Error(s) in re-building vignettes:
--- re-building ‘georob_vignette.Rnw’ using Sweave
Loading required package: parallel
Loading required package: snowfall
Loading required package: snow

Attaching package: ‘snow’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, clusterSplit, makeCluster, parApply,
    parCapply, parLapply, parRapply, parSapply, splitIndices,
    stopCluster

Loading required package: sp

Attaching package: ‘georob’

The following object is masked from ‘package:stats’:

    step


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

Traceback:
 1: RandomFieldsUtils::RFoptions()
 2: internal.rfoptions(..., RELAX = is(model, "formula"))
 3: rfeval(model = model, x = x, y = y, z = z, T = T, grid = grid,     params = params, distances = distances, dim = dim, ..., fctcall = "Fctn",     reg = MODEL_FCTN)
 4: RFfctn(x = lag.vectors[s[i]:e[i], ], model = model.list, dim = attr(lag.vectors,     "ndim.coords"), grid = FALSE)
 5: doTryCatch(return(expr), name, parentenv, handler)
 6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 7: tryCatchList(expr, classes, parentenv, handlers)
 8: tryCatch(expr, error = function(e) {    call <- conditionCall(e)    if (!is.null(call)) {        if (identical(call[[1L]], quote(doTryCatch)))             call <- sys.call(-4L)        dcall <- deparse(call, nlines = 1L)        prefix <- paste("Error in", dcall, ": ")        LONG <- 75L        sm <- strsplit(conditionMessage(e), "\n")[[1L]]        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")        if (is.na(w))             w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],                 type = "b")        if (w > LONG)             prefix <- paste0(prefix, "\n  ")    }    else prefix <- "Error : "    msg <- paste0(prefix, conditionMessage(e), "\n")    .Internal(seterrmessage(msg[1L]))    if (!silent && isTRUE(getOption("show.error.messages"))) {        cat(msg, file = outFile)        .Internal(printDeferredWarnings())    }    invisible(structure(msg, class = "try-error", condition = e))})
 9: try(RFfctn(x = lag.vectors[s[i]:e[i], ], model = model.list,     dim = attr(lag.vectors, "ndim.coords"), grid = FALSE), silent = TRUE)
10: FUN(X[[i]], ...)
11: lapply(X = X, FUN = FUN, ...)
12: mclapply(1L:k, f.aux, mc.cores = ncores)
13: FUN(X[[i]], ...)
14: lapply(1L:length(variogram.object), function(i, x, gcr.constant,     lag.vectors, control.pcmp) {    variogram.model <- x[[i]][["variogram.model"]]    param <- x[[i]][["param"]]    param <- param[!names(param) %in% c("variance", "snugget",         "nugget")]    aniso <- x[[i]][c("aniso", "sclmat", "rotmat")]    gcr.constant <- gcr.constant[[i]]    result <- list(error = TRUE)    if (NCOL(lag.vectors) > 1L) {        A <- aniso[["sclmat"]] * aniso[["rotmat"]]/param["scale"]        model.list <- list(variogram.model)        model.list <- c(model.list, as.list(param[-1L]))        model.list <- list("$", var = 1, A = A, model.list)        f.aux <- function(i) {            RFoptions(allow_duplicated_locations = TRUE, storing = FALSE)            result <- try(RFfctn(x = lag.vectors[s[i]:e[i], ],                 model = model.list, dim = attr(lag.vectors, "ndim.coords"),                 grid = FALSE), silent = TRUE)            RFoptions(allow_duplicated_locations = FALSE, storing = FALSE)            if (!(identical(class(result), "try-error") || any(is.na(result)))) {                if (!variogram.model %in% irf.models) {                  result <- result - model.list[["var"]]                }                result            }            else {                "RFvariogram.error"            }        }    }    else {        A <- 1/param["scale"]        model.list <- list(variogram.model)        model.list <- c(model.list, as.list(param[-1L]))        model.list <- list("$", var = 1, A = A, model.list)        f.aux <- function(i) {            RFoptions(allow_duplicated_locations = TRUE, storing = FALSE)            result <- try(RFfctn(x = lag.vectors[s[i]:e[i]],                 model = model.list, grid = FALSE), silent = TRUE)            RFoptions(allow_duplicated_locations = FALSE, storing = FALSE)            if (!(identical(class(result), "try-error") || any(is.na(result)))) {                if (!variogram.model %in% irf.models) {                  result <- result - model.list[["var"]]                }                result            }            else {                "RFvariogram.error"            }        }    }    ncores <- control.pcmp[["gcr.ncores"]]    if (!control.pcmp[["allow.recursive"]])         ncores <- 1L    k <- control.pcmp[["f"]] * ncores    n <- NROW(lag.vectors)    dn <- floor(n/k)    s <- ((0L:(k - 1L)) * dn) + 1L    e <- (1L:k) * dn    e[k] <- n    if (is.null(control.pcmp[["fork"]])) {        control.pcmp[["fork"]] <- !identical(.Platform[["OS.type"]],             "windows")    }    if (ncores > 1L && !control.pcmp[["fork"]]) {        if (!sfIsRunning()) {            options(error = f.stop.cluster)            junk <- sfInit(parallel = TRUE, cpus = ncores)            junk <- sfLibrary(georob, verbose = FALSE)            junk <- sfExport("s", "e", "lag.vectors", "model.list")        }        Valpha <- sfLapply(1L:k, f.aux)        if (control.pcmp[["sfstop"]]) {            junk <- sfStop()            options(error = NULL)        }    }    else {        Valpha <- mclapply(1L:k, f.aux, mc.cores = ncores)    }    not.ok <- any(sapply(Valpha, function(x) identical(x, "RFvariogram.error") ||         any(is.na(x))))    if (!not.ok) {        Valpha <- unlist(Valpha)        if (is.na(gcr.constant)) {            if (variogram.model %in% irf.models) {                gcr.constant <- -min(Valpha) * 2            }            else {                gcr.constant <- 1            }        }        Valpha <- gcr.constant + Valpha        if (symmetric) {            Valpha <- list(diag = rep(gcr.constant, 0.5 * (1 +                 sqrt(1 + 8L * length(Valpha)))), tri = Valpha)            attr(Valpha, "struc") <- "sym"        }        result[["error"]] <- FALSE        result[["gcr.constant"]] <- gcr.constant        result[["Valpha"]] <- Valpha    }    else {        warning("there were errors: call 'georob' with argument 'verbose' > 1")        if (verbose > 3)             cat("\n an error occurred when computing the negative semivariance matrix\n")    }    return(result)}, x = variogram.object, gcr.constant = gcr.constant, lag.vectors = lag.vectors,     control.pcmp = control.pcmp)
15: f.aux.gcr(lag.vectors = lag.vectors, variogram.object = x[["variogram.object"]],     symmetric = FALSE, control.pcmp = control.pcmp(max.ncores = 1L),     ...)
16: FUN(X[[i]], ...)
17: lapply(1L:NROW(angle), function(i, what, angle, lag.class, variogram.object,     nxy, nxz, ndim, col, pch, lty, ...) {    t.aux <- lag.class * sin(angle[i, "xz"])    lag.vectors <- cbind(t.aux * sin(angle[i, "xy"]), t.aux *         cos(angle[i, "xy"]), lag.class * cos(angle[i, "xz"]))    lag.vectors <- lag.vectors[, 1L:ndim, drop = FALSE]    attr(lag.vectors, "ndim.coords") <- NCOL(lag.vectors)    Valpha <- f.aux.gcr(lag.vectors = lag.vectors, variogram.object = x[["variogram.object"]],         symmetric = FALSE, control.pcmp = control.pcmp(max.ncores = 1L),         ...)    if (any(sapply(Valpha, function(x) x[["error"]])))         stop("\nan error occurred when computing semivariances\n")    r.gamma <- rowSums(sapply(1L:length(Valpha), function(i,         x, variogram.object) {        x <- Valpha[[i]]        -(x[["Valpha"]] - x[["gcr.constant"]]) * variogram.object[[i]][["param"]]["variance"]    }, x = Valpha, variogram.object = x[["variogram.object"]]))    sel <- sqrt(rowSums(lag.vectors^2)) > 0    r.gamma[sel] <- r.gamma[sel] + sum(x[["variogram.object"]][[1L]][["param"]][c("nugget",         "snugget")])    sel.pch <- ((i - 1L)%/%nxy) + 1L    sel.col <- i - (sel.pch - 1L) * nxy    type <- if (nxz > 1L)         "o"    else "l"    sill <- sum(unlist(lapply(x[["variogram.object"]], function(x) x[["param"]][names(x[["param"]]) %in%         c("variance", "snugget", "nugget")])))    r.gamma <- switch(what, variogram = r.gamma, covariance = sill -         r.gamma, correlation = (sill - r.gamma)/sill)    lines(lag.class, r.gamma, col = col[sel.col], pch = pch[sel.pch],         lty = lty, type = type, ...)}, what = what, angle = angle, lag.class = lag.class, variogram.object = x[["variogram.object"]],     nxy = length(xy.angle), nxz = length(xz.angle), ndim = ndim,     col = col, pch = pch, lty = lty)
18: lines.fitted.variogram(r.sv.spher)
19: lines(r.sv.spher)
20: eval(expr, .GlobalEnv)
21: eval(expr, .GlobalEnv)
22: withVisible(eval(expr, .GlobalEnv))
23: doTryCatch(return(expr), name, parentenv, handler)
24: tryCatchOne(expr, names, parentenv, handlers[[1L]])
25: tryCatchList(expr, classes, parentenv, handlers)
26: tryCatch(expr, error = function(e) {    call <- conditionCall(e)    if (!is.null(call)) {        if (identical(call[[1L]], quote(doTryCatch)))             call <- sys.call(-4L)        dcall <- deparse(call, nlines = 1L)        prefix <- paste("Error in", dcall, ": ")        LONG <- 75L        sm <- strsplit(conditionMessage(e), "\n")[[1L]]        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")        if (is.na(w))             w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],                 type = "b")        if (w > LONG)             prefix <- paste0(prefix, "\n  ")    }    else prefix <- "Error : "    msg <- paste0(prefix, conditionMessage(e), "\n")    .Internal(seterrmessage(msg[1L]))    if (!silent && isTRUE(getOption("show.error.messages"))) {        cat(msg, file = outFile)        .Internal(printDeferredWarnings())    }    invisible(structure(msg, class = "try-error", condition = e))})
27: try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE)
28: evalFunc(ce, options)
29: tryCatchList(expr, classes, parentenv, handlers)
30: tryCatch(evalFunc(ce, options), finally = {    cat("\n")    sink()})
31: driver$runcode(drobj, chunk, chunkopts)
32: utils::Sweave(...)
33: engine$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)    }    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)))})
38: tools:::buildVignettes(dir = "/data/gannet/ripley/R/packages/tests-devel/georob.Rcheck/vign_test/georob")
An irrecoverable exception occurred. R is aborting now ...