Package check result: ERROR Check: examples, Result: ERROR Running examples in ‘RSTr-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: add_neighbors > ### Title: Add neighbors to adjacency information > ### Aliases: add_neighbors > > ### ** Examples > > mamap <- sf::st_as_sf(mamap[order(mamap$GEOID), ]) > ma_adj <- spdep::poly2nb(mamap) *** 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(st_as_binary(x), ..., oriented = oriented) 5: s2::as_s2_geography(st_as_binary(x), ..., oriented = oriented) 6: st_as_s2.sfc(x, ..., oriented = oriented) 7: as_s2_geography.sfc(x) 8: as_s2_geography(x) 9: cpp_s2_intersects_matrix(as_s2_geography(x), as_s2_geography(y), options) 10: fn(x, y, s2::s2_options(model = model, ...)) 11: st_geos_binop("intersects", x, y, sparse = sparse, prepared = prepared, ...) 12: st_intersects.sfc(pl, sparse = TRUE, model = "closed") 13: st_intersects(pl, sparse = TRUE, model = "closed") 14: spdep::poly2nb(mamap) An irrecoverable exception occurred. R is aborting now ... Segmentation fault Check: re-building of vignette outputs, Result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘RSTr-adjacency.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(st_as_binary(x), ..., oriented = oriented) 5: s2::as_s2_geography(st_as_binary(x), ..., oriented = oriented) 6: st_as_s2.sfc(x, ..., oriented = oriented) 7: as_s2_geography.sfc(x) 8: as_s2_geography(x) 9: cpp_s2_intersects_matrix(as_s2_geography(x), as_s2_geography(y), options) 10: fn(x, y, s2::s2_options(model = model, ...)) 11: st_geos_binop("intersects", x, y, sparse = sparse, prepared = prepared, ...) 12: st_intersects.sfc(pl, sparse = TRUE, model = "closed") 13: st_intersects(pl, sparse = TRUE, model = "closed") 14: spdep::poly2nb(ma_shp) 15: eval(expr, envir) 16: eval(expr, envir) 17: withVisible(eval(expr, envir)) 18: 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$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)}) 19: eval(call) 20: eval(call) 21: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers) 22: doWithOneRestart(return(expr), restart) 23: withOneRestart(expr, restarts[[1L]]) 24: withRestartList(expr, restarts[-nr]) 25: doWithOneRestart(return(expr), restart) 26: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) 27: withRestartList(expr, restarts) 28: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) 29: evaluate::evaluate(...) 30: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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)) 31: in_dir(input_dir(), expr) 32: 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$render, options))) 33: eng_r(options) 34: block_exec(params) 35: call_block(x) 36: process_group(group) 37: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }) 38: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())) 39: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) 40: process_file(text, output) 41: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) 42: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...) 43: vweave_rmarkdown(...) 44: engine$weave(file, quiet = quiet, encoding = enc) 45: doTryCatch(return(expr), name, parentenv, handler) 46: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 47: tryCatchList(expr, classes, parentenv, handlers) 48: 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)))}) 49: tools:::.buildOneVignette("RSTr-adjacency.Rmd", "/home/hornik/tmp/CRAN_special_clang-san/RSTr.Rcheck/vign_test/RSTr", TRUE, FALSE, "RSTr-adjacency", "UTF-8", "/home/hornik/tmp/scratch/RtmpzHBJoO/working_dir/RtmpzzS14M/file19f1e2793a5a2e.rds") An irrecoverable exception occurred. R is aborting now ... Segmentation fault --- re-building ‘RSTr-agestandardize.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘RSTr-agestandardize.Rmd’ --- re-building ‘RSTr-car.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘RSTr-car.Rmd’ --- re-building ‘RSTr-event.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘RSTr-event.Rmd’ --- re-building ‘RSTr-informativeness.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘RSTr-informativeness.Rmd’ --- re-building ‘RSTr-initialvalues.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘RSTr-initialvalues.Rmd’ --- re-building ‘RSTr-models.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘RSTr-models.Rmd’ --- re-building ‘RSTr-priors.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘RSTr-priors.Rmd’ --- re-building ‘RSTr-reliability.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘RSTr-reliability.Rmd’ --- re-building ‘RSTr-samples.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘RSTr-samples.Rmd’ --- re-building ‘RSTr-troubleshoot.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘RSTr-troubleshoot.Rmd’ --- re-building ‘RSTr.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘RSTr.Rmd’ SUMMARY: processing the following file failed: ‘RSTr-adjacency.Rmd’ Error: Vignette re-building failed. Execution halted