Last updated on 2024-12-21 22:50:09 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.1.1 | 2.37 | 49.62 | 51.99 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.1.1 | 1.46 | 37.91 | 39.37 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.1.1 | 93.72 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 0.1.1 | 101.16 | ERROR | |||
| r-devel-windows-x86_64 | 0.1.1 | 4.00 | 75.00 | 79.00 | ERROR | |
| r-patched-linux-x86_64 | 0.1.1 | 1.77 | 53.47 | 55.24 | OK | |
| r-release-linux-x86_64 | 0.1.1 | 1.93 | 52.70 | 54.63 | OK | |
| r-release-macos-arm64 | 0.1.1 | 39.00 | OK | |||
| r-release-macos-x86_64 | 0.1.1 | 53.00 | OK | |||
| r-release-windows-x86_64 | 0.1.1 | 4.00 | 81.00 | 85.00 | OK | |
| r-oldrel-macos-arm64 | 0.1.1 | 39.00 | OK | |||
| r-oldrel-macos-x86_64 | 0.1.1 | 57.00 | OK | |||
| r-oldrel-windows-x86_64 | 0.1.1 | 5.00 | 86.00 | 91.00 | OK |
Version: 0.1.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘Getting-Started.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/plotmm.Rcheck/vign_test/plotmm/vignettes/Getting-Started_files/figure-html/unnamed-chunk-2-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 19300 bytes
Input file size = 19402 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 15737
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 15737
Output IDAT size = 15737 bytes (3563 bytes decrease)
Output file size = 15815 bytes (3587 bytes = 18.49% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/plotmm.Rcheck/vign_test/plotmm/vignettes/Getting-Started_files/figure-html/unnamed-chunk-3-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 18757 bytes
Input file size = 18859 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 13403
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 13403
Output IDAT size = 13403 bytes (5354 bytes decrease)
Output file size = 13481 bytes (5378 bytes = 28.52% decrease)
*** caught segfault ***
address 0x1, cause 'memory not mapped'
Traceback:
1: init.EM(x, nclass = 10, method = "em.EM")
2: eval(expr, envir)
3: eval(expr, envir)
4: withVisible(eval(expr, envir))
5: 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))})
6: eval(call)
7: eval(call)
8: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
9: doWithOneRestart(return(expr), restart)
10: withOneRestart(expr, restarts[[1L]])
11: withRestartList(expr, restarts[-nr])
12: doWithOneRestart(return(expr), restart)
13: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
14: withRestartList(expr, restarts[-nr])
15: doWithOneRestart(return(expr), restart)
16: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
17: withRestartList(expr, restarts)
18: withRestarts(with_handlers({ for (expr in tle$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) })
19: evaluate::evaluate(...)
20: 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$render, options))
21: in_dir(input_dir(), expr)
22: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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)))
23: eng_r(options)
24: block_exec(params)
25: call_block(x)
26: process_group(group)
27: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e))
28: 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)
29: process_file(text, output)
30: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
31: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
32: vweave_rmarkdown(...)
33: engine$weave(file, quiet = quiet, encoding = enc)
34: doTryCatch(return(expr), name, parentenv, handler)
35: tryCatchOne(expr, names, parentenv, handlers[[1L]])
36: tryCatchList(expr, classes, parentenv, handlers)
37: tryCatch({ engine$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)))})
38: tools::buildVignettes(dir = "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/plotmm.Rcheck/vign_test/plotmm", skip = TRUE, ser_elibs = "/home/hornik/tmp/scratch/Rtmpz3s69X/file30320f1451a432.rds")
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.1.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘Getting-Started.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/plotmm.Rcheck/vign_test/plotmm/vignettes/Getting-Started_files/figure-html/unnamed-chunk-2-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 19300 bytes
Input file size = 19402 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 15737
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 15737
Output IDAT size = 15737 bytes (3563 bytes decrease)
Output file size = 15815 bytes (3587 bytes = 18.49% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/plotmm.Rcheck/vign_test/plotmm/vignettes/Getting-Started_files/figure-html/unnamed-chunk-3-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 18757 bytes
Input file size = 18859 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 13403
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 13403
Output IDAT size = 13403 bytes (5354 bytes decrease)
Output file size = 13481 bytes (5378 bytes = 28.52% decrease)
*** caught segfault ***
address 0x1, cause 'memory not mapped'
Traceback:
1: init.EM(x, nclass = 10, method = "em.EM")
2: eval(expr, envir)
3: eval(expr, envir)
4: withVisible(eval(expr, envir))
5: 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))})
6: eval(call)
7: eval(call)
8: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
9: doWithOneRestart(return(expr), restart)
10: withOneRestart(expr, restarts[[1L]])
11: withRestartList(expr, restarts[-nr])
12: doWithOneRestart(return(expr), restart)
13: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
14: withRestartList(expr, restarts[-nr])
15: doWithOneRestart(return(expr), restart)
16: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
17: withRestartList(expr, restarts)
18: withRestarts(with_handlers({ for (expr in tle$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) })
19: evaluate::evaluate(...)
20: 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$render, options))
21: in_dir(input_dir(), expr)
22: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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)))
23: eng_r(options)
24: block_exec(params)
25: call_block(x)
26: process_group(group)
27: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e))
28: 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)
29: process_file(text, output)
30: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
31: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
32: vweave_rmarkdown(...)
33: engine$weave(file, quiet = quiet, encoding = enc)
34: doTryCatch(return(expr), name, parentenv, handler)
35: tryCatchOne(expr, names, parentenv, handlers[[1L]])
36: tryCatchList(expr, classes, parentenv, handlers)
37: tryCatch({ engine$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)))})
38: tools::buildVignettes(dir = "/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/plotmm.Rcheck/vign_test/plotmm", skip = TRUE, ser_elibs = "/tmp/Rtmp1SWXRK/file309e2432fbc3f.rds")
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.1.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘Getting-Started.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-clang/plotmm.Rcheck/vign_test/plotmm/vignettes/Getting-Started_files/figure-html/unnamed-chunk-2-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 19299 bytes
Input file size = 19401 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 15737
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 15737
Output IDAT size = 15737 bytes (3562 bytes decrease)
Output file size = 15815 bytes (3586 bytes = 18.48% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/plotmm.Rcheck/vign_test/plotmm/vignettes/Getting-Started_files/figure-html/unnamed-chunk-3-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 18757 bytes
Input file size = 18859 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 13403
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 13403
Output IDAT size = 13403 bytes (5354 bytes decrease)
Output file size = 13481 bytes (5378 bytes = 28.52% decrease)
*** caught segfault ***
address 0x1, cause 'memory not mapped'
Traceback:
1: init.EM(x, nclass = 10, method = "em.EM")
2: eval(expr, envir)
3: eval(expr, envir)
4: withVisible(eval(expr, envir))
5: 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))})
6: eval(call)
7: eval(call)
8: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
9: doWithOneRestart(return(expr), restart)
10: withOneRestart(expr, restarts[[1L]])
11: withRestartList(expr, restarts[-nr])
12: doWithOneRestart(return(expr), restart)
13: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
14: withRestartList(expr, restarts[-nr])
15: doWithOneRestart(return(expr), restart)
16: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
17: withRestartList(expr, restarts)
18: withRestarts(with_handlers({ for (expr in tle$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) })
19: evaluate::evaluate(...)
20: 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$render, options))
21: in_dir(input_dir(), expr)
22: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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)))
23: eng_r(options)
24: block_exec(params)
25: call_block(x)
26: process_group(group)
27: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e))
28: 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)
29: process_file(text, output)
30: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
31: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
32: vweave_rmarkdown(...)
33: engine$weave(file, quiet = quiet, encoding = enc)
34: doTryCatch(return(expr), name, parentenv, handler)
35: tryCatchOne(expr, names, parentenv, handlers[[1L]])
36: tryCatchList(expr, classes, parentenv, handlers)
37: tryCatch({ engine$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)))})
38: tools::buildVignettes(dir = "/data/gannet/ripley/R/packages/tests-clang/plotmm.Rcheck/vign_test/plotmm", skip = TRUE, ser_elibs = "/tmp/Rtmpq7DHUD/file2a59167d6ccf11.rds")
An irrecoverable exception occurred. R is aborting now ...
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.1.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘Getting-Started.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-devel/plotmm.Rcheck/vign_test/plotmm/vignettes/Getting-Started_files/figure-html/unnamed-chunk-2-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 19299 bytes
Input file size = 19401 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 15737
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 15737
Output IDAT size = 15737 bytes (3562 bytes decrease)
Output file size = 15815 bytes (3586 bytes = 18.48% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/plotmm.Rcheck/vign_test/plotmm/vignettes/Getting-Started_files/figure-html/unnamed-chunk-3-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 18757 bytes
Input file size = 18859 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 13403
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 13403
Output IDAT size = 13403 bytes (5354 bytes decrease)
Output file size = 13481 bytes (5378 bytes = 28.52% decrease)
*** caught segfault ***
address 0x1, cause 'memory not mapped'
Traceback:
1: init.EM(x, nclass = 10, method = "em.EM")
2: eval(expr, envir)
3: eval(expr, envir)
4: withVisible(eval(expr, envir))
5: 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))})
6: eval(call)
7: eval(call)
8: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
9: doWithOneRestart(return(expr), restart)
10: withOneRestart(expr, restarts[[1L]])
11: withRestartList(expr, restarts[-nr])
12: doWithOneRestart(return(expr), restart)
13: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
14: withRestartList(expr, restarts[-nr])
15: doWithOneRestart(return(expr), restart)
16: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
17: withRestartList(expr, restarts)
18: withRestarts(with_handlers({ for (expr in tle$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) })
19: evaluate::evaluate(...)
20: 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$render, options))
21: in_dir(input_dir(), expr)
22: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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)))
23: eng_r(options)
24: block_exec(params)
25: call_block(x)
26: process_group(group)
27: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e))
28: 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)
29: process_file(text, output)
30: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
31: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
32: vweave_rmarkdown(...)
33: engine$weave(file, quiet = quiet, encoding = enc)
34: doTryCatch(return(expr), name, parentenv, handler)
35: tryCatchOne(expr, names, parentenv, handlers[[1L]])
36: tryCatchList(expr, classes, parentenv, handlers)
37: tryCatch({ engine$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)))})
38: tools::buildVignettes(dir = "/data/gannet/ripley/R/packages/tests-devel/plotmm.Rcheck/vign_test/plotmm", skip = TRUE, ser_elibs = "/tmp/RtmpBmalZo/file74ad316d51273.rds")
An irrecoverable exception occurred. R is aborting now ...
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.1.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building 'Getting-Started.Rmd' using rmarkdown
Flavor: r-devel-windows-x86_64