* using log directory ‘/home/hornik/tmp/CRAN_special_clang-san/hexify.Rcheck’
* using R Under development (unstable) (2026-01-20 r89309)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 21.1.8 (1)
    Debian flang version 21.1.8 (1)
* running under: Debian GNU/Linux forky/sid
* using session charset: UTF-8
* checking for file ‘hexify/DESCRIPTION’ ... OK
* this is package ‘hexify’ version ‘0.3.7’
* 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 ‘hexify’ can be installed ... [43s/44s] OK
* used C++ compiler: ‘Debian clang version 21.1.8 (1+b1)’
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
* checking loading without being on the library search path ... [1s/1s] 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 ... [24s/24s] OK
* checking Rd files ... [2s/2s] 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [1s/1s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... 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 ... [20s/20s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [57s/57s] OK
  Running ‘testthat.R’ [57s/57s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [61s/61s] ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘quickstart.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘quickstart.Rmd’

--- re-building ‘visualization.Rmd’ using rmarkdown
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "point_alpha" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "point_alpha" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "point_alpha" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "point_alpha" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "point_alpha" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "point_alpha" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "jitter" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "jitter" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "jitter" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "jitter" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "jitter" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "jitter" is not a graphical parameter
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘visualization.Rmd’

--- re-building ‘workflows.Rmd’ using rmarkdown

 *** caught segfault ***
address 0xfffffffffffffff8, cause 'memory not mapped'

Traceback:
 1: wk_handle.wk_wkb(wkb, s2_geography_writer(oriented = oriented,     check = check, tessellate_tol = if (planar) {        tessellate_tol_m/s2_earth_radius_meters()    } else {        Inf    }))
 2: wk::wk_handle(wkb, s2_geography_writer(oriented = oriented, check = check,     tessellate_tol = if (planar) {        tessellate_tol_m/s2_earth_radius_meters()    } else {        Inf    }))
 3: s2_geog_from_wkb(x, oriented = oriented, check = check)
 4: as_s2_geography.WKB(b, ..., oriented = oriented)
 5: s2::as_s2_geography(b, ..., oriented = oriented)
 6: as_s2_geography.sfg(y)
 7: as_s2_geography(y)
 8: recycle_common(as_s2_geography(x), as_s2_geography(y))
 9: fn(x, yy, s2::s2_options(model = model, ...))
10: FUN(X[[i]], ...)
11: lapply(y, function(yy) fn(x, yy, s2::s2_options(model = model,     ...)))
12: unlist(lapply(y, function(yy) fn(x, yy, s2::s2_options(model = model,     ...))), recursive = FALSE)
13: structure(unlist(lapply(y, function(yy) fn(x, yy, s2::s2_options(model = model,     ...))), recursive = FALSE), class = "s2_geography")
14: geos_op2_geom("intersection", x, y, ...)
15: geos_op2_df(x, y, geos_op2_geom("intersection", x, y, ...))
16: st_intersection.sf(france_grid, st_geometry(france))
17: st_intersection(france_grid, st_geometry(france))
18: eval(expr, envir)
19: eval(expr, envir)
20: withVisible(eval(expr, envir))
21: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) {    watcher$capture_plot_and_output()    if (on_message$capture) {        watcher$push(cnd)    }    if (on_message$silence) {        invokeRestart("muffleMessage")    }}, warning = function (cnd) {    if (getOption("warn") >= 2 || getOption("warn") < 0) {        return()    }    watcher$capture_plot_and_output()    if (on_warning$capture) {        cnd <- sanitize_call(cnd)        watcher$push(cnd)    }    if (on_warning$silence) {        invokeRestart("muffleWarning")    }}, error = function (cnd) {    watcher$capture_plot_and_output()    cnd <- sanitize_call(cnd)    watcher$push(cnd)    switch(on_error, continue = invokeRestart("eval_continue"),         stop = invokeRestart("eval_stop"), error = NULL)})
22: eval(call)
23: eval(call)
24: with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE}, handlers)
25: doWithOneRestart(return(expr), restart)
26: withOneRestart(expr, restarts[[1L]])
27: withRestartList(expr, restarts[-nr])
28: doWithOneRestart(return(expr), restart)
29: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
30: withRestartList(expr, restarts)
31: withRestarts(with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
32: evaluate::evaluate(...)
33: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,     keep_message = if (is.numeric(options$message)) TRUE else options$message,     stop_on_error = if (is.numeric(options$error)) options$error else {        if (options$error && options$include)             0L        else 2L    }, output_handler = knit_handlers(options$render, options))
34: in_dir(input_dir(), expr)
35: in_input_dir(evaluate(code, envir = env, new_device = FALSE,     keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,     keep_message = if (is.numeric(options$message)) TRUE else options$message,     stop_on_error = if (is.numeric(options$error)) options$error else {        if (options$error && options$include)             0L        else 2L    }, output_handler = knit_handlers(options$render, options)))
36: eng_r(options)
37: block_exec(params)
38: call_block(x)
39: process_group(group)
40: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    })
41: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    }), list(rlang_trace_top_env = knit_global()))
42: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    }), list(rlang_trace_top_env = knit_global())), function(loc) {    setwd(wd)    write_utf8(res, output %n% stdout())    paste0("\nQuitting from ", loc, if (!is.null(error))         paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
43: process_file(text, output)
44: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
45: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),     output_dir = getwd(), ...)
46: vweave_rmarkdown(...)
47: engine$weave(file, quiet = quiet, encoding = enc)
48: doTryCatch(return(expr), name, parentenv, handler)
49: tryCatchOne(expr, names, parentenv, handlers[[1L]])
50: tryCatchList(expr, classes, parentenv, handlers)
51: tryCatch({    engine$weave(file, quiet = quiet, encoding = enc)    setwd(startdir)    output <- find_vignette_product(name, by = "weave", engine = engine)    if (!have.makefile && vignette_is_tex(output)) {        texi2pdf(file = output, clean = FALSE, quiet = quiet)        output <- find_vignette_product(name, by = "texi2pdf",             engine = engine)    }}, error = function(e) {    OK <<- FALSE    message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",         file, conditionMessage(e)))})
52: tools:::.buildOneVignette("workflows.Rmd", "/home/hornik/tmp/CRAN_special_clang-san/hexify.Rcheck/vign_test/hexify",     TRUE, FALSE, "workflows", "UTF-8", "/home/hornik/tmp/scratch/RtmprD43Ak/working_dir/RtmpOVjJlD/file16df2e5b6180c2.rds")
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
SUMMARY: processing the following file failed:
  ‘workflows.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [7s/7s] OK
* checking HTML version of manual ... [15s/15s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR