Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: lme4
Loading required package: Matrix

 *** caught segfault ***
address 3c9cc455, cause 'memory not mapped'

Traceback:
 1: .Call(glmerLaplace, pp$ptr(), resp$ptr(), nAGQ, tol, as.integer(maxit),     verbose)
 2: pwrssUpdate(pp, resp, tol = tolPwrss, GQmat = GQmat, compDev = compDev,     grpFac = fac, maxit = maxit, verbose = verbose)
 3: fn(nM$xeval())
 4: stopifnot(length(value <- as.numeric(value)) == 1L)
 5: nM$newf(fn(nM$xeval()))
 6: (function (fn, par, lower = rep.int(-Inf, n), upper = rep.int(Inf,     n), control = list()) {    n <- length(par)    if (is.null(xst <- control[["xst"]]))         xst <- rep.int(0.02, n)    if (is.null(xt <- control[["xt"]]))         xt <- xst * 5e-04    control[["xst"]] <- control[["xt"]] <- NULL    if (is.null(verbose <- control[["verbose"]]))         verbose <- 0    control[["verbose"]] <- NULL    if (is.null(control[["iprint"]])) {        control[["iprint"]] <- switch(as.character(min(as.numeric(verbose),             3L)), `0` = 0, `1` = 20, `2` = 10, `3` = 1)    }    stopifnot(is.function(fn), length(formals(fn)) == 1L, (n <- length(par <- as.numeric(par))) ==         length(lower <- as.numeric(lower)), length(upper <- as.numeric(upper)) ==         n, length(xst <- as.numeric(xst)) == n, all(xst != 0),         length(xt <- as.numeric(xt)) == n)    nM <- NelderMead$new(lower = lower, upper = upper, x0 = par,         xst = xst, xt = xt)    cc <- do.call(function(iprint = 0L, maxfun = 10000L, FtolAbs = 1e-05,         FtolRel = 1e-15, XtolRel = 1e-07, MinfMax = -.Machine$double.xmax,         warnOnly = FALSE, ...) {        if (length(list(...)) > 0)             warning("unused control arguments ignored")        list(iprint = iprint, maxfun = maxfun, FtolAbs = FtolAbs,             FtolRel = FtolRel, XtolRel = XtolRel, MinfMax = MinfMax,             warnOnly = warnOnly)    }, control)    nM$setFtolAbs(cc$FtolAbs)    nM$setFtolRel(cc$FtolRel)    nM$setIprint(cc$iprint)    nM$setMaxeval(cc$maxfun)    nM$setMinfMax(cc$MinfMax)    it <- 0    repeat {        it <- it + 1        nMres <- nM$newf(fn(nM$xeval()))        if (nMres != 0L)             break    }    cmsg <- "reached max evaluations"    if (nMres == -4) {        cmsg <- warning(sprintf("failure to converge in %d evaluations",             cc$maxfun))        nMres <- 4    }    msgvec <- c("nm_forced", "cannot generate a feasible simplex",         "initial x is not feasible", "active", "objective function went below allowed minimum",         "objective function values converged to within tolerance",         "parameter values converged to within tolerance", cmsg)    if (nMres < 0) {        (if (cc$warnOnly)             warning        else stop)(msgvec[nMres + 4])    }    list(fval = nM$value(), par = nM$xpos(), convergence = pmin(0,         nMres), NM.result = nMres, message = msgvec[nMres + 4],         control = c(cc, xst = xst, xt = xt), feval = it)})(fn = function (pars) {    resp$setOffset(baseOffset)    resp$updateMu(lp0)    pp$setTheta(as.double(pars[dpars]))    spars <- as.numeric(pars[-dpars])    offset <- if (length(spars) == 0)         baseOffset    else baseOffset + pp$X %*% spars    resp$setOffset(offset)    p <- pwrssUpdate(pp, resp, tol = tolPwrss, GQmat = GQmat,         compDev = compDev, grpFac = fac, maxit = maxit, verbose = verbose)    resp$updateWts()    p}, par = c(0, -4.3594189053278, -1.05523260109027, -1.60531062884395, -20.4608670943758, 0.0391805878733845), lower = c(0, -Inf, -Inf, -Inf, -Inf, -Inf), upper = c(Inf, Inf, Inf, Inf, Inf, Inf), control = list(    xst = c(0.02, 0.220552032343092, 0.160495994305595, 0.216643313125654,     2, 0.00936288093030652), xt = c(1e-05, 0.000110276016171546,     8.02479971527973e-05, 0.000108321656562827, 0.001, 4.68144046515326e-06    ), verbose = 0L))
 7: do.call(optfun, arglist)
 8: withCallingHandlers(do.call(optfun, arglist), warning = function(w) {    curWarnings <<- append(curWarnings, list(w$message))})
 9: optwrap(optimizer, devfun, start, rho$lower, control = control,     adj = adj, verbose = verbose, ...)
10: optimizeGlmer(devfun, optimizer = control$optimizer[[2]], restart_edge = control$restart_edge,     boundary.tol = control$boundary.tol, control = control$optCtrl,     start = start, nAGQ = nAGQ, verbose = verbose, stage = 2,     calc.derivs = control$calc.derivs, use.last.params = control$use.last.params)
11: glmer(formula = cbind(incidence, size - incidence) ~ period +     size + (1 | herd), data = list(herd = c(1L, 1L, 1L, 1L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L, 6L, 6L, 6L, 6L, 7L, 7L, 7L, 7L, 8L, 9L, 9L, 9L, 9L, 10L, 10L, 10L, 10L, 11L, 11L, 11L, 11L, 12L, 12L, 12L, 12L, 13L, 13L, 13L, 13L, 14L, 14L, 14L, 14L, 15L, 15L, 15L, 15L), incidence = c(1, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 1, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0), size = c(14, 12, 9, 5, 22, 18, 21, 22, 16, 16, 20, 10, 10, 9, 6, 18, 25, 24, 4, 17, 17, 18, 20, 16, 10, 9, 5, 34, 9, 6, 8, 6, 22, 22, 18, 22, 25, 27, 22, 22, 10, 8, 6, 5, 21, 24, 19, 23, 19, 2, 3, 2, 19, 15, 15, 15),     period = c(1L, 2L, 3L, 4L, 1L, 2L, 3L, 1L, 2L, 3L, 4L, 1L,     2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L,     1L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L,     3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L),     obs = 1:56), family = binomial)
12: eval(expr, envir, enclos)
13: eval(newCall)
14: doFit.glmerMod(c(1, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 1, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0),     <S4 object of class "glmerMod">)
15: (function (y, fit, subset, ...) UseMethod("doFit", fit))(c(1, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 1, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0), <S4 object of class "glmerMod">)
16: do.call(doFit, c(list(y, fit), fitOpts))
17: eval(expr, p)
18: eval.parent(thing)
19: withCallingHandlers(eval.parent(thing), warning = function(w) {    w$tag <- tag    warning(w)    invokeRestart("muffleWarning")})
20: doTryCatch(return(expr), name, parentenv, handler)
21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
22: tryCatchList(expr, classes, parentenv, handlers)
23: tryCatch(withCallingHandlers(eval.parent(thing), warning = function(w) {    w$tag <- tag    warning(w)    invokeRestart("muffleWarning")}), error = function(e) {    e$tag <- tag    stop(e)})
24: tag(z <- do.call(doFit, c(list(y, fit), fitOpts)), tag = "Fitting")
25: f()
26: f(...)
27: withCallingHandlers(f(...), warning = function(w) {    warningValue <<- append(warningValue, w$message)    wtag <- if (is.null(w$tag))         ""    else w$tag    warningTag <<- append(warningTag, wtag)    invokeRestart("muffleWarning")})
28: doTryCatch(return(expr), name, parentenv, handler)
29: tryCatchOne(expr, names, parentenv, handlers[[1L]])
30: tryCatchList(expr, classes, parentenv, handlers)
31: tryCatch(withCallingHandlers(f(...), warning = function(w) {    warningValue <<- append(warningValue, w$message)    wtag <- if (is.null(w$tag))         ""    else w$tag    warningTag <<- append(warningTag, wtag)    invokeRestart("muffleWarning")}), error = function(e) {    errorValue <<- e$message    errorTag <<- if (is.null(e$tag))         ""    else e$tag    return(NULL)})
32: .fun(piece, ...)
33: (function (i) {    piece <- pieces[[i]]    if (.inform) {        res <- try(.fun(piece, ...))        if (inherits(res, "try-error")) {            piece <- paste(utils::capture.output(print(piece)),                 collapse = "\n")            stop("with piece ", i, ": \n", piece, call. = FALSE)        }    }    else {        res <- .fun(piece, ...)    }    progress$step()    res})(2L)
34: .Call(loop_apply_, as.integer(n), f, env)
35: loop_apply(n, do.ply)
36: llply(.data$value[!maybenot], maybe(.fun), ..., .progress = .progress)
37: maybe_llply(...)
38: maybe_laply(seq_len(.N), eval.parent(substitute(function(.) .thing)),     ...)
39: maybe_raply(nsim, f(), .text = "Simulating")
40: powerSim(gm2, fixed("size", "z"), nsim = 50)
41: eval(expr, envir, enclos)
42: eval(expr, envir, enclos)
43: withVisible(eval(expr, envir, enclos))
44: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler,     error = eHandler, message = mHandler)
45: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir,     enclos)), warning = wHandler, error = eHandler, message = mHandler))
46: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr,     envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
47: evaluate_call(expr, parsed$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)
48: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning),     keep_message = !isFALSE(options$message), stop_on_error = if (options$error &&         options$include) 0L else 2L, output_handler = knit_handlers(options$render,         options))
49: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE,     keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message),     stop_on_error = if (options$error && options$include) 0L else 2L,     output_handler = knit_handlers(options$render, options)))
50: block_exec(params)
51: call_block(x)
52: process_group.block(group)
53: process_group(group)
54: 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$get("infile"),             ") ")    })
55: process_file(text, output)
56: knit(input, text = text, envir = envir, encoding = encoding,     quiet = quiet)
57: knit2html(..., force_v1 = TRUE)
58: (if (grepl("\\.[Rr]md$", file)) knit2html_v1 else if (grepl("\\.[Rr]rst$",     file)) knit2pdf else knit)(file, encoding = encoding, quiet = quiet,     envir = globalenv())
59: vweave(...)
60: engine$weave(file, quiet = quiet, encoding = enc)
61: doTryCatch(return(expr), name, parentenv, handler)
62: tryCatchOne(expr, names, parentenv, handlers[[1L]])
63: tryCatchList(expr, classes, parentenv, handlers)
64: tryCatch({    engine$weave(file, quiet = quiet, encoding = enc)    setwd(startdir)    find_vignette_product(name, by = "weave", engine = engine)}, error = function(e) {    stop(gettextf("processing vignette '%s' failed with diagnostics:\n%s",         file, conditionMessage(e)), domain = NA, call. = FALSE)})
65: buildVignettes(dir = "/home/ripley/R/packages/tests32/simr.Rcheck/vign_test/simr")
An irrecoverable exception occurred. R is aborting now ...