• using R Under development (unstable) (2024-11-15 r87338)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-14 (GCC) 14.2.0     GNU Fortran (GCC) 14.2.0
• running under: Fedora Linux 36 (Workstation Edition)
• using session charset: UTF-8
• using option ‘--no-stop-on-test-error’
• checking for file ‘BuyseTest/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘BuyseTest’ version ‘3.0.5’
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘BuyseTest’ can be installed ... [194s/174s] OK See the install log for details.
• used C++ compiler: ‘g++-14 (GCC) 14.2.0’
• checking package directory ... OK
• checking ‘build’ directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking for left-over files ... OK
• checking index information ... OK
• checking package subdirectories ... OK
• checking code files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... OK
• checking whether the package can be loaded with stated dependencies ... OK
• checking whether the package can be unloaded cleanly ... OK
• checking whether the namespace can be loaded with stated dependencies ... OK
• checking whether the namespace can be unloaded cleanly ... OK
• checking loading without being on the library search path ... OK
• checking whether startup messages can be suppressed ... OK
• checking use of S3 registration ... OK
• checking dependencies in R code ... OK
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... [81s/100s] OK
• checking Rd files ... OK
• checking Rd metadata ... OK
• checking Rd line widths ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking line endings in C/C++/Fortran sources/headers ... OK
• checking line endings in Makefiles ... OK
• checking compilation flags in Makevars ... OK
• checking for GNU extensions in Makefiles ... OK
• checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
• checking use of PKG_*FLAGS in Makefiles ... OK
• checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
• checking pragmas in C/C++ headers and code ... OK
• checking compilation flags used ... OK
• checking compiled code ... OK
• checking sizes of PDF files under ‘inst/doc’ ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... ERROR Running examples in ‘BuyseTest-Ex.R’ failed The error most likely occurred in: > ### Name: BuyseMultComp > ### Title: Adjustment for Multiple Comparisons > ### Aliases: BuyseMultComp > ### Keywords: htest > > ### ** Examples > > #### simulate data #### > set.seed(10) > df.data <- simBuyseTest(1e2, n.strata = 3) Error in cbind(idxM, pidxM) : cannot get data pointer of 'NULL' objects Calls: simBuyseTest ... exogenous<- -> exogenous<-.lvm -> reindex -> mat.lvm -> cbind Execution halted
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [32s/39s] ERROR   Running ‘testthat.R’ [31s/38s] Running the tests in ‘tests/testthat.R’ failed. Complete output:   > ## * load packages   > library(testthat)   > library(BuyseTest)   Loading required package: Rcpp   BuyseTest version 3.0.5   >   > library(lava)      Attaching package: 'lava'      The following object is masked from 'package:testthat':          compare      > library(data.table)   > library(survival)      Attaching package: 'survival'      The following object is masked from 'package:BuyseTest':          brier      > xx <- capture.output(print(veteran))   > library(riskRegression)   riskRegression version 2023.12.21   > library(prodlim)   > library(mvtnorm)   >   > ## * run tests   > ## setwd("~/Documents/GitHub/BuyseTest/tests/")   > ## source("~/Documents/GitHub/BuyseTest/tests/testthat/test-BuyseTest-engine.R")   > test_check("BuyseTest")   [ FAIL 15 | WARN 6 | SKIP 0 | PASS 553 ]      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Error ('test-BuysePower.R:78:5'): 1 tte endpoint - Gehan ────────────────────   Error in `cbind(idxM, pidxM)`: cannot get data pointer of 'NULL' objects   Backtrace:        ▆     1. └─BuyseTest::powerBuyseTest(...) at test-BuysePower.R:78:5     2. └─BuyseTest (local) sim(n.C = 10, n.T = 10)     3. ├─lava::`distribution<-`(...)     4. └─lava:::`distribution<-.lvm`(...)     5. ├─lava::`addvar<-`(`*tmp*`, value = as.formula(paste("~", variable)))     6. └─lava:::`addvar<-.lvm`(...)     7. ├─lava::`regression<-`(`*tmp*`, ..., value = value)     8. └─lava:::`regression<-.lvm`(`*tmp*`, ..., value = value)     9. └─lava::procformula(object, value, ...)    10. ├─lava::`exogenous<-`(...)    11. └─lava:::`exogenous<-.lvm`(...)    12. └─lava::reindex(x)    13. └─lava:::mat.lvm(x, res)    14. └─base::cbind(idxM, pidxM)   ── Error ('test-BuysePower.R:118:5'): 1 tte endpoint - Peron ───────────────────   Error in `cbind(idxM, pidxM)`: cannot get data pointer of 'NULL' objects   Backtrace:        ▆     1. └─BuyseTest::powerBuyseTest(...) at test-BuysePower.R:118:5     2. └─BuyseTest (local) sim(n.C = 10, n.T = 10)     3. ├─lava::`distribution<-`(...)     4. └─lava:::`distribution<-.lvm`(...)     5. ├─lava::`addvar<-`(`*tmp*`, value = as.formula(paste("~", variable)))     6. └─lava:::`addvar<-.lvm`(...)     7. ├─lava::`regression<-`(`*tmp*`, ..., value = value)     8. └─lava:::`regression<-.lvm`(`*tmp*`, ..., value = value)     9. └─lava::procformula(object, value, ...)    10. ├─lava::`exogenous<-`(...)    11. └─lava:::`exogenous<-.lvm`(...)    12. └─lava::reindex(x)    13. └─lava:::mat.lvm(x, res)    14. └─base::cbind(idxM, pidxM)   ── Error ('test-BuysePower.R:160:5'): Multiple endpoints ───────────────────────   Error in `cbind(idxM, pidxM)`: cannot get data pointer of 'NULL' objects   Backtrace:        ▆     1. └─BuyseTest::powerBuyseTest(...) at test-BuysePower.R:160:5     2. └─BuyseTest (local) sim(n.C = 10, n.T = 10)     3. ├─lava::`distribution<-`(...)     4. └─lava:::`distribution<-.lvm`(...)     5. ├─lava::`addvar<-`(`*tmp*`, value = as.formula(paste("~", variable)))     6. └─lava:::`addvar<-.lvm`(...)     7. ├─lava::`regression<-`(`*tmp*`, ..., value = value)     8. └─lava:::`regression<-.lvm`(`*tmp*`, ..., value = value)     9. └─lava::procformula(object, value, ...)    10. ├─lava::`exogenous<-`(...)    11. └─lava:::`exogenous<-.lvm`(...)    12. └─lava::reindex(x)    13. └─lava:::mat.lvm(x, res)    14. └─base::cbind(idxM, pidxM)   ── Error ('test-BuyseTTEM.R:33:1'): (code run outside of `test_that()`) ────────   Error in `cbind(idxM, pidxM)`: cannot get data pointer of 'NULL' objects   Backtrace:        ▆     1. └─BuyseTest::simBuyseTest(100) at test-BuyseTTEM.R:33:1     2. ├─lava::`distribution<-`(...)     3. └─lava:::`distribution<-.lvm`(...)     4. ├─lava::`addvar<-`(`*tmp*`, value = as.formula(paste("~", variable)))     5. └─lava:::`addvar<-.lvm`(...)     6. ├─lava::`regression<-`(`*tmp*`, ..., value = value)     7. └─lava:::`regression<-.lvm`(`*tmp*`, ..., value = value)     8. └─lava::procformula(object, value, ...)     9. ├─lava::`exogenous<-`(...)    10. └─lava:::`exogenous<-.lvm`(...)    11. └─lava::reindex(x)    12. └─lava:::mat.lvm(x, res)    13. └─base::cbind(idxM, pidxM)   ── Error ('test-BuyseTest-PairScore.R:38:1'): (code run outside of `test_that()`) ──   Error in `cbind(idxM, pidxM)`: cannot get data pointer of 'NULL' objects   Backtrace:        ▆     1. └─BuyseTest::simBuyseTest(...) at test-BuyseTest-PairScore.R:38:1     2. ├─lava::`distribution<-`(...)     3. └─lava:::`distribution<-.lvm`(...)     4. ├─lava::`addvar<-`(`*tmp*`, value = as.formula(paste("~", variable)))     5. └─lava:::`addvar<-.lvm`(...)     6. ├─lava::`regression<-`(`*tmp*`, ..., value = value)     7. └─lava:::`regression<-.lvm`(`*tmp*`, ..., value = value)     8. └─lava::procformula(object, value, ...)     9. ├─lava::`exogenous<-`(...)    10. └─lava:::`exogenous<-.lvm`(...)    11. └─lava::reindex(x)    12. └─lava:::mat.lvm(x, res)    13. └─base::cbind(idxM, pidxM)   ── Error ('test-BuyseTest-checkValues.R:20:1'): (code run outside of `test_that()`) ──   Error in `cbind(idxM, pidxM)`: cannot get data pointer of 'NULL' objects   Backtrace:        ▆     1. └─BuyseTest::simBuyseTest(...) at test-BuyseTest-checkValues.R:20:1     2. ├─lava::`distribution<-`(...)     3. └─lava:::`distribution<-.lvm`(...)     4. ├─lava::`addvar<-`(`*tmp*`, value = as.formula(paste("~", variable)))     5. └─lava:::`addvar<-.lvm`(...)     6. ├─lava::`regression<-`(`*tmp*`, ..., value = value)     7. └─lava:::`regression<-.lvm`(`*tmp*`, ..., value = value)     8. └─lava::procformula(object, value, ...)     9. ├─lava::`exogenous<-`(...)    10. └─lava:::`exogenous<-.lvm`(...)    11. └─lava::reindex(x)    12. └─lava:::mat.lvm(x, res)    13. └─base::cbind(idxM, pidxM)   ── Error ('test-BuyseTest-correctionTTE.R:194:1'): (code run outside of `test_that()`) ──   Error in `cbind(idxM, pidxM)`: cannot get data pointer of 'NULL' objects   Backtrace:        ▆     1. └─BuyseTest::simBuyseTest(n.T = 20, n.C = 20) at test-BuyseTest-correctionTTE.R:194:1     2. ├─lava::`distribution<-`(...)     3. └─lava:::`distribution<-.lvm`(...)     4. ├─lava::`addvar<-`(`*tmp*`, value = as.formula(paste("~", variable)))     5. └─lava:::`addvar<-.lvm`(...)     6. ├─lava::`regression<-`(`*tmp*`, ..., value = value)     7. └─lava:::`regression<-.lvm`(`*tmp*`, ..., value = value)     8. └─lava::procformula(object, value, ...)     9. ├─lava::`exogenous<-`(...)    10. └─lava:::`exogenous<-.lvm`(...)    11. └─lava::reindex(x)    12. └─lava:::mat.lvm(x, res)    13. └─base::cbind(idxM, pidxM)   ── Error ('test-BuyseTest-engine.R:36:1'): (code run outside of `test_that()`) ──   Error in `cbind(idxM, pidxM)`: cannot get data pointer of 'NULL' objects   Backtrace:        ▆     1. └─BuyseTest::simBuyseTest(...) at test-BuyseTest-engine.R:36:1     2. ├─lava::`distribution<-`(...)     3. └─lava:::`distribution<-.lvm`(...)     4. ├─lava::`addvar<-`(`*tmp*`, value = as.formula(paste("~", variable)))     5. └─lava:::`addvar<-.lvm`(...)     6. ├─lava::`regression<-`(`*tmp*`, ..., value = value)     7. └─lava:::`regression<-.lvm`(`*tmp*`, ..., value = value)     8. └─lava::procformula(object, value, ...)     9. ├─lava::`exogenous<-`(...)    10. └─lava:::`exogenous<-.lvm`(...)    11. └─lava::reindex(x)    12. └─lava:::mat.lvm(x, res)    13. └─base::cbind(idxM, pidxM)   ── Error ('test-BuyseTest-iid.R:222:1'): (code run outside of `test_that()`) ───   Error in `cbind(idxM, pidxM)`: cannot get data pointer of 'NULL' objects   Backtrace:        ▆     1. └─BuyseTest::simBuyseTest(n, name.cluster = NULL) at test-BuyseTest-iid.R:222:1     2. └─lava::`categorical<-`(`*tmp*`, labels = level.treatment[1], value = name.treatment)     3. └─lava::categorical(x, value, ...)     4. ├─lava::`ordinal<-`(...)     5. └─lava:::`ordinal<-.lvm`(...)     6. ├─lava::ordinal(x, value, ...)     7. └─lava:::ordinal.lvm(x, value, ...)     8. ├─lava::`addvar<-`(`*tmp*`, value = var)     9. └─lava:::`addvar<-.lvm`(`*tmp*`, value = var)    10. ├─lava::addvar(x, var = value, ...)    11. └─lava:::addvar.lvm(x, var = value, ...)    12. └─lava::reindex(x)    13. └─lava:::mat.lvm(x, res)    14. └─base::cbind(idxM, pidxM)   ── Error ('test-BuyseTest-multcomp.R:36:1'): (code run outside of `test_that()`) ──   Error in `cbind(idxM, pidxM)`: cannot get data pointer of 'NULL' objects   Backtrace:        ▆     1. └─BuyseTest::simBuyseTest(n) at test-BuyseTest-multcomp.R:36:1     2. ├─lava::`distribution<-`(...)     3. └─lava:::`distribution<-.lvm`(...)     4. ├─lava::`addvar<-`(`*tmp*`, value = as.formula(paste("~", variable)))     5. └─lava:::`addvar<-.lvm`(...)     6. ├─lava::`regression<-`(`*tmp*`, ..., value = value)     7. └─lava:::`regression<-.lvm`(`*tmp*`, ..., value = value)     8. └─lava::procformula(object, value, ...)     9. ├─lava::`exogenous<-`(...)    10. └─lava:::`exogenous<-.lvm`(...)    11. └─lava::reindex(x)    12. └─lava:::mat.lvm(x, res)    13. └─base::cbind(idxM, pidxM)   ── Error ('test-BuyseTest-previousBug.R:259:1'): (code run outside of `test_that()`) ──   Error in `cbind(idxM, pidxM)`: cannot get data pointer of 'NULL' objects   Backtrace:        ▆     1. └─BuyseTest::simBuyseTest(50) at test-BuyseTest-previousBug.R:259:1     2. ├─lava::`distribution<-`(...)     3. └─lava:::`distribution<-.lvm`(...)     4. ├─lava::`addvar<-`(`*tmp*`, value = as.formula(paste("~", variable)))     5. └─lava:::`addvar<-.lvm`(...)     6. ├─lava::`regression<-`(`*tmp*`, ..., value = value)     7. └─lava:::`regression<-.lvm`(`*tmp*`, ..., value = value)     8. └─lava::procformula(object, value, ...)     9. ├─lava::`exogenous<-`(...)    10. └─lava:::`exogenous<-.lvm`(...)    11. └─lava::reindex(x)    12. └─lava:::mat.lvm(x, res)    13. └─base::cbind(idxM, pidxM)   ── Error ('test-BuyseTest-resampling.R:38:1'): (code run outside of `test_that()`) ──   Error in `cbind(idxM, pidxM)`: cannot get data pointer of 'NULL' objects   Backtrace:        ▆     1. └─BuyseTest::simBuyseTest(...) at test-BuyseTest-resampling.R:38:1     2. ├─lava::`distribution<-`(...)     3. └─lava:::`distribution<-.lvm`(...)     4. ├─lava::`addvar<-`(`*tmp*`, value = as.formula(paste("~", variable)))     5. └─lava:::`addvar<-.lvm`(...)     6. ├─lava::`regression<-`(`*tmp*`, ..., value = value)     7. └─lava:::`regression<-.lvm`(`*tmp*`, ..., value = value)     8. └─lava::procformula(object, value, ...)     9. ├─lava::`exogenous<-`(...)    10. └─lava:::`exogenous<-.lvm`(...)    11. └─lava::reindex(x)    12. └─lava:::mat.lvm(x, res)    13. └─base::cbind(idxM, pidxM)   ── Error ('test-BuyseTest-restricted.R:35:1'): (code run outside of `test_that()`) ──   Error in `cbind(idxM, pidxM)`: cannot get data pointer of 'NULL' objects   Backtrace:        ▆     1. ├─base::as.data.frame(simBuyseTest(n.obs)) at test-BuyseTest-restricted.R:35:1     2. └─BuyseTest::simBuyseTest(n.obs)     3. ├─lava::`distribution<-`(...)     4. └─lava:::`distribution<-.lvm`(...)     5. ├─lava::`addvar<-`(`*tmp*`, value = as.formula(paste("~", variable)))     6. └─lava:::`addvar<-.lvm`(...)     7. ├─lava::`regression<-`(`*tmp*`, ..., value = value)     8. └─lava:::`regression<-.lvm`(`*tmp*`, ..., value = value)     9. └─lava::procformula(object, value, ...)    10. ├─lava::`exogenous<-`(...)    11. └─lava:::`exogenous<-.lvm`(...)    12. └─lava::reindex(x)    13. └─lava:::mat.lvm(x, res)    14. └─base::cbind(idxM, pidxM)   ── Error ('test-BuyseTest-strata.R:34:1'): (code run outside of `test_that()`) ──   Error in `cbind(idxM, pidxM)`: cannot get data pointer of 'NULL' objects   Backtrace:        ▆     1. └─BuyseTest::simBuyseTest(...) at test-BuyseTest-strata.R:34:1     2. ├─lava::`distribution<-`(...)     3. └─lava:::`distribution<-.lvm`(...)     4. ├─lava::`addvar<-`(`*tmp*`, value = as.formula(paste("~", variable)))     5. └─lava:::`addvar<-.lvm`(...)     6. ├─lava::`regression<-`(`*tmp*`, ..., value = value)     7. └─lava:::`regression<-.lvm`(`*tmp*`, ..., value = value)     8. └─lava::procformula(object, value, ...)     9. ├─lava::`exogenous<-`(...)    10. └─lava:::`exogenous<-.lvm`(...)    11. └─lava::reindex(x)    12. └─lava:::mat.lvm(x, res)    13. └─base::cbind(idxM, pidxM)   ── Error ('test-initThreshold.R:32:1'): (code run outside of `test_that()`) ────   Error in `cbind(idxM, pidxM)`: cannot get data pointer of 'NULL' objects   Backtrace:        ▆     1. └─BuyseTest::simBuyseTest(10) at test-initThreshold.R:32:1     2. ├─lava::`distribution<-`(...)     3. └─lava:::`distribution<-.lvm`(...)     4. ├─lava::`addvar<-`(`*tmp*`, value = as.formula(paste("~", variable)))     5. └─lava:::`addvar<-.lvm`(...)     6. ├─lava::`regression<-`(`*tmp*`, ..., value = value)     7. └─lava:::`regression<-.lvm`(`*tmp*`, ..., value = value)     8. └─lava::procformula(object, value, ...)     9. ├─lava::`exogenous<-`(...)    10. └─lava:::`exogenous<-.lvm`(...)    11. └─lava::reindex(x)    12. └─lava:::mat.lvm(x, res)    13. └─base::cbind(idxM, pidxM)      [ FAIL 15 | WARN 6 | SKIP 0 | PASS 553 ]   Error: Test failures   Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [15s/19s] OK
• checking PDF version of manual ... [14s/20s] OK
• checking HTML version of manual ... OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE

Status: 2 ERRORs