hornik/tmp/scratch/RtmpvOs9zt/RLIBS_295cec53440c60/haploR/unitTests"
Executing test function test_queryHaploreg ... done successfully.
Executing test function test_queryRegulome ... <simpleError in file(con, "r"): cannot open the connection>
Timing stopped at: 0.175 0.013 1.587
Error in regulomeSummary(c("rs4791078", "rs10048158"), timeout = 1e+05) :
object 'out' not found
In addition: Warning messages:
1: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: Marsaglia-Multicarry has poor statistical properties
2: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
3: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: Marsaglia-Multicarry has poor statistical properties
4: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
done successfully.
RUNIT TEST PROTOCOL -- Sun Feb 23 00:13:48 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_queryRegulome: Error in regulomeSummary(c("rs4791078", "rs10048158"), timeout = 1e+05) :
object 'out' not found
Error:
Unit testing failed (#test failures: 0,
#R errors: 1)
Execution halted
Flavor: r-release-linux-x86_64