- using R Under development (unstable) (2024-11-01 r87285)
- 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 ‘treeheatr/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘treeheatr’ version ‘0.2.1’
- 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 ‘treeheatr’ can be installed ... [9s/14s] OK
See the install log for details.
- 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 ... [13s/18s] 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 contents of ‘data’ directory ... OK
- checking data for non-ASCII characters ... OK
- checking LazyData ... OK
- checking data for ASCII and uncompressed saves ... OK
- checking installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... [6s/15s] ERROR
Running examples in ‘treeheatr-Ex.R’ failed
The error most likely occurred in:
> ### Name: compute_tree
> ### Title: Compute decision tree from data set
> ### Aliases: compute_tree
>
> ### ** Examples
>
> fit_tree <- compute_tree(penguins, target_lab = 'species')
*** caught segfault ***
address 0x1, cause 'memory not mapped'
Traceback:
1: method$fun(x, control = control)
2: system.time(order <- method$fun(x, control = control))
3: seriate.dist(., method = "ARSA")
4: seriation::seriate(., method = "ARSA")
5: seriation::get_order(.)
6: df[, clust_vec] %>% cluster::daisy(metric = "gower") %>% seriation::seriate(method = "ARSA") %>% seriation::get_order()
7: FUN(X[[i]], ...)
8: lapply(unique(.$node_id), clust_samp_func, dat = ., clust_vec = if (clust_target) colnames(data) else setdiff(colnames(data), fit$target_lab), clust_samps = clust_samps)
9: list2(...)
10: bind_rows(.)
11: mutate(., Sample = row_number())
12: data %>% cbind(node_id = node_pred, y_hat = y_pred) %>% lapply(unique(.$node_id), clust_samp_func, dat = ., clust_vec = if (clust_target) colnames(data) else setdiff(colnames(data), fit$target_lab), clust_samps = clust_samps) %>% bind_rows() %>% mutate(Sample = row_number())
13: prediction_df(fit, task, clust_samps, clust_target)
14: compute_tree(penguins, target_lab = "species")
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 ... [20s/35s] ERROR
Error(s) in re-building vignettes:
--- re-building ‘explore.Rmd’ using rmarkdown
*** caught segfault ***
address 0x1, cause 'memory not mapped'
Traceback:
1: method$fun(x, control = control)
2: system.time(order <- method$fun(x, control = control))
3: seriate.dist(., method = "ARSA")
4: seriation::seriate(., method = "ARSA")
5: seriation::get_order(.)
6: df[, clust_vec] %>% cluster::daisy(metric = "gower") %>% seriation::seriate(method = "ARSA") %>% seriation::get_order()
7: FUN(X[[i]], ...)
8: lapply(unique(.$node_id), clust_samp_func, dat = ., clust_vec = if (clust_target) colnames(data) else setdiff(colnames(data), fit$target_lab), clust_samps = clust_samps)
9: list2(...)
10: bind_rows(.)
11: mutate(., Sample = row_number())
12: data %>% cbind(node_id = node_pred, y_hat = y_pred) %>% lapply(unique(.$node_id), clust_samp_func, dat = ., clust_vec = if (clust_target) colnames(data) else setdiff(colnames(data), fit$target_lab), clust_samps = clust_samps) %>% bind_rows() %>% mutate(Sample = row_number())
13: prediction_df(fit, task, clust_samps, clust_target)
14: compute_tree(x = penguins, target_lab = "species")
15: eval(ctree_result, parent.frame())
16: eval(ctree_result, parent.frame())
17: heat_tree(penguins, target_lab = "species")
18: eval(expr, envir)
19: eval(expr, envir)
20: withVisible(eval(expr, envir))
21: withCallingHandlers(code, 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 = invokeRestart("eval_error", cnd))})
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$visible, envir) } TRUE}, handlers)
25: doWithOneRestart(return(expr), restart)
26: withOneRestart(expr, restarts[[1L]])
27: withRestartList(expr, restarts[-nr])
28: doWithOneRestart(return(expr), restart)
29: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
30: withRestartList(expr, restarts[-nr])
31: doWithOneRestart(return(expr), restart)
32: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
33: withRestartList(expr, restarts)
34: withRestarts(with_handlers({ for (expr in tle$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, eval_error = function(cnd) { signalCondition(cnd) stop(cnd) })
35: evaluate::evaluate(...)
36: 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$render, options))
37: in_dir(input_dir(), expr)
38: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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)))
39: eng_r(options)
40: block_exec(params)
41: call_block(x)
42: process_group(group)
43: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e))
44: xfun:::handle_error(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e)), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from lines ", loc) }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
45: process_file(text, output)
46: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
47: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
48: vweave_rmarkdown(...)
49: engine$weave(file, quiet = quiet, encoding = enc)
50: doTryCatch(return(expr), name, parentenv, handler)
51: tryCatchOne(expr, names, parentenv, handlers[[1L]])
52: tryCatchList(expr, classes, parentenv, handlers)
53: tryCatch({ engine$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) } outputs <- c(outputs, output)}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
54: tools::buildVignettes(dir = "/data/gannet/ripley/R/packages/tests-devel/treeheatr.Rcheck/vign_test/treeheatr", skip = TRUE, ser_elibs = "/tmp/RtmpfwmDj4/file3cb365e980bc8.rds")
An irrecoverable exception occurred. R is aborting now ...
- checking PDF version of manual ... [7s/12s] 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