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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data MBECS
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* checking for file ‘MBECS/DESCRIPTION’ ... OK
* preparing ‘MBECS’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ...sh: line 1: 19606 Segmentation fault: 11 '/Library/Frameworks/R.framework/Resources/bin/Rscript' --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)" > '/tmp/RtmpmkB8ih/xshell410e4b75d79c' 2>&1
ERROR
--- re-building ‘mbecs_vignette.Rmd’ using knitr
2024-03-27 17:14:57.031 R[19606:1358436305] XType: com.apple.fonts is not accessible.
2024-03-27 17:14:57.032 R[19606:1358436305] XType: XTFontStaticRegistry is enabled.
*** caught segfault ***
address 0x0, cause 'unknown'
Traceback:
1: .Call(merPredDCreate, as(X, "matrix"), Lambdat, LamtUt, Lind, RZX, Ut, Utr, V, VtV, Vtr, Xwts, Zt, beta0, delb, delu, theta, u0)
2: initializePtr()
3: .Object$initialize(...)
4: initialize(value, ...)
5: initialize(value, ...)
6: methods::new(def, ...)
7: (new("refMethodDef", .Data = function (...) { methods::new(def, ...)}, mayCall = c("methods", "new"), name = "new", refClassName = "refGeneratorSlot", superClassMethod = ""))(Zt = new("dgCMatrix", i = c(0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L), p = 0:40, Dim = c(2L, 40L), Dimnames = list( c("B1", "B2"), c("S1", "S2", "S3", "S4", "S5", "S6", "S7", "S8", "S9", "S10", "S11", "S12", "S13", "S14", "S15", "S16", "S17", "S18", "S19", "S20", "S21", "S22", "S23", "S24", "S25", "S26", "S27", "S28", "S29", "S30", "S31", "S32", "S33", "S34", "S35", "S36", "S37", "S38", "S39", "S40")), x = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), factors = list()), theta = 1, Lambdat = new("dgCMatrix", i = 0:1, p = 0:2, Dim = c(2L, 2L), Dimnames = list(NULL, NULL), x = c(1, 1), factors = list()), Lind = c(1L, 1L), n = 40L, X = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1))
8: do.call(merPredD$new, c(reTrms[c("Zt", "theta", "Lambdat", "Lind")], n = nrow(X), list(X = X)))
9: (function (fr, X, reTrms, REML = TRUE, start = NULL, verbose = 0, control = lmerControl(), ...) { p <- ncol(X) rho <- new.env(parent = parent.env(environment())) rho$pp <- do.call(merPredD$new, c(reTrms[c("Zt", "theta", "Lambdat", "Lind")], n = nrow(X), list(X = X))) REMLpass <- if (REML) p else 0L rho$resp <- if (missing(fr)) mkRespMod(REML = REMLpass, ...) else mkRespMod(fr, REML = REMLpass) pp <- resp <- NULL rho$lmer_Deviance <- lmer_Deviance devfun <- function(theta) .Call(lmer_Deviance, pp$ptr(), resp$ptr(), as.double(theta)) environment(devfun) <- rho if (is.null(start) && all(reTrms$cnms == "(Intercept)") && length(reTrms$flist) == length(reTrms$lower) && !is.null(y <- model.response(fr))) { v <- sapply(reTrms$flist, function(f) var(ave(y, f))) v.e <- var(y) - sum(v) if (!is.na(v.e) && v.e > 0) { v.rel <- v/v.e if (all(v.rel >= reTrms$lower^2)) rho$pp$setTheta(sqrt(v.rel)) } } if (length(rho$resp$y) > 0) devfun(rho$pp$theta) rho$lower <- reTrms$lower devfun})(fr = list(y = c(-0.312755488043344, 2.74206122461871, -0.312755488043344, 2.74206122461871, -3.35200197589873, -2.80013482859142, -3.35200197589873, -2.80013482859142, -0.754080049399043, -1.53172113691453, -0.754080049399043, -1.53172113691453, -1.59825302029062, 1.93925348587903, -1.59825302029062, 1.93925348587903, 8.5055997339663, 6.914118366545, 8.5055997339663, 6.914118366545, 5.00728283534373, 3.5884762794777, 5.00728283534373, 3.5884762794777, 1.59143893128236, 2.38233122373385, 1.59143893128236, 2.38233122373385, -3.78530194941442, 1.04411626922334, -3.78530194941442, 1.04411626922334, 2.94051161373089, -3.74664037402877, 2.94051161373089, -3.74664037402877, 1.37052677227415, 1.69418567147827, 1.37052677227415, 1.69418567147827), group = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L), batch = c(1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L)), X = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), reTrms = list(Zt = new("dgCMatrix", i = c(0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L), p = 0:40, Dim = c(2L, 40L), Dimnames = list(c("B1", "B2"), c("S1", "S2", "S3", "S4", "S5", "S6", "S7", "S8", "S9", "S10", "S11", "S12", "S13", "S14", "S15", "S16", "S17", "S18", "S19", "S20", "S21", "S22", "S23", "S24", "S25", "S26", "S27", "S28", "S29", "S30", "S31", "S32", "S33", "S34", "S35", "S36", "S37", "S38", "S39", "S40")), x = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), factors = list()), theta = 1, Lind = c(1L, 1L), Gp = c(0L, 2L), lower = 0, Lambdat = new("dgCMatrix", i = 0:1, p = 0:2, Dim = c(2L, 2L), Dimnames = list(NULL, NULL), x = c(1, 1), factors = list()), flist = list( batch = c(1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L)), cnms = list(batch = "(Intercept)"), Ztlist = list( `1 | batch` = new("dgCMatrix", i = c(0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L), p = 0:40, Dim = c(2L, 40L), Dimnames = list(c("B1", "B2"), c("S1", "S2", "S3", "S4", "S5", "S6", "S7", "S8", "S9", "S10", "S11", "S12", "S13", "S14", "S15", "S16", "S17", "S18", "S19", "S20", "S21", "S22", "S23", "S24", "S25", "S26", "S27", "S28", "S29", "S30", "S31", "S32", "S33", "S34", "S35", "S36", "S37", "S38", "S39", "S40")), x = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), factors = list())), nl = c(batch = 2L)), REML = TRUE, wmsgs = character(0), start = NULL, verbose = 0L, control = list(optimizer = "nloptwrap", restart_edge = TRUE, boundary.tol = 1e-05, calc.derivs = TRUE, use.last.params = FALSE, checkControl = list(check.nobs.vs.rankZ = "ignore", check.nobs.vs.nlev = "stop", check.nlev.gtreq.5 = "ignore", check.nlev.gtr.1 = "stop", check.nobs.vs.nRE = "stop", check.rankX = "stop.deficient", check.scaleX = "warning", check.formula.LHS = "stop"), checkConv = list(check.conv.grad = list(action = "warning", tol = 0.002, relTol = NULL), check.conv.singular = list( action = "message", tol = 1e-04), check.conv.hess = list( action = "warning", tol = 1e-06)), optCtrl = list()))
10: do.call(mkLmerDevfun, c(lmod, list(start = start, verbose = verbose, control = control)))
11: lme4::lmer(tmp.formula, data = tmp.meta, control = control)
12: mbecModelVarianceLMM(model.form, model.vars, tmp.cnts, tmp.meta, type)
13: mbecModelVariance(input.obj = mbec.obj, model.vars = c("batch", "group"), method = "lmm", type = "cor", label = "ruv3")
14: eval(expr, envir, enclos)
15: eval(expr, envir, enclos)
16: eval_with_user_handlers(expr, envir, enclos, user_handlers)
17: withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers))
18: withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler)
19: handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler))
20: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler)))
21: 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)
22: evaluate::evaluate(...)
23: 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$render, options))
24: in_dir(input_dir(), expr)
25: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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)))
26: eng_r(options)
27: block_exec(params)
28: call_block(x)
29: process_group.block(group)
30: process_group(group)
31: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e))
32: withCallingHandlers(expr, error = function(e) { loc = paste0(current_lines(), label, sprintf(" (%s)", knit_concord$get("infile"))) message(one_string(handler(e, loc)))})
33: handle_error(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e)), function(e, loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from lines ", loc) }, if (labels[i] != "") sprintf(" [%s]", labels[i]))
34: process_file(text, output)
35: knit(input, text = text, envir = envir, quiet = quiet)
36: (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$", file)) knit2pandoc else knit)(file, encoding = encoding, quiet = quiet, envir = globalenv(), ...)
37: engine$weave(file, quiet = quiet, encoding = enc)
38: doTryCatch(return(expr), name, parentenv, handler)
39: tryCatchOne(expr, names, parentenv, handlers[[1L]])
40: tryCatchList(expr, classes, parentenv, handlers)
41: 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)))})
42: tools::buildVignettes(dir = ".", tangle = TRUE)
An irrecoverable exception occurred. R is aborting now ...
