* using log directory ‘/data/localhost/ripley/R/packages/tests-clang-trunk/TBRDist.Rcheck’
* using R Under development (unstable) (2026-08-08 r90378)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    clang version 23.1.0-rc2
    flang version 23.1.0-rc2
* running under: Fedora Linux 44 (Server Edition)
* using session charset: UTF-8
* current time: 2026-08-08 12:18:37 UTC
* using option ‘--no-stop-on-test-error’
* checking for file ‘TBRDist/DESCRIPTION’ ... OK
* this is package ‘TBRDist’ version ‘2.0.1’
* 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 ‘TBRDist’ can be installed ... [32s/22s] OK
* used C++ compiler: ‘clang version 23.1.0-rc2’
* checking C++ specification ... INFO
  specified C++17
* checking installed package size ... OK
* 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 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 ... 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 for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘TBRDist-Ex.R’ failed
The error most likely occurred in:

> ### Name: RSPRDist
> ### Title: Calculate rSPR distance between rooted trees
> ### Aliases: RSPRDist
> 
> ### ** Examples
> 
> library(ape)
> set.seed(1)
> tree1 <- rtree(8)
> tree2 <- rtree(8)
> tree1$tip.label <- tree2$tip.label <- paste0("t", 1:8)
> 
> RSPRDist(tree1, tree2)

 *** caught segfault ***
address (nil), cause 'memory not mapped'

Traceback:
 1: rspr_dist(treeLists[[1]], treeLists[[2]], approx = approx, exact = !approx)
 2: RSPRDist(tree1, tree2)
An irrecoverable exception occurred. R is aborting now ...
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’/data/localhost/ripley/R/R-clang-trunk/bin/BATCH: line 60: 1868474 Segmentation fault         (core dumped) ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1

 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library('testthat')
  > library('TBRDist')
  > 
  > test_check("TBRDist")
  
   *** caught segfault ***
  address (nil), cause 'memory not mapped'
  
  Traceback:
   1: rspr_dist(treeLists[[1]], treeLists[[2]], approx = approx, exact = !approx)
   2: RSPRDist(t, t)
   3: eval_bare(expr, quo_get_env(quo))
   4: quasi_label(enquo(object), label)
   5: expect_identical(RSPRDist(t, t), 0L)
   6: eval(code, test_env)
   7: eval(code, test_env)
   8: withCallingHandlers({    eval(code, test_env)    new_expectations <- the$test_expectations > starting_expectations    if (snapshot_skipped) {        skip("On CRAN")    }    else if (!new_expectations && skip_on_empty) {        skip_empty()    }}, expectation = handle_expectation, packageNotFoundError = function(e) {    if (on_cran()) {        skip(paste0("{", e$package, "} is not installed."))    }}, snapshot_on_cran = function(cnd) {    snapshot_skipped <<- TRUE    invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message,     error = handle_error, interrupt = handle_interrupt)
   9: doTryCatch(return(expr), name, parentenv, handler)
  10: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  11: tryCatchList(expr, classes, parentenv, handlers)
  12: tryCatch(withCallingHandlers({    eval(code, test_env)    new_expectations <- the$test_expectations > starting_expectations    if (snapshot_skipped) {        skip("On CRAN")    }    else if (!new_expectations && skip_on_empty) {        skip_empty()    }}, expectation = handle_expectation, packageNotFoundError = function(e) {    if (on_cran()) {        skip(paste0("{", e$package, "} is not installed."))    }}, snapshot_on_cran = function(cnd) {    snapshot_skipped <<- TRUE    invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message,     error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
  13: doWithOneRestart(return(expr), restart)
  14: withOneRestart(expr, restarts[[1L]])
  15: withRestarts(tryCatch(withCallingHandlers({    eval(code, test_env)    new_expectations <- the$test_expectations > starting_expectations    if (snapshot_skipped) {        skip("On CRAN")    }    else if (!new_expectations && skip_on_empty) {        skip_empty()    }}, expectation = handle_expectation, packageNotFoundError = function(e) {    if (on_cran()) {        skip(paste0("{", e$package, "} is not installed."))    }}, snapshot_on_cran = function(cnd) {    snapshot_skipped <<- TRUE    invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message,     error = handle_error, interrupt = handle_interrupt), error = handle_fatal),     end_test = function() {    })
  16: test_code(code, parent.frame())
  17: test_that("distance between identical trees is 0", {    t <- Tree("((((1,2),(3,4)),((5,6),(7,8))),(((9,10),(11,12)),((13,14),(15,16))));")    expect_identical(RSPRDist(t, t), 0L)})
  18: eval(code, test_env)
  19: eval(code, test_env)
  20: withCallingHandlers({    eval(code, test_env)    new_expectations <- the$test_expectations > starting_expectations    if (snapshot_skipped) {        skip("On CRAN")    }    else if (!new_expectations && skip_on_empty) {        skip_empty()    }}, expectation = handle_expectation, packageNotFoundError = function(e) {    if (on_cran()) {        skip(paste0("{", e$package, "} is not installed."))    }}, snapshot_on_cran = function(cnd) {    snapshot_skipped <<- TRUE    invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message,     error = handle_error, interrupt = handle_interrupt)
  21: doTryCatch(return(expr), name, parentenv, handler)
  22: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  23: tryCatchList(expr, classes, parentenv, handlers)
  24: tryCatch(withCallingHandlers({    eval(code, test_env)    new_expectations <- the$test_expectations > starting_expectations    if (snapshot_skipped) {        skip("On CRAN")    }    else if (!new_expectations && skip_on_empty) {        skip_empty()    }}, expectation = handle_expectation, packageNotFoundError = function(e) {    if (on_cran()) {        skip(paste0("{", e$package, "} is not installed."))    }}, snapshot_on_cran = function(cnd) {    snapshot_skipped <<- TRUE    invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message,     error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
  25: doWithOneRestart(return(expr), restart)
  26: withOneRestart(expr, restarts[[1L]])
  27: withRestarts(tryCatch(withCallingHandlers({    eval(code, test_env)    new_expectations <- the$test_expectations > starting_expectations    if (snapshot_skipped) {        skip("On CRAN")    }    else if (!new_expectations && skip_on_empty) {        skip_empty()    }}, expectation = handle_expectation, packageNotFoundError = function(e) {    if (on_cran()) {        skip(paste0("{", e$package, "} is not installed."))    }}, snapshot_on_cran = function(cnd) {    snapshot_skipped <<- TRUE    invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message,     error = handle_error, interrupt = handle_interrupt), error = handle_fatal),     end_test = function() {    })
  28: test_code(code = exprs, env = env, reporter = get_reporter() %||%     StopReporter$new())
  29: source_file(path, env = env(env), desc = desc, shuffle = shuffle,     error_call = error_call)
  30: FUN(X[[i]], ...)
  31: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle,     error_call = error_call)
  32: doTryCatch(return(expr), name, parentenv, handler)
  33: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  34: tryCatchList(expr, classes, parentenv, handlers)
  35: tryCatch(code, testthat_abort_reporter = function(cnd) {    cat(conditionMessage(cnd), "\n")    NULL})
  36: with_reporter(reporters$multi, lapply(test_paths, test_one_file,     env = env, desc = desc, shuffle = shuffle, error_call = error_call))
  37: test_files_serial(test_dir = test_dir, test_package = test_package,     test_paths = test_paths, load_helpers = load_helpers, reporter = reporter,     env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     desc = desc, load_package = load_package, shuffle = shuffle,     error_call = error_call)
  38: test_files(test_dir = path, test_paths = test_paths, test_package = package,     reporter = reporter, load_helpers = load_helpers, env = env,     stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     load_package = load_package, parallel = parallel, shuffle = shuffle)
  39: test_dir("testthat", package = package, reporter = reporter,     ..., load_package = "installed")
  40: test_check("TBRDist")
  An irrecoverable exception occurred. R is aborting now ...
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... 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
See
  ‘/data/localhost/ripley/R/packages/tests-clang-trunk/TBRDist.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 1:12.48, 63.62 + 7.57