* using log directory ‘/Users/ripley/R/packages/tests-Accelerate/isoWater.Rcheck’
* using R Under development (unstable) (2023-09-17 r85158)
* using platform: aarch64-apple-darwin22.6.0
* R was compiled by
    Apple clang version 15.0.0 (clang-1500.0.40.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.5.2
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘isoWater/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘isoWater’ version ‘1.1.2’
* 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 ‘isoWater’ can be installed ... OK
* checking installed package size ... OK
* 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 R 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... 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 R/sysdata.rda ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘isoWater.Rmd’ using rmarkdown

 *** caught segfault ***
address 0x110, cause 'invalid permissions'

Traceback:
 1: ar.yw.default(x, aic = aic, order.max = order.max, na.action = na.action,     series = series, ...)
 2: ar.yw(x, aic = aic, order.max = order.max, na.action = na.action,     series = series, ...)
 3: ar(x[, i], aic = TRUE)
 4: spectrum0.ar(x)
 5: doTryCatch(return(expr), name, parentenv, handler)
 6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 7: tryCatchList(expr, classes, parentenv, handlers)
 8: 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, nlines = 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))})
 9: try(spectrum0.ar(x)$spec)
10: safespec0(x[[i]][, j])
11: summary.mcmc.list(x)
12: summary(x)
13: mcmc2bugs(samples, model.file = model.file, program = "jags",     DIC = DIC, DICOutput = NULL, n.iter = n.iter, n.burnin = n.burnin,     n.thin = n.thin)
14: jags(data = data, parameters.to.save = parameters.to.save, model.file = model.file,     n.chains = 1, n.iter = n.iter, n.burnin = n.burnin, n.thin = n.thin)
15: eval(c.expr, envir = args, enclos = envir)
16: eval(c.expr, envir = args, enclos = envir)
17: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)
20: tryCatch(eval(c.expr, envir = args, enclos = envir), error = function(e) e)
21: FUN(X[[i]], ...)
22: lapply(X = S, FUN = FUN, ...)
23: doTryCatch(return(expr), name, parentenv, handler)
24: tryCatchOne(expr, names, parentenv, handlers[[1L]])
25: tryCatchList(expr, classes, parentenv, handlers)
26: 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, nlines = 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))})
27: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
28: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
29: FUN(X[[i]], ...)
30: lapply(seq_len(cores), inner.do)
31: mclapply(argsList, FUN, mc.preschedule = preschedule, mc.set.seed = set.seed,     mc.silent = silent, mc.cores = cores)
32: e$fun(obj, substitute(ex), parent.frame(), e$data)
33: foreach(i = 1:n.cluster) %dopar% {    jags(data = data, parameters.to.save = parameters.to.save,         model.file = model.file, n.chains = 1, n.iter = n.iter,         n.burnin = n.burnin, n.thin = n.thin)}
34: jags.parallel(data = d, parameters.to.save = p, model.file = tmf,     n.iter = n.iter, n.chains = ncores, n.burnin = n.burnin,     n.thin = n.thin)
35: mixSource(obs, sources, slope, ngens = 20000, ncores = 2)
36: eval(expr, envir, enclos)
37: eval(expr, envir, enclos)
38: eval_with_user_handlers(expr, envir, enclos, user_handlers)
39: withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers))
40: withCallingHandlers(withVisible(eval_with_user_handlers(expr,     envir, enclos, user_handlers)), warning = wHandler, error = eHandler,     message = mHandler)
41: handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr,     envir, enclos, user_handlers)), warning = wHandler, error = eHandler,     message = mHandler))
42: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr,     envir, enclos, user_handlers)), warning = wHandler, error = eHandler,     message = mHandler)))
43: evaluate_call(expr, parsed$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,     log_echo = log_echo, log_warning = log_warning, output_handler = output_handler,     include_timing = include_timing)
44: evaluate::evaluate(...)
45: 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$render, options))
46: in_dir(input_dir(), expr)
47: in_input_dir(evaluate(code, envir = env, new_device = FALSE,     keep_warning = if (is.numeric(options$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)))
48: eng_r(options)
49: block_exec(params)
50: call_block(x)
51: process_group.block(group)
52: process_group(group)
53: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e))
54: withCallingHandlers(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e)),     error = function(e) {        setwd(wd)        write_utf8(res, output %n% stdout())        message("\nQuitting from lines ", paste(current_lines(i),             collapse = "-"), if (labels[i] != "")             sprintf(" [%s]", labels[i]), sprintf(" (%s)", knit_concord$get("infile")))    })
55: process_file(text, output)
56: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
57: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),     output_dir = getwd(), ...)
58: vweave_rmarkdown(...)
59: engine$weave(file, quiet = quiet, encoding = enc)
60: doTryCatch(return(expr), name, parentenv, handler)
61: tryCatchOne(expr, names, parentenv, handlers[[1L]])
62: tryCatchList(expr, classes, parentenv, handlers)
63: 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)))})
64: tools::buildVignettes(dir = "/Users/ripley/R/packages/tests-Accelerate/isoWater.Rcheck/vign_test/isoWater",     skip = TRUE, ser_elibs = "/var/folders/pk/n4bndnt1287ctrd_ftthnnnr0000gp/T//Rtmppvn8nf/fileff855330a1fb.rds")
An irrecoverable exception occurred. R is aborting now ...

 *** caught segfault ***
address 0x110, cause 'invalid permissions'

Traceback:
 1: ar.yw.default(x, aic = aic, order.max = order.max, na.action = na.action,     series = series, ...)
 2: ar.yw(x, aic = aic, order.max = order.max, na.action = na.action,     series = series, ...)
 3: ar(x[, i], aic = TRUE)
 4: spectrum0.ar(x)
 5: doTryCatch(return(expr), name, parentenv, handler)
 6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 7: tryCatchList(expr, classes, parentenv, handlers)
 8: 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, nlines = 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))})
 9: try(spectrum0.ar(x)$spec)
10: safespec0(x[[i]][, j])
11: summary.mcmc.list(x)
12: summary(x)
13: mcmc2bugs(samples, model.file = model.file, program = "jags",     DIC = DIC, DICOutput = NULL, n.iter = n.iter, n.burnin = n.burnin,     n.thin = n.thin)
14: jags(data = data, parameters.to.save = parameters.to.save, model.file = model.file,     n.chains = 1, n.iter = n.iter, n.burnin = n.burnin, n.thin = n.thin)
15: eval(c.expr, envir = args, enclos = envir)
16: eval(c.expr, envir = args, enclos = envir)
17: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)
20: tryCatch(eval(c.expr, envir = args, enclos = envir), error = function(e) e)
21: FUN(X[[i]], ...)
22: lapply(X = S, FUN = FUN, ...)
23: doTryCatch(return(expr), name, parentenv, handler)
24: tryCatchOne(expr, names, parentenv, handlers[[1L]])
25: tryCatchList(expr, classes, parentenv, handlers)
26: 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, nlines = 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))})
27: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
28: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
29: FUN(X[[i]], ...)
30: lapply(seq_len(cores), inner.do)
31: mclapply(argsList, FUN, mc.preschedule = preschedule, mc.set.seed = set.seed,     mc.silent = silent, mc.cores = cores)
32: e$fun(obj, substitute(ex), parent.frame(), e$data)
33: foreach(i = 1:n.cluster) %dopar% {    jags(data = data, parameters.to.save = parameters.to.save,         model.file = model.file, n.chains = 1, n.iter = n.iter,         n.burnin = n.burnin, n.thin = n.thin)}
34: jags.parallel(data = d, parameters.to.save = p, model.file = tmf,     n.iter = n.iter, n.chains = ncores, n.burnin = n.burnin,     n.thin = n.thin)
35: mixSource(obs, sources, slope, ngens = 20000, ncores = 2)
36: eval(expr, envir, enclos)
37: eval(expr, envir, enclos)
38: eval_with_user_handlers(expr, envir, enclos, user_handlers)
39: withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers))
40: withCallingHandlers(withVisible(eval_with_user_handlers(expr,     envir, enclos, user_handlers)), warning = wHandler, error = eHandler,     message = mHandler)
41: handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr,     envir, enclos, user_handlers)), warning = wHandler, error = eHandler,     message = mHandler))
42: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr,     envir, enclos, user_handlers)), warning = wHandler, error = eHandler,     message = mHandler)))
43: evaluate_call(expr, parsed$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,     log_echo = log_echo, log_warning = log_warning, output_handler = output_handler,     include_timing = include_timing)
44: evaluate::evaluate(...)
45: 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$render, options))
46: in_dir(input_dir(), expr)
47: in_input_dir(evaluate(code, envir = env, new_device = FALSE,     keep_warning = if (is.numeric(options$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)))
48: eng_r(options)
49: block_exec(params)
50: call_block(x)
51: process_group.block(group)
52: process_group(group)
53: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e))
54: withCallingHandlers(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e)),     error = function(e) {        setwd(wd)        write_utf8(res, output %n% stdout())        message("\nQuitting from lines ", paste(current_lines(i),             collapse = "-"), if (labels[i] != "")             sprintf(" [%s]", labels[i]), sprintf(" (%s)", knit_concord$get("infile")))    })
55: process_file(text, output)
56: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
57: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),     output_dir = getwd(), ...)
58: vweave_rmarkdown(...)
59: engine$weave(file, quiet = quiet, encoding = enc)
60: doTryCatch(return(expr), name, parentenv, handler)
61: tryCatchOne(expr, names, parentenv, handlers[[1L]])
62: tryCatchList(expr, classes, parentenv, handlers)
63: 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)))})
64: tools::buildVignettes(dir = "/Users/ripley/R/packages/tests-Accelerate/isoWater.Rcheck/vign_test/isoWater",     skip = TRUE, ser_elibs = "/var/folders/pk/n4bndnt1287ctrd_ftthnnnr0000gp/T//Rtmppvn8nf/fileff855330a1fb.rds")
An irrecoverable exception occurred. R is aborting now ...

Quitting from lines 177-179 [mixSource1] (isoWater.Rmd)
Error: processing vignette 'isoWater.Rmd' failed with diagnostics:
argument of length 0
--- failed re-building ‘isoWater.Rmd’

SUMMARY: processing the following file failed:
  ‘isoWater.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* checking HTML version of manual ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 ERROR
See
  ‘/Users/ripley/R/packages/tests-Accelerate/isoWater.Rcheck/00check.log’
for details.

       25.05 real        17.00 user         3.39 sys