CRAN Package Check Results for Package glmmTMB

Last updated on 2021-10-26 20:50:54 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.1.2.3 169.99 274.46 444.45 OK
r-devel-linux-x86_64-debian-gcc 1.1.2.3 153.83 218.47 372.30 OK
r-devel-linux-x86_64-fedora-clang 1.1.2.3 600.31 NOTE
r-devel-linux-x86_64-fedora-gcc 1.1.2.3 619.11 OK
r-devel-windows-x86_64 1.1.2.3 183.00 300.00 483.00 NOTE --no-vignettes
r-devel-windows-x86_64-gcc10-UCRT 1.1.2.3 OK
r-patched-linux-x86_64 1.1.2.3 169.29 298.09 467.38 OK
r-patched-solaris-x86 1.1.2 380.60 ERROR
r-release-linux-x86_64 1.1.2.3 152.71 299.45 452.16 OK
r-release-macos-arm64 1.1.2.3 NOTE
r-release-macos-x86_64 1.1.2.3 NOTE
r-release-windows-ix86+x86_64 1.1.2.3 235.00 499.00 734.00 NOTE --no-vignettes
r-oldrel-macos-x86_64 1.1.2.3 NOTE
r-oldrel-windows-ix86+x86_64 1.1.2.3 342.00 479.00 821.00 NOTE --no-vignettes

Check Details

Version: 1.1.2.3
Check: installed package size
Result: NOTE
     installed size is 48.8Mb
     sub-directories of 1Mb or more:
     libs 44.1Mb
     test_data 2.2Mb
     vignette_data 1.1Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-x86_64

Version: 1.1.2.3
Flags: --no-vignettes
Check: installed package size
Result: NOTE
     installed size is 18.4Mb
     sub-directories of 1Mb or more:
     libs 13.7Mb
     test_data 2.1Mb
     vignette_data 1.1Mb
Flavors: r-devel-windows-x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.1.2
Check: installed package size
Result: NOTE
     installed size is 6.9Mb
     sub-directories of 1Mb or more:
     libs 1.9Mb
     test_data 2.2Mb
     vignette_data 1.3Mb
Flavor: r-patched-solaris-x86

Version: 1.1.2
Check: examples
Result: ERROR
    Running examples in ‘glmmTMB-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: VarCorr.glmmTMB
    > ### Title: Extract variance and correlation components
    > ### Aliases: VarCorr.glmmTMB VarCorr
    > ### Keywords: internal
    >
    > ### ** Examples
    >
    > ## Comparing variance-covariance matrix with manual computation
    > data("sleepstudy",package="lme4")
    > fm4 <- glmmTMB(Reaction ~ Days + (Days|Subject), sleepstudy)
    
     *** caught segfault ***
    address 4539ec45, cause 'memory not mapped'
    
     *** caught segfault ***
    address 1140000a, cause 'memory not mapped'
    
    Traceback:
     1: retape(set.defaults = TRUE)
     2: MakeADFun(data.tmb, parameters, map = mapArg, random = randomArg, profile = NULL, silent = !verbose, DLL = "glmmTMB")
     3: eval(substitute(expr), data, enclos = parent.frame())
     4: eval(substitute(expr), data, enclos = parent.frame())
     5: with.default(TMBStruc, MakeADFun(data.tmb, parameters, map = mapArg, random = randomArg, profile = NULL, silent = !verbose, DLL = "glmmTMB"))
     6: with(TMBStruc, MakeADFun(data.tmb, parameters, map = mapArg, random = randomArg, profile = NULL, silent = !verbose, DLL = "glmmTMB"))
     7: fitTMB(TMBStruc)
     8: glmmTMB(Reaction ~ Days + (Days | Subject), sleepstudy)
    An irrecoverable exception occurred. R is aborting now ...
    
    Traceback:
     1: retape(set.defaults = TRUE)
     2: MakeADFun(data.tmb, parameters, map = mapArg, random = randomArg, profile = NULL, silent = !verbose, DLL = "glmmTMB")
     3: eval(substitute(expr), data, enclos = parent.frame())
     4: eval(substitute(expr), data, enclos = parent.frame())
     5: with.default(TMBStruc, MakeADFun(data.tmb, parameters, map = mapArg, random = randomArg, profile = NULL, silent = !verbose, DLL = "glmmTMB"))
     6: with(TMBStruc, MakeADFun(data.tmb, parameters, map = mapArg, random = randomArg, profile = NULL, silent = !verbose, DLL = "glmmTMB"))
     7: fitTMB(TMBStruc)
     8: glmmTMB(Reaction ~ Days + (Days | Subject), sleepstudy)
    An irrecoverable exception occurred. R is aborting now ...
Flavor: r-patched-solaris-x86

Version: 1.1.2
Check: tests
Result: ERROR
     Running ‘AAAtest-all.R’ [9s/40s]
    Running the tests in ‘tests/AAAtest-all.R’ failed.
    Complete output:
     > if (require("testthat")) {
     + pkg <- "glmmTMB"
     + require(pkg, character.only=TRUE)
     + print(sessionInfo())
     + test_check(pkg, reporter="summary")
     + print(warnings()) # TODO? catch most of these by expect_warning(..)
     + } else {
     + warnings("Package 'testthat' not available, cannot run unit tests for package",
     + sQuote(pkg))
     + }
     Loading required package: testthat
     Loading required package: glmmTMB
     R version 4.1.1 Patched (2021-08-19 r80801)
     Platform: i386-pc-solaris2.10 (32-bit)
     Running under: Solaris 10
    
     Matrix products: default
     BLAS: /home/ripley/R/cc/lib/libRblas.so
     LAPACK: /home/ripley/R/cc/lib/libRlapack.so
    
     locale:
     [1] /en_GB.UTF-8/C/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
    
     attached base packages:
     [1] stats graphics grDevices utils datasets methods base
    
     other attached packages:
     [1] glmmTMB_1.1.2 testthat_3.0.4
    
     loaded via a namespace (and not attached):
     [1] Rcpp_1.0.7 TMB_1.7.20 magrittr_2.0.1
     [4] splines_4.1.1 MASS_7.3-54 xtable_1.8-4
     [7] lattice_0.20-44 R6_2.5.1 rlang_0.4.11
     [10] multcomp_1.4-17 minqa_1.2.4 grid_4.1.1
     [13] nlme_3.1-152 TH.data_1.0-10 coda_0.19-4
     [16] emmeans_1.6.2-1 survival_3.2-12 lme4_1.1-27.1
     [19] numDeriv_2016.8-1.1 Matrix_1.3-4 nloptr_1.2.2.2
     [22] codetools_0.2-18 sandwich_3.0-1 estimability_1.3
     [25] compiler_4.1.1 boot_1.3-28 mvtnorm_1.1-2
     [28] zoo_1.8-9
     Warning: namespace 'GLMMadaptive' is not available and has been replaced
     by .GlobalEnv when processing object 'fit'
     Anova: ..
     *** caught segfault ***
     address 0, cause 'memory not mapped'
    
     *** caught segfault ***
     address 2d48db14, cause 'memory not mapped'
    
     Traceback:
     1: retape(set.defaults = TRUE)
     2: MakeADFun(data.tmb, parameters, map = mapArg, random = randomArg, profile = NULL, silent = !verbose, DLL = "glmmTMB")
     3: eval(substitute(expr), data, enclos = parent.frame())
     4: eval(substitute(expr), data, enclos = parent.frame())
     5: with.default(TMBStruc, MakeADFun(data.tmb, parameters, map = mapArg, random = randomArg, profile = NULL, silent = !verbose, DLL = "glmmTMB"))
     6: with(TMBStruc, MakeADFun(data.tmb, parameters, map = mapArg, random = randomArg, profile = NULL, silent = !verbose, DLL = "glmmTMB"))
     7: fitTMB(TMBStruc)
     8: glmmTMB(Reaction ~ Days + (1 | Subject), disp = ~I(Days > 5), sleepstudy, REML = FALSE)
     9: eval(code, test_env)
     10: eval(code, test_env)
     11: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)
     12: doTryCatch(return(expr), name, parentenv, handler)
     13: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     14: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
     15: doTryCatch(return(expr), name, parentenv, handler)
     16: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
     17: tryCatchList(expr, classes, parentenv, handlers)
     18: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
     19: test_code(NULL, exprs, env)
     20: source_file(path, child_env(env), wrap = wrap)
     21: FUN(X[[i]], ...)
     22: lapply(test_paths, test_one_file, env = env, wrap = wrap)
     23: force(code)
     Traceback:
     1: retape(set.defaults = TRUE)
     2: MakeADFun(data.tmb, parameters, map = mapArg, random = randomArg, profile = NULL, silent = !verbose, DLL = "glmmTMB")
     3: eval(substitute(expr), data, enclos = parent.frame())
     4: eval(substitute(expr), data, enclos = parent.frame())
     5: with.default(TMBStruc, MakeADFun(data.tmb, parameters, map = mapArg, random = randomArg, profile = NULL, silent = !verbose, DLL = "glmmTMB"))
     6: with(TMBStruc, MakeADFun(data.tmb, parameters, map = mapArg, random = randomArg, profile = NULL, silent = !verbose, DLL = "glmmTMB"))
     7: fitTMB(TMBStruc)
     8: glmmTMB(Reaction ~ Days + (1 | Subject), disp = ~I(Days > 5), sleepstudy, REML = FALSE)
     9: eval(code, test_env)
     10: eval(code, test_env)
     11: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)
     12: doTryCatch(return(expr), name, parentenv, handler)
     13: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     14: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
     15: doTryCatch(return(expr), name, parentenv, handler)
     16: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
     17: tryCatchList(expr, classes, parentenv, handlers)
     18: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
     19: test_code(NULL, exprs, env)
     20: source_file(path, child_env(env), wrap = wrap)
     21: FUN(X[[i]], ...)
     22: lapply(test_paths, test_one_file, env = env, wrap = wrap)
     23: force(code)
     24: doWithOneRestart(return(expr), restart)
     25: withOneRestart(expr, restarts[[1L]])
     26: withRestarts(testthat_abort_reporter = function() NULL, force(code))
     27: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, wrap = wrap))
     28: test_files(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap, load_package = load_package)
     29: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap, load_package = load_package, parallel = parallel)
     30: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
     31: test_check(pkg, reporter = "summary")
     An irrecoverable exception occurred. R is aborting now ...
    
     24: doWithOneRestart(return(expr), restart)
     25: withOneRestart(expr, restarts[[1L]])
     26: withRestarts(testthat_abort_reporter = function() NULL, force(code))
     27: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, wrap = wrap))
     28: test_files(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap, load_package = load_package)
     29: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap, load_package = load_package, parallel = parallel)
     30: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
     31: test_check(pkg, reporter = "summary")
     An irrecoverable exception occurred. R is aborting now ...
Flavor: r-patched-solaris-x86

Version: 1.1.2
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘covstruct.rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
    --- finished re-building ‘covstruct.rmd’
    
    --- re-building ‘mcmc.rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
    --- finished re-building ‘mcmc.rmd’
    
    Segmentation Fault - core dumped
    --- re-building ‘miscEx.rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
    
     *** caught segfault ***
    address 0, cause 'memory not mapped'
    
    Traceback:
     1: retape(set.defaults = TRUE)
     2: MakeADFun(data.tmb, parameters, map = mapArg, random = randomArg, profile = NULL, silent = !verbose, DLL = "glmmTMB")
     3: eval(substitute(expr), data, enclos = parent.frame())
     4: eval(substitute(expr), data, enclos = parent.frame())
     5: with.default(TMBStruc, MakeADFun(data.tmb, parameters, map = mapArg, random = randomArg, profile = NULL, silent = !verbose, DLL = "glmmTMB"))
     6: with(TMBStruc, MakeADFun(data.tmb, parameters, map = mapArg, random = randomArg, profile = NULL, silent = !verbose, DLL = "glmmTMB"))
     7: fitTMB(TMBStruc)
     8: glmmTMB(y ~ x, family = beta_family(), data = dd)
     9: eval(expr, envir, enclos)
    10: eval(expr, envir, enclos)
    11: withVisible(eval(expr, envir, enclos))
    12: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)
    13: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler))
    14: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
    15: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, output_handler = output_handler, include_timing = include_timing)
    16: evaluate::evaluate(...)
    17: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(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))
    18: 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 (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)))
    19: eng_r(options)
    20: block_exec(params)
    21: call_block(x)
    22: process_group.block(group)
    23: process_group(group)
    24: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { setwd(wd) cat(res, sep = "\n", file = output %n% "") message("Quitting from lines ", paste(current_lines(i), collapse = "-"), " (", knit_concord$get("infile"), ") ") })
    25: process_file(text, output)
    26: knit(input, text = text, envir = envir, quiet = quiet)
    27: (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$", file)) knit2pandoc else knit)(file, encoding = encoding, quiet = quiet, envir = globalenv(), ...)
    28: vweave(...)
    29: engine$weave(file, quiet = quiet, encoding = enc)
    30: doTryCatch(return(expr), name, parentenv, handler)
    31: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    32: tryCatchList(expr, classes, parentenv, handlers)
    33: tryCatch({ engine$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)))})
    34: tools:::.buildOneVignette("miscEx.rmd", "/home/ripley/R/packages/tests32/glmmTMB.Rcheck/vign_test/glmmTMB", TRUE, FALSE, "miscEx", "UTF-8", "/tmp/RtmpDDaWL2/working_dir/Rtmp9naWZS/file599e37d0269d.rds")
    An irrecoverable exception occurred. R is aborting now ...
    --- re-building ‘parallel.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
    --- finished re-building ‘parallel.Rmd’
    
    Segmentation Fault - core dumped
    --- re-building ‘sim.rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
    
     *** caught segfault ***
    address 0, cause 'memory not mapped'
    
    Traceback:
     1: retape(set.defaults = TRUE)
     2: MakeADFun(data.tmb, parameters, map = mapArg, random = randomArg, profile = NULL, silent = !verbose, DLL = "glmmTMB")
     3: eval(substitute(expr), data, enclos = parent.frame())
     4: eval(substitute(expr), data, enclos = parent.frame())
     5: with.default(TMBStruc, MakeADFun(data.tmb, parameters, map = mapArg, random = randomArg, profile = NULL, silent = !verbose, DLL = "glmmTMB"))
     6: with(TMBStruc, MakeADFun(data.tmb, parameters, map = mapArg, random = randomArg, profile = NULL, silent = !verbose, DLL = "glmmTMB"))
     7: fitTMB(TMBStruc)
     8: glmmTMB(SiblingNegotiation ~ FoodTreatment * SexParent + (1 | Nest) + offset(log(BroodSize)), family = nbinom1, ziformula = ~1, data = Owls)
     9: eval(expr, envir, enclos)
    10: eval(expr, envir, enclos)
    11: withVisible(eval(expr, envir, enclos))
    12: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)
    13: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler))
    14: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
    15: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, output_handler = output_handler, include_timing = include_timing)
    16: evaluate::evaluate(...)
    17: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(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))
    18: 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 (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)))
    19: eng_r(options)
    20: block_exec(params)
    21: call_block(x)
    22: process_group.block(group)
    23: process_group(group)
    24: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { setwd(wd) cat(res, sep = "\n", file = output %n% "") message("Quitting from lines ", paste(current_lines(i), collapse = "-"), " (", knit_concord$get("infile"), ") ") })
    25: process_file(text, output)
    26: knit(input, text = text, envir = envir, quiet = quiet)
    27: (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$", file)) knit2pandoc else knit)(file, encoding = encoding, quiet = quiet, envir = globalenv(), ...)
    28: vweave(...)
    29: engine$weave(file, quiet = quiet, encoding = enc)
    30: doTryCatch(return(expr), name, parentenv, handler)
    31: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    32: tryCatchList(expr, classes, parentenv, handlers)
    33: tryCatch({ engine$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)))})
    34: tools:::.buildOneVignette("sim.rmd", "/home/ripley/R/packages/tests32/glmmTMB.Rcheck/vign_test/glmmTMB", TRUE, FALSE, "sim", "UTF-8", "/tmp/RtmpDDaWL2/working_dir/Rtmp9naWZS/file599ed9e7f23.rds")
    An irrecoverable exception occurred. R is aborting now ...
    
     *** caught segfault ***
    address 0, cause 'memory not mapped'
    
    Traceback:
     1: retape(set.defaults = TRUE)
     2: MakeADFun(data.tmb, parameters, map = mapArg, random = randomArg, profile = NULL, silent = !verbose, DLL = "glmmTMB")
     3: eval(substitute(expr), data, enclos = parent.frame())
     4: eval(substitute(expr), data, enclos = parent.frame())
     5: with.default(TMBStruc, MakeADFun(data.tmb, parameters, map = mapArg, random = randomArg, profile = NULL, silent = !verbose, DLL = "glmmTMB"))
     6: with(TMBStruc, MakeADFun(data.tmb, parameters, map = mapArg, random = randomArg, profile = NULL, silent = !verbose, DLL = "glmmTMB"))
     7: fitTMB(TMBStruc)
     8: glmmTMB(SiblingNegotiation ~ FoodTreatment * SexParent + (1 | Nest) + offset(log(BroodSize)), family = nbinom1, ziformula = ~1, data = Owls)
     9: eval(expr, envir, enclos)
    10: eval(expr, envir, enclos)
    11: withVisible(eval(expr, envir, enclos))
    12: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)
    13: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler))
    14: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
    15: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, output_handler = output_handler, include_timing = include_timing)
    16: evaluate::evaluate(...)
    17: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(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))
    18: 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 (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)))
    19: eng_r(options)
    20: block_exec(params)
    21: call_block(x)
    22: process_group.block(group)
    23: process_group(group)
    24: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { setwd(wd) cat(res, sep = "\n", file = output %n% "") message("Quitting from lines ", paste(current_lines(i), collapse = "-"), " (", knit_concord$get("infile"), ") ") })
    25: process_file(text, output)
    26: knit(input, text = text, envir = envir, quiet = quiet)
    27: (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$", file)) knit2pandoc else knit)(file, encoding = encoding, quiet = quiet, envir = globalenv(), ...)
    28: vweave(...)
    29: engine$weave(file, quiet = quiet, encoding = enc)
    30: doTryCatch(return(expr), name, parentenv, handler)
    31: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    32: tryCatchList(expr, classes, parentenv, handlers)
    33: tryCatch({ engine$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)))})
    34: tools:::.buildOneVignette("sim.rmd", "/home/ripley/R/packages/tests32/glmmTMB.Rcheck/vign_test/glmmTMB", TRUE, FALSE, "sim", "UTF-8", "/tmp/RtmpDDaWL2/working_dir/Rtmp9naWZS/file599ed9e7f23.rds")
    An irrecoverable exception occurred. R is aborting now ...
    Segmentation Fault - core dumped
    --- re-building ‘troubleshooting.rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
    
     *** caught segfault ***
    address 0, cause 'memory not mapped'
    
    Traceback:
     1: retape(set.defaults = TRUE)
     2: MakeADFun(data.tmb, parameters, map = mapArg, random = randomArg, profile = NULL, silent = !verbose, DLL = "glmmTMB")
     3: eval(substitute(expr), data, enclos = parent.frame())
     4: eval(substitute(expr), data, enclos = parent.frame())
     5: with.default(TMBStruc, MakeADFun(data.tmb, parameters, map = mapArg, random = randomArg, profile = NULL, silent = !verbose, DLL = "glmmTMB"))
     6: with(TMBStruc, MakeADFun(data.tmb, parameters, map = mapArg, random = randomArg, profile = NULL, silent = !verbose, DLL = "glmmTMB"))
     7: fitTMB(TMBStruc)
     8: glmmTMB(formula = taeCPUE ~ Avg.Relief + (1 | site.name/reef.name), data = dd, family = nbinom1, ziformula = ~0, dispformula = ~1, control = glmmTMBControl(optimizer = optim, optArgs = list(method = "BFGS")))
     9: eval(call, parent.frame())
    10: eval(call, parent.frame())
    11: update.default(mod2, control = glmmTMBControl(optimizer = optim, optArgs = list(method = "BFGS")))
    12: update(mod2, control = glmmTMBControl(optimizer = optim, optArgs = list(method = "BFGS")))
    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$message), stop_on_error = if (is.numeric(options$error)) options$error else { if (options$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 (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)))
    23: eng_r(options)
    24: block_exec(params)
    25: call_block(x)
    26: process_group.block(group)
    27: process_group(group)
    28: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { setwd(wd) cat(res, sep = "\n", file = output %n% "") message("Quitting from lines ", paste(current_lines(i), collapse = "-"), " (", knit_concord$get("infile"), ") ") })
    29: process_file(text, output)
    30: knit(input, text = text, envir = envir, quiet = quiet)
    31: (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$", file)) knit2pandoc else knit)(file, encoding = encoding, quiet = quiet, envir = globalenv(), ...)
    32: vweave(...)
    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) }}, error = function(e) { OK <<- FALSE message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
    38: tools:::.buildOneVignette("troubleshooting.rmd", "/home/ripley/R/packages/tests32/glmmTMB.Rcheck/vign_test/glmmTMB", TRUE, FALSE, "troubleshooting", "UTF-8", "/tmp/RtmpDDaWL2/working_dir/Rtmp9naWZS/file599e16071098.rds")
    An irrecoverable exception occurred. R is aborting now ...
    --- re-building ‘glmmTMB.Rnw’ using knitr
    Loading required package: stats4
    --- finished re-building ‘glmmTMB.Rnw’
    
    Segmentation Fault - core dumped
    --- re-building ‘model_evaluation.Rnw’ using knitr
    Loading required package: carData
    lattice theme set by effectsTheme()
    See ?effectsTheme for details.
    Loading required package: mvtnorm
    Loading required package: survival
    Loading required package: TH.data
    Loading required package: MASS
    
    Attaching package: 'TH.data'
    
    The following object is masked from 'package:MASS':
    
     geyser
    
    This is DHARMa 0.4.3. For overview type '?DHARMa'. For recent changes, type news(package = 'DHARMa') Note: Syntax of plotResiduals has changed in 0.3.0, see ?plotResiduals for details
    Loading required package: ggplot2
    Version: 1.37.5
    Date: 2020-06-17
    Author: Philip Leifeld (University of Essex)
    
    Consider submitting praise using the praise or praise_interactive functions.
    Please cite the JSS article in your publications -- see citation("texreg").
    
     *** caught segfault ***
    address 0, cause 'memory not mapped'
    
    Traceback:
     1: retape(set.defaults = TRUE)
     2: MakeADFun(data.tmb, parameters, map = mapArg, random = randomArg, profile = NULL, silent = !verbose, DLL = "glmmTMB")
     3: eval(substitute(expr), data, enclos = parent.frame())
     4: eval(substitute(expr), data, enclos = parent.frame())
     5: with.default(TMBStruc, MakeADFun(data.tmb, parameters, map = mapArg, random = randomArg, profile = NULL, silent = !verbose, DLL = "glmmTMB"))
     6: with(TMBStruc, MakeADFun(data.tmb, parameters, map = mapArg, random = randomArg, profile = NULL, silent = !verbose, DLL = "glmmTMB"))
     7: fitTMB(TMBStruc)
     8: glmmTMB(SiblingNegotiation ~ FoodTreatment * SexParent + (1 | Nest) + offset(log(BroodSize)), contrasts = list(FoodTreatment = "contr.sum", SexParent = "contr.sum"), family = nbinom1, zi = ~1, data = Owls)
     9: eval(expr, envir, enclos)
    10: eval(expr, envir, enclos)
    11: withVisible(eval(expr, envir, enclos))
    12: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)
    13: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler))
    14: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
    15: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, output_handler = output_handler, include_timing = include_timing)
    16: evaluate::evaluate(...)
    17: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(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))
    18: 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 (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)))
    19: eng_r(options)
    20: block_exec(params)
    21: call_block(x)
    22: process_group.block(group)
    23: process_group(group)
    24: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { setwd(wd) cat(res, sep = "\n", file = output %n% "") message("Quitting from lines ", paste(current_lines(i), collapse = "-"), " (", knit_concord$get("infile"), ") ") })
    25: process_file(text, output)
    26: (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$", file)) knit2pandoc else knit)(file, encoding = encoding, quiet = quiet, envir = globalenv(), ...)
    27: engine$weave(file, quiet = quiet, encoding = enc)
    28: doTryCatch(return(expr), name, parentenv, handler)
    29: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    30: tryCatchList(expr, classes, parentenv, handlers)
    31: tryCatch({ engine$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)))})
    32: tools:::.buildOneVignette("model_evaluation.Rnw", "/home/ripley/R/packages/tests32/glmmTMB.Rcheck/vign_test/glmmTMB", TRUE, FALSE, "model_evaluation", "UTF-8", "/tmp/RtmpDDaWL2/working_dir/Rtmp9naWZS/file599e7e7f92.rds")
    An irrecoverable exception occurred. R is aborting now ...
    
     *** caught segfault ***
    address 0, cause 'memory not mapped'
    
    Traceback:
     1: retape(set.defaults = TRUE)
     2: MakeADFun(data.tmb, parameters, map = mapArg, random = randomArg, profile = NULL, silent = !verbose, DLL = "glmmTMB")
     3: eval(substitute(expr), data, enclos = parent.frame())
     4: eval(substitute(expr), data, enclos = parent.frame())
     5: with.default(TMBStruc, MakeADFun(data.tmb, parameters, map = mapArg, random = randomArg, profile = NULL, silent = !verbose, DLL = "glmmTMB"))
     6: with(TMBStruc, MakeADFun(data.tmb, parameters, map = mapArg, random = randomArg, profile = NULL, silent = !verbose, DLL = "glmmTMB"))
     7: fitTMB(TMBStruc)
     8: glmmTMB(SiblingNegotiation ~ FoodTreatment * SexParent + (1 | Nest) + offset(log(BroodSize)), contrasts = list(FoodTreatment = "contr.sum", SexParent = "contr.sum"), family = nbinom1, zi = ~1, data = Owls)
     9: eval(expr, envir, enclos)
    10: eval(expr, envir, enclos)
    11: withVisible(eval(expr, envir, enclos))
    12: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)
    13: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler))
    14: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
    15: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, output_handler = output_handler, include_timing = include_timing)
    16: evaluate::evaluate(...)
    17: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(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))
    18: 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 (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)))
    19: eng_r(options)
    20: block_exec(params)
    21: call_block(x)
    22: process_group.block(group)
    23: process_group(group)
    24: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { setwd(wd) cat(res, sep = "\n", file = output %n% "") message("Quitting from lines ", paste(current_lines(i), collapse = "-"), " (", knit_concord$get("infile"), ") ") })
    25: process_file(text, output)
    26: (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$", file)) knit2pandoc else knit)(file, encoding = encoding, quiet = quiet, envir = globalenv(), ...)
    27: engine$weave(file, quiet = quiet, encoding = enc)
    28: doTryCatch(return(expr), name, parentenv, handler)
    29: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    30: tryCatchList(expr, classes, parentenv, handlers)
    31: tryCatch({ engine$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)))})
    32: tools:::.buildOneVignette("model_evaluation.Rnw", "/home/ripley/R/packages/tests32/glmmTMB.Rcheck/vign_test/glmmTMB", TRUE, FALSE, "model_evaluation", "UTF-8", "/tmp/RtmpDDaWL2/working_dir/Rtmp9naWZS/file599e7e7f92.rds")
    An irrecoverable exception occurred. R is aborting now ...
    SUMMARY: processing the following files failed:
     ‘miscEx.rmd’ ‘sim.rmd’ ‘troubleshooting.rmd’ ‘model_evaluation.Rnw’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-patched-solaris-x86