Last updated on 2026-10-24 01:51:38 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2024.5-17 | 1.73 | 31.19 | 32.92 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2024.5-17 | 1.48 | 23.63 | 25.11 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 2024.5-17 | 27.35 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2024.5-17 | 29.01 | OK | |||
| r-devel-windows-x86_64 | 2024.5-17 | 5.00 | 55.00 | 60.00 | OK | |
| r-patched-linux-x86_64 | 2024.5-17 | 1.79 | 27.94 | 29.73 | OK | |
| r-release-linux-x86_64 | 2024.5-17 | 1.71 | 27.99 | 29.70 | OK | |
| r-release-macos-arm64 | 2024.5-17 | 1.00 | 15.00 | 16.00 | OK | |
| r-release-macos-x86_64 | 2024.5-17 | 2.00 | 60.00 | 62.00 | OK | |
| r-release-windows-x86_64 | 2024.5-17 | 3.00 | 51.00 | 54.00 | OK | |
| r-oldrel-macos-arm64 | 2024.5-17 | OK | ||||
| r-oldrel-macos-x86_64 | 2024.5-17 | 1.00 | 46.00 | 47.00 | OK | |
| r-oldrel-windows-x86_64 | 2024.5-17 | 4.00 | 54.00 | 58.00 | OK |
Version: 2024.5-17
Check: examples
Result: ERROR
Running examples in ‘marginalizedRisk-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: marginalized.risk
> ### Title: Compute Maringalized Risk
> ### Aliases: marginalized.risk marginalizedRisk marginalized.risk.cat
> ### marginalized.risk.cont marginalized.risk.cont.2
>
> ### ** Examples
>
>
>
> #### suppose wt.loss is the marker of interest
>
> if(requireNamespace("survival")) {
+
+ library(survival)
+
+ dat=subset(lung, !is.na(wt.loss) & !is.na(ph.ecog))
+
+ f1=Surv(time, status) ~ wt.loss + ph.ecog + age + sex
+
+ fit.risk = coxph(f1, data=dat)
+
+ ss=quantile(dat$wt.loss, seq(.05,.95,by=0.01))
+ t0=1000
+ prob = marginalized.risk(fit.risk, "wt.loss", dat, categorical.s=FALSE, t = t0, ss=ss)
+
+ plot(ss, prob, type="l", xlab="Weight loss", ylab=paste0("Probability of survival at day ", t0))
+
+ }
Loading required namespace: survival
Error in a$specials[[i]] : subscript out of bounds
Calls: marginalized.risk ... model.matrix -> model.matrix.coxph -> delete.response -> off
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2024.5-17
Check: tests
Result: ERROR
Running ‘doRUnit.R’ [1s/2s]
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 <- "marginalizedRisk" # <-- 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 <- tempdir()
+
+ ## 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] "marginalizedRisk"
$getwd
[1] "/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/marginalizedRisk.Rcheck/tests"
$pathToUnitTests
[1] "/home/hornik/tmp/scratch/RtmpORqfO5/RLIBS_3d05c84036e7ec/marginalizedRisk/unitTests"
Executing test function test.marginalized.risk ... Timing stopped at: 1.004 0.076 1.178
Error in a$specials[[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.
------------------- UNIT TEST SUMMARY ---------------------
RUNIT TEST PROTOCOL -- Fri Oct 23 18:33:49 2026
***********************************************
Number of test functions: 1
Number of errors: 1
Number of failures: 0
1 Test Suite :
marginalizedRisk unit testing - 1 test function, 1 error, 0 failures
ERROR in test.marginalized.risk: Error in a$specials[[i]] : subscript out of bounds
Error:
unit testing failed (#test failures: 0, #R errors: 1)
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc