CRAN Package Check Results for Package bamp

Last updated on 2019-06-07 02:50:43 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.0.7 11.00 162.82 173.82 OK
r-devel-linux-x86_64-debian-gcc 2.0.7 7.23 132.51 139.74 OK
r-devel-linux-x86_64-fedora-clang 2.0.7 176.94 OK
r-devel-linux-x86_64-fedora-gcc 2.0.7 187.14 OK
r-devel-windows-ix86+x86_64 2.0.7 41.00 248.00 289.00 OK
r-patched-linux-x86_64 2.0.7 9.22 192.18 201.40 OK
r-patched-solaris-x86 2.0.7 446.20 OK
r-release-linux-x86_64 2.0.7 9.34 32.94 42.28 WARN
r-release-windows-ix86+x86_64 2.0.7 40.00 265.00 305.00 OK
r-release-osx-x86_64 2.0.7 OK
r-oldrel-windows-ix86+x86_64 2.0.7 37.00 251.00 288.00 OK
r-oldrel-osx-x86_64 2.0.7 OK

Check Details

Version: 2.0.7
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-release-gcc/Work/PKGS/bamp.Rcheck/vign_test/bamp", TRUE, FALSE, "bamp", "UTF-8", "/tmp/RtmpbPlfJt/file1fe52ce00a63.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-release-gcc/Work/PKGS/bamp.Rcheck/vign_test/bamp", TRUE, FALSE, "bamp", "UTF-8", "/tmp/RtmpbPlfJt/file1fe52ce00a63.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-release-linux-x86_64