Last updated on 2019-04-23 10:47:57 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.6 | 11.22 | 131.59 | 142.81 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.0.6 | 7.39 | 29.06 | 36.45 | WARN | |
| r-devel-linux-x86_64-fedora-clang | 2.0.6 | 160.96 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.0.6 | 168.99 | OK | |||
| r-devel-windows-ix86+x86_64 | 2.0.6 | 40.00 | 198.00 | 238.00 | OK | |
| r-patched-linux-x86_64 | 2.0.6 | 10.05 | 31.76 | 41.81 | WARN | |
| r-patched-solaris-x86 | 2.0.6 | 395.70 | OK | |||
| r-release-linux-x86_64 | 2.0.6 | 8.55 | 28.26 | 36.81 | WARN | |
| r-release-windows-ix86+x86_64 | 2.0.6 | 26.00 | 231.00 | 257.00 | OK | |
| r-release-osx-x86_64 | 2.0.6 | OK | ||||
| r-oldrel-osx-x86_64 | 2.0.6 | ERROR |
Version: 2.0.6
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building ‘bamp.Rmd’ using rmarkdown
*** caught segfault ***
address 0x1, cause 'memory not mapped'
Traceback:
1: FUN(X[[i]], ...)
2: lapply(X = S, FUN = FUN, ...)
3: doTryCatch(return(expr), name, parentenv, handler)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
5: tryCatchList(expr, classes, parentenv, handlers)
6: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call)[1L] prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
7: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
8: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
9: FUN(X[[i]], ...)
10: lapply(seq_len(cores), inner.do)
11: parallel::mclapply(1:chains, singlerun, cases, population, blocks, numbers, periods_per_agegroup, numbersmcmc, modelsettings, allhyper, theta.sample, phi.sample, psi.sample, theta2.sample, phi2.sample, psi2.sample, ksi, delta.sample, kappa.sample, kappa2.sample, lambda.sample, lambda2.sample, ny.sample, ny2.sample, my.sample, dev.sample, verbose, mc.cores = cores)
12: bamp(cases, population, age = "rw1", period = "rw1", cohort = "rw1", periods_per_agegroup = 5)
13: eval(expr, envir, enclos)
14: eval(expr, envir, enclos)
15: withVisible(eval(expr, envir, enclos))
16: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)
17: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler))
18: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
19: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, output_handler = output_handler, include_timing = include_timing)
20: evaluate::evaluate(...)
21: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (options$error && options$include) 0L else 2L, output_handler = knit_handlers(options$render, options))
22: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (options$error && options$include) 0L else 2L, output_handler = knit_handlers(options$render, options)))
23: block_exec(params)
24: call_block(x)
25: process_group.block(group)
26: process_group(group)
27: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { setwd(wd) cat(res, sep = "\n", file = output %n% "") message("Quitting from lines ", paste(current_lines(i), collapse = "-"), " (", knit_concord$get("infile"), ") ") })
28: process_file(text, output)
29: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet, encoding = encoding)
30: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), ...)
31: vweave_rmarkdown(...)
32: engine$weave(file, quiet = quiet, encoding = enc)
33: doTryCatch(return(expr), name, parentenv, handler)
34: tryCatchOne(expr, names, parentenv, handlers[[1L]])
35: tryCatchList(expr, classes, parentenv, handlers)
36: tryCatch({ engine$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)))})
37: tools:::.buildOneVignette("bamp.Rmd", "/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/bamp.Rcheck/vign_test/bamp", TRUE, FALSE, "bamp", "UTF-8", "/home/hornik/tmp/scratch/RtmpElQlNB/file687c3bca04fb.rds")
An irrecoverable exception occurred. R is aborting now ...
*** caught segfault ***
address 0x1, cause 'memory not mapped'
Traceback:
1: FUN(X[[i]], ...)
2: lapply(X = S, FUN = FUN, ...)
3: doTryCatch(return(expr), name, parentenv, handler)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
5: tryCatchList(expr, classes, parentenv, handlers)
6: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call)[1L] prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
7: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
8: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
9: FUN(X[[i]], ...)
10: lapply(seq_len(cores), inner.do)
11: parallel::mclapply(1:chains, singlerun, cases, population, blocks, numbers, periods_per_agegroup, numbersmcmc, modelsettings, allhyper, theta.sample, phi.sample, psi.sample, theta2.sample, phi2.sample, psi2.sample, ksi, delta.sample, kappa.sample, kappa2.sample, lambda.sample, lambda2.sample, ny.sample, ny2.sample, my.sample, dev.sample, verbose, mc.cores = cores)
12: bamp(cases, population, age = "rw1", period = "rw1", cohort = "rw1", periods_per_agegroup = 5)
13: eval(expr, envir, enclos)
14: eval(expr, envir, enclos)
15: withVisible(eval(expr, envir, enclos))
16: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)
17: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler))
18: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
19: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, output_handler = output_handler, include_timing = include_timing)
20: evaluate::evaluate(...)
21: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (options$error && options$include) 0L else 2L, output_handler = knit_handlers(options$render, options))
22: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (options$error && options$include) 0L else 2L, output_handler = knit_handlers(options$render, options)))
23: block_exec(params)
24: call_block(x)
25: process_group.block(group)
26: process_group(group)
27: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { setwd(wd) cat(res, sep = "\n", file = output %n% "") message("Quitting from lines ", paste(current_lines(i), collapse = "-"), " (", knit_concord$get("infile"), ") ") })
28: process_file(text, output)
29: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet, encoding = encoding)
30: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), ...)
31: vweave_rmarkdown(...)
32: engine$weave(file, quiet = quiet, encoding = enc)
33: doTryCatch(return(expr), name, parentenv, handler)
34: tryCatchOne(expr, names, parentenv, handlers[[1L]])
35: tryCatchList(expr, classes, parentenv, handlers)
36: tryCatch({ engine$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)))})
37: tools:::.buildOneVignette("bamp.Rmd", "/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/bamp.Rcheck/vign_test/bamp", TRUE, FALSE, "bamp", "UTF-8", "/home/hornik/tmp/scratch/RtmpElQlNB/file687c3bca04fb.rds")
An irrecoverable exception occurred. R is aborting now ...
Quitting from lines 31-33 (bamp.Rmd)
Error: processing vignette 'bamp.Rmd' failed with diagnostics:
attempt to set an attribute on NULL
--- failed re-building ‘bamp.Rmd’
--- re-building ‘modeling.html.asis’ using asis
--- finished re-building ‘modeling.html.asis’
--- re-building ‘prediction.html.asis’ using asis
--- finished re-building ‘prediction.html.asis’
--- re-building ‘simulation.html.asis’ using asis
--- finished re-building ‘simulation.html.asis’
SUMMARY: processing the following file failed:
‘bamp.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2.0.6
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building ‘bamp.Rmd’ using rmarkdown
*** caught segfault ***
address 0x1, cause 'memory not mapped'
Traceback:
1: FUN(X[[i]], ...)
2: lapply(X = S, FUN = FUN, ...)
3: doTryCatch(return(expr), name, parentenv, handler)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
5: tryCatchList(expr, classes, parentenv, handlers)
6: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call)[1L] prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
7: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
8: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
9: FUN(X[[i]], ...)
10: lapply(seq_len(cores), inner.do)
11: parallel::mclapply(1:chains, singlerun, cases, population, blocks, numbers, periods_per_agegroup, numbersmcmc, modelsettings, allhyper, theta.sample, phi.sample, psi.sample, theta2.sample, phi2.sample, psi2.sample, ksi, delta.sample, kappa.sample, kappa2.sample, lambda.sample, lambda2.sample, ny.sample, ny2.sample, my.sample, dev.sample, verbose, mc.cores = cores)
12: bamp(cases, population, age = "rw1", period = "rw1", cohort = "rw1", periods_per_agegroup = 5)
13: eval(expr, envir, enclos)
14: eval(expr, envir, enclos)
15: withVisible(eval(expr, envir, enclos))
16: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)
17: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler))
18: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
19: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, output_handler = output_handler, include_timing = include_timing)
20: evaluate::evaluate(...)
21: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (options$error && options$include) 0L else 2L, output_handler = knit_handlers(options$render, options))
22: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (options$error && options$include) 0L else 2L, output_handler = knit_handlers(options$render, options)))
23: block_exec(params)
24: call_block(x)
25: process_group.block(group)
26: process_group(group)
27: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { setwd(wd) cat(res, sep = "\n", file = output %n% "") message("Quitting from lines ", paste(current_lines(i), collapse = "-"), " (", knit_concord$get("infile"), ") ") })
28: process_file(text, output)
29: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet, encoding = encoding)
30: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), ...)
31: vweave_rmarkdown(...)
32: engine$weave(file, quiet = quiet, encoding = enc)
33: doTryCatch(return(expr), name, parentenv, handler)
34: tryCatchOne(expr, names, parentenv, handlers[[1L]])
35: tryCatchList(expr, classes, parentenv, handlers)
36: tryCatch({ engine$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)))})
37: tools:::.buildOneVignette("bamp.Rmd", "/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/bamp.Rcheck/vign_test/bamp", TRUE, FALSE, "bamp", "UTF-8", "/tmp/RtmpS8GLss/file8a23ffdc03c.rds")
An irrecoverable exception occurred. R is aborting now ...
*** caught segfault ***
address 0x1, cause 'memory not mapped'
Traceback:
1: FUN(X[[i]], ...)
2: lapply(X = S, FUN = FUN, ...)
3: doTryCatch(return(expr), name, parentenv, handler)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
5: tryCatchList(expr, classes, parentenv, handlers)
6: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call)[1L] prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
7: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
8: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
9: FUN(X[[i]], ...)
10: lapply(seq_len(cores), inner.do)
11: parallel::mclapply(1:chains, singlerun, cases, population, blocks, numbers, periods_per_agegroup, numbersmcmc, modelsettings, allhyper, theta.sample, phi.sample, psi.sample, theta2.sample, phi2.sample, psi2.sample, ksi, delta.sample, kappa.sample, kappa2.sample, lambda.sample, lambda2.sample, ny.sample, ny2.sample, my.sample, dev.sample, verbose, mc.cores = cores)
12: bamp(cases, population, age = "rw1", period = "rw1", cohort = "rw1", periods_per_agegroup = 5)
13: eval(expr, envir, enclos)
14: eval(expr, envir, enclos)
15: withVisible(eval(expr, envir, enclos))
16: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)
17: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler))
18: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
19: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, output_handler = output_handler, include_timing = include_timing)
20: evaluate::evaluate(...)
21: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (options$error && options$include) 0L else 2L, output_handler = knit_handlers(options$render, options))
22: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (options$error && options$include) 0L else 2L, output_handler = knit_handlers(options$render, options)))
23: block_exec(params)
24: call_block(x)
25: process_group.block(group)
26: process_group(group)
27: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { setwd(wd) cat(res, sep = "\n", file = output %n% "") message("Quitting from lines ", paste(current_lines(i), collapse = "-"), " (", knit_concord$get("infile"), ") ") })
28: process_file(text, output)
29: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet, encoding = encoding)
30: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), ...)
31: vweave_rmarkdown(...)
32: engine$weave(file, quiet = quiet, encoding = enc)
33: doTryCatch(return(expr), name, parentenv, handler)
34: tryCatchOne(expr, names, parentenv, handlers[[1L]])
35: tryCatchList(expr, classes, parentenv, handlers)
36: tryCatch({ engine$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)))})
37: tools:::.buildOneVignette("bamp.Rmd", "/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/bamp.Rcheck/vign_test/bamp", TRUE, FALSE, "bamp", "UTF-8", "/tmp/RtmpS8GLss/file8a23ffdc03c.rds")
An irrecoverable exception occurred. R is aborting now ...
Quitting from lines 31-33 (bamp.Rmd)
Error: processing vignette 'bamp.Rmd' failed with diagnostics:
attempt to set an attribute on NULL
--- failed re-building ‘bamp.Rmd’
--- re-building ‘modeling.html.asis’ using asis
--- finished re-building ‘modeling.html.asis’
--- re-building ‘prediction.html.asis’ using asis
--- finished re-building ‘prediction.html.asis’
--- re-building ‘simulation.html.asis’ using asis
--- finished re-building ‘simulation.html.asis’
SUMMARY: processing the following file failed:
‘bamp.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-patched-linux-x86_64
Version: 2.0.6
Check: re-building of vignette outputs
Result: WARN
Error in re-building vignettes:
...
*** caught segfault ***
address 0x1, cause 'memory not mapped'
Traceback:
1: FUN(X[[i]], ...)
2: lapply(X = S, FUN = FUN, ...)
3: doTryCatch(return(expr), name, parentenv, handler)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
5: tryCatchList(expr, classes, parentenv, handlers)
6: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call)[1L] prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
7: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
8: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
9: FUN(X[[i]], ...)
10: lapply(seq_len(cores), inner.do)
11: parallel::mclapply(1:chains, singlerun, cases, population, blocks, numbers, periods_per_agegroup, numbersmcmc, modelsettings, allhyper, theta.sample, phi.sample, psi.sample, theta2.sample, phi2.sample, psi2.sample, ksi, delta.sample, kappa.sample, kappa2.sample, lambda.sample, lambda2.sample, ny.sample, ny2.sample, my.sample, dev.sample, verbose, mc.cores = cores)
12: bamp(cases, population, age = "rw1", period = "rw1", cohort = "rw1", periods_per_agegroup = 5)
13: eval(expr, envir, enclos)
14: eval(expr, envir, enclos)
15: withVisible(eval(expr, envir, enclos))
16: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)
17: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler))
18: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
19: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, output_handler = output_handler, include_timing = include_timing)
20: evaluate::evaluate(...)
21: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (options$error && options$include) 0L else 2L, output_handler = knit_handlers(options$render, options))
22: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (options$error && options$include) 0L else 2L, output_handler = knit_handlers(options$render, options)))
23: block_exec(params)
24: call_block(x)
25: process_group.block(group)
26: process_group(group)
27: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { setwd(wd) cat(res, sep = "\n", file = output %n% "") message("Quitting from lines ", paste(current_lines(i), collapse = "-"), " (", knit_concord$get("infile"), ") ") })
28: process_file(text, output)
29: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet, encoding = encoding)
30: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), ...)
31: vweave_rmarkdown(...)
32: engine$weave(file, quiet = quiet, encoding = enc)
33: doTryCatch(return(expr), name, parentenv, handler)
34: tryCatchOne(expr, names, parentenv, handlers[[1L]])
35: tryCatchList(expr, classes, parentenv, handlers)
36: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) find_vignette_product(name, by = "weave", engine = engine)}, error = function(e) { stop(gettextf("processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)), domain = NA, call. = FALSE)})
37: buildVignettes(dir = "/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/bamp.Rcheck/vign_test/bamp")
An irrecoverable exception occurred. R is aborting now ...
*** caught segfault ***
address 0x1, cause 'memory not mapped'
Traceback:
1: FUN(X[[i]], ...)
2: lapply(X = S, FUN = FUN, ...)
3: doTryCatch(return(expr), name, parentenv, handler)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
5: tryCatchList(expr, classes, parentenv, handlers)
6: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call)[1L] prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
7: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
8: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
9: FUN(X[[i]], ...)
10: lapply(seq_len(cores), inner.do)
11: parallel::mclapply(1:chains, singlerun, cases, population, blocks, numbers, periods_per_agegroup, numbersmcmc, modelsettings, allhyper, theta.sample, phi.sample, psi.sample, theta2.sample, phi2.sample, psi2.sample, ksi, delta.sample, kappa.sample, kappa2.sample, lambda.sample, lambda2.sample, ny.sample, ny2.sample, my.sample, dev.sample, verbose, mc.cores = cores)
12: bamp(cases, population, age = "rw1", period = "rw1", cohort = "rw1", periods_per_agegroup = 5)
13: eval(expr, envir, enclos)
14: eval(expr, envir, enclos)
15: withVisible(eval(expr, envir, enclos))
16: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)
17: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler))
18: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
19: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, output_handler = output_handler, include_timing = include_timing)
20: evaluate::evaluate(...)
21: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (options$error && options$include) 0L else 2L, output_handler = knit_handlers(options$render, options))
22: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (options$error && options$include) 0L else 2L, output_handler = knit_handlers(options$render, options)))
23: block_exec(params)
24: call_block(x)
25: process_group.block(group)
26: process_group(group)
27: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { setwd(wd) cat(res, sep = "\n", file = output %n% "") message("Quitting from lines ", paste(current_lines(i), collapse = "-"), " (", knit_concord$get("infile"), ") ") })
28: process_file(text, output)
29: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet, encoding = encoding)
30: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), ...)
31: vweave_rmarkdown(...)
32: engine$weave(file, quiet = quiet, encoding = enc)
33: doTryCatch(return(expr), name, parentenv, handler)
34: tryCatchOne(expr, names, parentenv, handlers[[1L]])
35: tryCatchList(expr, classes, parentenv, handlers)
36: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) find_vignette_product(name, by = "weave", engine = engine)}, error = function(e) { stop(gettextf("processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)), domain = NA, call. = FALSE)})
37: buildVignettes(dir = "/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/bamp.Rcheck/vign_test/bamp")
An irrecoverable exception occurred. R is aborting now ...
Quitting from lines 31-33 (bamp.Rmd)
Error: processing vignette ‘bamp.Rmd’ failed with diagnostics:
attempt to set an attribute on NULL
Execution halted
Flavor: r-release-linux-x86_64
Version: 2.0.6
Check: whether package can be installed
Result: ERROR
Installation failed.
Flavor: r-oldrel-osx-x86_64