Error(s) in re-building vignettes:
--- re-building ‘spcosa.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-clang/spcosa.Rcheck/vign_test/spcosa/vignettes/spcosa_files/figure-html/unnamed-chunk-7-1.png
672x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 29571 bytes
Input file size = 29685 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 21909
  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 = 21909

Output IDAT size = 21909 bytes (7662 bytes decrease)
Output file size = 21987 bytes (7698 bytes = 25.93% decrease)

** Processing: /data/gannet/ripley/R/packages/tests-clang/spcosa.Rcheck/vign_test/spcosa/vignettes/spcosa_files/figure-html/unnamed-chunk-8-1.png
672x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 32369 bytes
Input file size = 32483 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 23908
  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 = 23908

Output IDAT size = 23908 bytes (8461 bytes decrease)
Output file size = 23986 bytes (8497 bytes = 26.16% decrease)

** Processing: /data/gannet/ripley/R/packages/tests-clang/spcosa.Rcheck/vign_test/spcosa/vignettes/spcosa_files/figure-html/unnamed-chunk-10-1.png
672x384 pixels, 8 bits/pixel, 215 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 8991 bytes
Input file size = 9738 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 7498
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 7419
  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 = 1  f = 0		IDAT size = 7419

Output IDAT size = 7419 bytes (1572 bytes decrease)
Output file size = 7497 bytes (2241 bytes = 23.01% decrease)

** Processing: /data/gannet/ripley/R/packages/tests-clang/spcosa.Rcheck/vign_test/spcosa/vignettes/spcosa_files/figure-html/unnamed-chunk-11-1.png
672x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 40069 bytes
Input file size = 40195 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 29976
  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 = 29976

Output IDAT size = 29976 bytes (10093 bytes decrease)
Output file size = 30054 bytes (10141 bytes = 25.23% decrease)

** Processing: /data/gannet/ripley/R/packages/tests-clang/spcosa.Rcheck/vign_test/spcosa/vignettes/spcosa_files/figure-html/unnamed-chunk-16-1.png
672x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 35456 bytes
Input file size = 35582 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 26150
  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 = 26150

Output IDAT size = 26150 bytes (9306 bytes decrease)
Output file size = 26228 bytes (9354 bytes = 26.29% decrease)

** Processing: /data/gannet/ripley/R/packages/tests-clang/spcosa.Rcheck/vign_test/spcosa/vignettes/spcosa_files/figure-html/unnamed-chunk-18-1.png
672x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 19527 bytes
Input file size = 19629 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 15302
  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 = 15302

Output IDAT size = 15302 bytes (4225 bytes decrease)
Output file size = 15380 bytes (4249 bytes = 21.65% decrease)

** Processing: /data/gannet/ripley/R/packages/tests-clang/spcosa.Rcheck/vign_test/spcosa/vignettes/spcosa_files/figure-html/unnamed-chunk-20-1.png
672x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 26615 bytes
Input file size = 26729 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 21182
  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 = 21182

Output IDAT size = 21182 bytes (5433 bytes decrease)
Output file size = 21260 bytes (5469 bytes = 20.46% decrease)

** Processing: /data/gannet/ripley/R/packages/tests-clang/spcosa.Rcheck/vign_test/spcosa/vignettes/spcosa_files/figure-html/unnamed-chunk-27-1.png
576x480 pixels, 8 bits/pixel, 252 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 7412 bytes
Input file size = 8258 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 6199
  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 = 6199

Output IDAT size = 6199 bytes (1213 bytes decrease)
Output file size = 6277 bytes (1981 bytes = 23.99% decrease)

** Processing: /data/gannet/ripley/R/packages/tests-clang/spcosa.Rcheck/vign_test/spcosa/vignettes/spcosa_files/figure-html/unnamed-chunk-27-2.png
576x480 pixels, 8 bits/pixel, 252 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 7399 bytes
Input file size = 8245 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 6170
  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 = 6170

Output IDAT size = 6170 bytes (1229 bytes decrease)
Output file size = 6248 bytes (1997 bytes = 24.22% decrease)

[gannet:3701688:0:3701688] Caught signal 11 (Segmentation fault: address not mapped to object at address 0xc)
==== backtrace (tid:3701688) ====
 0  /lib64/libucs.so.0(ucs_handle_error+0x2e4) [0x7fa5877cd144]
 1  /lib64/libucs.so.0(+0x2880d) [0x7fa5877ce80d]
 2  /lib64/libucs.so.0(+0x289dd) [0x7fa5877ce9dd]
 3  [0x7fa64fbd17e9]
=================================

 *** caught segfault ***
address 0x4d200387bb8, cause 'unknown'

Traceback:
 1: .jcall("RJavaTools", "Ljava/lang/Object;", "newInstance", class,     .jarray(p, "java/lang/Object", dispatch = FALSE), .jarray(pc,         "java/lang/Class", dispatch = FALSE), evalString = FALSE,     evalArray = FALSE, use.true.class = TRUE)
 2: .J(Class, ...)
 3: new(J("partition/CompactSpatialPartitionSwop"), cellCenters,     .jarray(as(sample(x = rep(x = 0:(nStrata - 1), length = nCells)),         "integer")))
 4: new(J("partition/CompactSpatialPartitionSwop"), cellCenters,     .jarray(as(sample(x = rep(x = 0:(nStrata - 1), length = nCells)),         "integer")))
 5: .local(object, ...)
 6: stratify(object = object, nStrata = nStrata, priorPoints = priorPoints,     maxIterations = maxIterations, nTry = nTry, equalArea = equalArea,     verbose = verbose)
 7: stratify(object = object, nStrata = nStrata, priorPoints = priorPoints,     maxIterations = maxIterations, nTry = nTry, equalArea = equalArea,     verbose = verbose)
 8: .local(object, ...)
 9: stratify(shp_farmsum, nStrata = 20, equalArea = TRUE, nTry = 10)
10: stratify(shp_farmsum, nStrata = 20, equalArea = TRUE, nTry = 10)
11: eval(expr, envir)
12: eval(expr, envir)
13: withVisible(eval(expr, envir))
14: withCallingHandlers(code, message = function (cnd) {    watcher$capture_plot_and_output()    if (on_message$capture) {        watcher$push(cnd)    }    if (on_message$silence) {        invokeRestart("muffleMessage")    }}, warning = function (cnd) {    if (getOption("warn") >= 2 || getOption("warn") < 0) {        return()    }    watcher$capture_plot_and_output()    if (on_warning$capture) {        cnd <- sanitize_call(cnd)        watcher$push(cnd)    }    if (on_warning$silence) {        invokeRestart("muffleWarning")    }}, error = function (cnd) {    watcher$capture_plot_and_output()    cnd <- sanitize_call(cnd)    watcher$push(cnd)    switch(on_error, continue = invokeRestart("eval_continue"),         stop = invokeRestart("eval_stop"), error = NULL)})
15: eval(call)
16: eval(call)
17: with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE}, handlers)
18: doWithOneRestart(return(expr), restart)
19: withOneRestart(expr, restarts[[1L]])
20: withRestartList(expr, restarts[-nr])
21: doWithOneRestart(return(expr), restart)
22: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
23: withRestartList(expr, restarts)
24: withRestarts(with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
25: evaluate::evaluate(...)
26: 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$render, options))
27: in_dir(input_dir(), expr)
28: in_input_dir(evaluate(code, envir = env, new_device = FALSE,     keep_warning = if (is.numeric(options$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)))
29: eng_r(options)
30: block_exec(params)
31: call_block(x)
32: process_group(group)
33: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e))
34: 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)
35: process_file(text, output)
36: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
37: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),     output_dir = getwd(), ...)
38: vweave_rmarkdown(...)
39: engine$weave(file, quiet = quiet, encoding = enc)
40: doTryCatch(return(expr), name, parentenv, handler)
41: tryCatchOne(expr, names, parentenv, handlers[[1L]])
42: tryCatchList(expr, classes, parentenv, handlers)
43: tryCatch({    engine$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)))})
44: tools::buildVignettes(dir = "/data/gannet/ripley/R/packages/tests-clang/spcosa.Rcheck/vign_test/spcosa",     skip = TRUE, ser_elibs = "/tmp/RtmpRirSjT/file37faa341e6a182.rds")
An irrecoverable exception occurred. R is aborting now ...