* using log directory ‘/data/gannet/ripley/R/packages/tests-Intel/bssm.Rcheck’
* using R Under development (unstable) (2024-06-24 r86824)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Intel(R) oneAPI DPC++/C++ Compiler 2024.2.0 (2024.2.0.20240602)
    ifx (IFX) 2024.2.0 20240602
* running under: Fedora Linux 36 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘bssm/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘bssm’ version ‘2.0.2’
* 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 ‘bssm’ can be installed ... [16m/63m] WARNING
Found the following significant warnings:
  /usr/lib/gcc/x86_64-redhat-linux/12/../../../../include/c++/12/bits/stl_tempbuf.h:263:8: warning: 'get_temporary_buffer<arma::arma_sort_index_packet<double>>' is deprecated [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-Intel/bssm.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Intel(R) oneAPI DPC++/C++ Compiler 2024.2.0 (2024.2.0.20240602)’
* 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [3s/23s] OK
* checking whether the package can be loaded with stated dependencies ... [3s/19s] OK
* checking whether the package can be unloaded cleanly ... [2s/19s] OK
* checking whether the namespace can be loaded with stated dependencies ... [2s/19s] OK
* checking whether the namespace can be unloaded cleanly ... [3s/23s] OK
* checking loading without being on the library search path ... [3s/24s] 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 ... [38s/215s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [4s/18s] ERROR
Running examples in ‘bssm-Ex.R’ failed
The error most likely occurred in:

> ### Name: ar1_lg
> ### Title: Univariate Gaussian model with AR(1) latent process
> ### Aliases: ar1_lg
> 
> ### ** Examples
> 
> set.seed(1)
> mu <- 2
> rho <- 0.7
> sd_y <- 0.1
> sigma <- 0.5
> beta <- -1
> x <- rnorm(30)
> z <- y <- numeric(30)
> z[1] <- rnorm(1, mu, sigma / sqrt(1 - rho^2))
> y[1] <- rnorm(1, beta * x[1] + z[1], sd_y)
> for(i in 2:30) {
+   z[i] <- rnorm(1, mu * (1 - rho) + rho * z[i - 1], sigma)
+   y[i] <- rnorm(1, beta * x[i] + z[i], sd_y)
+ }
> model <- ar1_lg(y, rho = uniform(0.5, -1, 1), 
+   sigma = halfnormal(1, 10), mu = normal(0, 0, 1), 
+   sd_y = halfnormal(1, 10), 
+   xreg = x,  beta = normal(0, 0, 1))
> out <- run_mcmc(model, iter = 2e4)

 *** caught segfault ***
address (nil), cause 'unknown'

Traceback:
 1: gaussian_mcmc(model, output_type, iter, burnin, thin, gamma,     target_acceptance, S, seed, end_adaptive_phase, threads,     model_type(model), verbose)
 2: run_mcmc.lineargaussian(model, iter = 20000)
 3: run_mcmc(model, iter = 20000)
An irrecoverable exception occurred. R is aborting now ...
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test_all.R’/data/gannet/ripley/R/Intel/bin/BATCH: line 60: 1335273 Segmentation fault      (core dumped) ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1
 [5s/32s]
 [6s/34s] ERROR
Running the tests in ‘tests/test_all.R’ failed.
Complete output:
  > Sys.setenv("OMP_NUM_THREADS" = 2)
  > 
  > library("testthat")
  > test_check("bssm")
  Loading required package: bssm
  
  Attaching package: 'bssm'
  
  The following object is masked from 'package:base':
  
      gamma
  
  
   *** caught segfault ***
  address (nil), cause 'unknown'
  
  Traceback:
   1: gaussian_mcmc(model, output_type, iter, burnin, thin, gamma,     target_acceptance, S, seed, end_adaptive_phase, threads,     model_type(model), verbose)
   2: run_mcmc.lineargaussian(model_bssm, iter = 50, seed = 1)
   3: run_mcmc(model_bssm, iter = 50, seed = 1)
   4: eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   5: withCallingHandlers({    code    NULL}, error = function(cnd) {    if (can_entrace(cnd)) {        cnd <- cnd_entrace(cnd)    }    return_from(env, cnd)})
   6: .capture(act$val <- eval_bare(quo_get_expr(.quo), quo_get_env(.quo)),     ...)
   7: quasi_capture(enquo(object), label, capture_error, entrace = TRUE)
   8: expect_error(mcmc_bsm <- run_mcmc(model_bssm, iter = 50, seed = 1),     NA)
   9: eval(code, test_env)
  10: eval(code, test_env)
  11: withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error)
  12: doTryCatch(return(expr), name, parentenv, handler)
  13: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  14: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
  15: doTryCatch(return(expr), name, parentenv, handler)
  16: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
  17: tryCatchList(expr, classes, parentenv, handlers)
  18: tryCatch(withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error), error = handle_fatal,     skip = function(e) {    })
  19: test_code(desc, code, env = parent.frame(), default_reporter = local_interactive_reporter())
  20: test_that("expanded and not expanded data frame work equally for theta",     {        expect_error(mcmc_bsm <- run_mcmc(model_bssm, iter = 50,             seed = 1), NA)        d <- expect_error(as.data.frame(mcmc_bsm), NA)        expect_equal(colnames(d), c("iter", "value", "variable",             "weight"))        expect_equal(unique(d$variable), c("sd_y", "sd_level"))        expect_equal(mean(d$value[d$variable == "sd_level"]),             weighted.mean(mcmc_bsm$theta[, 2], mcmc_bsm$counts))        d <- expect_error(as.data.frame(mcmc_bsm, expand = FALSE),             NA)        expect_equal(colnames(d), c("iter", "value", "variable",             "weight"))        expect_equal(unique(d$variable), c("sd_y", "sd_level"))        expect_equal(weighted.mean(d$value[d$variable == "sd_level"],             d$weight[d$variable == "sd_level"]), weighted.mean(mcmc_bsm$theta[,             2], mcmc_bsm$counts))    })
  21: eval(code, test_env)
  22: eval(code, test_env)
  23: withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error)
  24: doTryCatch(return(expr), name, parentenv, handler)
  25: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  26: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
  27: doTryCatch(return(expr), name, parentenv, handler)
  28: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
  29: tryCatchList(expr, classes, parentenv, handlers)
  30: tryCatch(withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error), error = handle_fatal,     skip = function(e) {    })
  31: test_code(test = NULL, code = exprs, env = env, default_reporter = StopReporter$new())
  32: source_file(path, env = env(env), desc = desc, error_call = error_call)
  33: FUN(X[[i]], ...)
  34: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)
  35: doTryCatch(return(expr), name, parentenv, handler)
  36: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  37: tryCatchList(expr, classes, parentenv, handlers)
  38: tryCatch(code, testthat_abort_reporter = function(cnd) {    cat(conditionMessage(cnd), "\n")    NULL})
  39: with_reporter(reporters$multi, lapply(test_paths, test_one_file,     env = env, desc = desc, error_call = error_call))
  40: test_files_serial(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,     desc = desc, load_package = load_package, error_call = error_call)
  41: 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,     load_package = load_package, parallel = parallel)
  42: test_dir("testthat", package = package, reporter = reporter,     ..., load_package = "installed")
  43: test_check("bssm")
  An irrecoverable exception occurred. R is aborting now ...
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [5m/17m] ERROR
Error(s) in re-building vignettes:
--- re-building ‘bssm.Rmd’ using rmarkdown

 *** caught segfault ***
address (nil), cause 'unknown'

Traceback:
 1: gaussian_mcmc(model, output_type, iter, burnin, thin, gamma,     target_acceptance, S, seed, end_adaptive_phase, threads,     model_type(model), verbose)
 2: run_mcmc.lineargaussian(UKgas_model, iter = 40000, seed = 1)
 3: run_mcmc(UKgas_model, iter = 40000, seed = 1)
 4: eval(expr, envir, enclos)
 5: eval(expr, envir, enclos)
 6: eval_with_user_handlers(expr, envir, enclos, user_handlers)
 7: withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers))
 8: withCallingHandlers(withVisible(eval_with_user_handlers(expr,     envir, enclos, user_handlers)), warning = wHandler, error = eHandler,     message = mHandler)
 9: handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr,     envir, enclos, user_handlers)), warning = wHandler, error = eHandler,     message = mHandler))
10: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr,     envir, enclos, user_handlers)), warning = wHandler, error = eHandler,     message = mHandler)))
11: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos,     debug = debug, last = i == length(out), use_try = stop_on_error !=         2L, keep_warning = keep_warning, keep_message = keep_message,     log_echo = log_echo, log_warning = log_warning, output_handler = output_handler,     include_timing = include_timing)
12: evaluate::evaluate(...)
13: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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))
14: in_dir(input_dir(), expr)
15: 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$render, options)))
16: eng_r(options)
17: block_exec(params)
18: call_block(x)
19: process_group(group)
20: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e))
21: xfun:::handle_error(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e)),     function(loc) {        setwd(wd)        write_utf8(res, output %n% stdout())        paste0("\nQuitting from lines ", loc)    }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
22: process_file(text, output)
23: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
24: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),     output_dir = getwd(), ...)
25: vweave_rmarkdown(...)
26: engine$weave(file, quiet = quiet, encoding = enc)
27: doTryCatch(return(expr), name, parentenv, handler)
28: tryCatchOne(expr, names, parentenv, handlers[[1L]])
29: tryCatchList(expr, classes, parentenv, handlers)
30: 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)))})
31: tools:::.buildOneVignette("bssm.Rmd", "/data/gannet/ripley/R/packages/tests-Intel/bssm.Rcheck/vign_test/bssm",     TRUE, FALSE, "bssm", "UTF-8", "/tmp/RtmpfbfnFs/working_dir/RtmpaUq0a9/file1468fd6f3c739.rds")
An irrecoverable exception occurred. R is aborting now ...
--- re-building ‘growth_model.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-Intel/bssm.Rcheck/vign_test/bssm/vignettes/growth_model_files/figure-html/ekf-1.png
1344x960 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 44150 bytes
Input file size = 44288 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 36883
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 36883

Output IDAT size = 36883 bytes (7267 bytes decrease)
Output file size = 36961 bytes (7327 bytes = 16.54% decrease)

** Processing: /data/gannet/ripley/R/packages/tests-Intel/bssm.Rcheck/vign_test/bssm/vignettes/growth_model_files/figure-html/ekf-2.png
1344x960 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 86719 bytes
Input file size = 86917 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5		IDAT size = 81690
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 5		IDAT size = 81690

Output IDAT size = 81690 bytes (5029 bytes decrease)
Output file size = 81768 bytes (5149 bytes = 5.92% decrease)


 *** caught segfault ***
address (nil), cause 'unknown'

Traceback:
 1: nonlinear_is_mcmc(t(model$y), model$Z, model$H, model$T, model$R,     model$Z_gn, model$T_gn, model$a1, model$P1, model$theta,     model$log_prior_pdf, model$known_params, model$known_tv_params,     as.integer(model$time_varying), model$n_states, model$n_etas,     seed, particles, iter, burnin, thin, gamma, target_acceptance,     S, end_adaptive_phase, threads, pmatch(mcmc_type, paste0("is",         1:3)), sampling_method, max_iter, conv_tol, iekf_iter,     output_type, FALSE, verbose)
 2: run_mcmc.ssm_nlg(model, iter = 6000, burnin = 1000, particles = 10,     mcmc_type = "is2", sampling_method = "psi", S = S)
 3: run_mcmc(model, iter = 6000, burnin = 1000, particles = 10, mcmc_type = "is2",     sampling_method = "psi", S = S)
 4: eval(expr, envir, enclos)
 5: eval(expr, envir, enclos)
 6: eval_with_user_handlers(expr, envir, enclos, user_handlers)
 7: withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers))
 8: withCallingHandlers(withVisible(eval_with_user_handlers(expr,     envir, enclos, user_handlers)), warning = wHandler, error = eHandler,     message = mHandler)
 9: handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr,     envir, enclos, user_handlers)), warning = wHandler, error = eHandler,     message = mHandler))
10: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr,     envir, enclos, user_handlers)), warning = wHandler, error = eHandler,     message = mHandler)))
11: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos,     debug = debug, last = i == length(out), use_try = stop_on_error !=         2L, keep_warning = keep_warning, keep_message = keep_message,     log_echo = log_echo, log_warning = log_warning, output_handler = output_handler,     include_timing = include_timing)
12: evaluate::evaluate(...)
13: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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))
14: in_dir(input_dir(), expr)
15: 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$render, options)))
16: eng_r(options)
17: block_exec(params)
18: call_block(x)
19: process_group(group)
20: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e))
21: xfun:::handle_error(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e)),     function(loc) {        setwd(wd)        write_utf8(res, output %n% stdout())        paste0("\nQuitting from lines ", loc)    }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
22: process_file(text, output)
23: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
24: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),     output_dir = getwd(), ...)
25: vweave_rmarkdown(...)
26: engine$weave(file, quiet = quiet, encoding = enc)
27: doTryCatch(return(expr), name, parentenv, handler)
28: tryCatchOne(expr, names, parentenv, handlers[[1L]])
29: tryCatchList(expr, classes, parentenv, handlers)
30: 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)))})
31: tools:::.buildOneVignette("growth_model.Rmd", "/data/gannet/ripley/R/packages/tests-Intel/bssm.Rcheck/vign_test/bssm",     TRUE, FALSE, "growth_model", "UTF-8", "/tmp/RtmpfbfnFs/working_dir/RtmpaUq0a9/file1468fd4923ab3f.rds")
An irrecoverable exception occurred. R is aborting now ...
--- re-building ‘psi_pf.Rmd’ using rmarkdown
--- finished re-building ‘psi_pf.Rmd’

--- re-building ‘sde_model.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-Intel/bssm.Rcheck/vign_test/bssm/vignettes/sde_model_files/figure-html/unnamed-chunk-5-1.png
1344x960 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 115977 bytes
Input file size = 116223 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 102996
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 102996

Output IDAT size = 102996 bytes (12981 bytes decrease)
Output file size = 103074 bytes (13149 bytes = 11.31% decrease)

--- finished re-building ‘sde_model.Rmd’

SUMMARY: processing the following files failed:
  ‘bssm.Rmd’ ‘growth_model.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [11s/42s] OK
* checking HTML version of manual ... [5s/16s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 3 ERRORs, 1 WARNING
See
  ‘/data/gannet/ripley/R/packages/tests-Intel/bssm.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 1:33:13, 1357.52 + 70.38