Error(s) in re-building vignettes:
--- re-building ‘UsingSpikeSlabGAM.Rnw’ using Sweave
Loading required package: parallel
Loading required package: stabs
This is mboost 2.9-1. See 'package?mboost' and 'news(package  = "mboost")'
for a complete list of changes.


Attaching package: 'ggplot2'

The following object is masked from 'package:mboost':

    %+%

Warning in model.matrix.default(~0 + model$groupIndicators, contrasts.arg = contr.treatment) :
  non-list contrasts argument ignored
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
spikeSlabGAM
 --- call from context --- 
FUN(X[[i]], ...)
 --- call from argument --- 
if (class(tmp) == "try-error") {
    tmp <- (ginv(qr.R(model$predvars[[label]]$qrB)) %*% t(qr.Q(model$predvars[[label]]$qrB))) %*% 
        fhat
}
 --- R stacktrace ---
where 1: FUN(X[[i]], ...)
where 2: lapply(trms, evalTerm, model = m, newdata = grid, aggregate = aggregate, 
    quantiles = quantiles, returnData = FALSE)
where 3: Reduce("+", lapply(trms, evalTerm, model = m, newdata = grid, 
    aggregate = aggregate, quantiles = quantiles, returnData = FALSE))
where 4: data.frame(if (cumulative) {
    Reduce("+", lapply(trms, evalTerm, model = m, newdata = grid, 
        aggregate = aggregate, quantiles = quantiles, returnData = FALSE))
} else {
    evalTerm(label, model = m, newdata = grid, aggregate = aggregate, 
        quantiles = quantiles, returnData = FALSE)
})
where 5: FUN(X[[i]], ...)
where 6: lapply(as.list(plotLabels), plotTerm, m = x, cumulative = cumulative, 
    aggregate = aggregate, quantiles = quantiles, gridlength = gridlength, 
    ggElems = ggElems)
where 7: plot.spikeSlabGAM(m, nrow = 4, ncol = 3, ggElems = list(theme(legend.key.size = grid:::unit(0.01, 
    "npc"), legend.text = element_text(size = 7), legend.title = element_text(size = 8, 
    hjust = 0), axis.text.x = element_text(size = 8), axis.text.y = element_text(size = 8, 
    hjust = 1), plot.margin = grid:::unit(c(0.5, 0, 0, 0), "lines"))))
where 8: plot(m, nrow = 4, ncol = 3, ggElems = list(theme(legend.key.size = grid:::unit(0.01, 
    "npc"), legend.text = element_text(size = 7), legend.title = element_text(size = 8, 
    hjust = 0), axis.text.x = element_text(size = 8), axis.text.y = element_text(size = 8, 
    hjust = 1), plot.margin = grid:::unit(c(0.5, 0, 0, 0), "lines"))))
where 9: eval(expr, .GlobalEnv)
where 10: eval(expr, .GlobalEnv)
where 11: withVisible(eval(expr, .GlobalEnv))
where 12: doTryCatch(return(expr), name, parentenv, handler)
where 13: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 14: tryCatchList(expr, classes, parentenv, handlers)
where 15: 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)[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))
})
where 16: try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE)
where 17: evalFunc(ce, options)
where 18: tryCatchList(expr, classes, parentenv, handlers)
where 19: tryCatch(evalFunc(ce, options), finally = {
    cat("\n")
    sink()
})
where 20: driver$runcode(drobj, chunk, chunkopts)
where 21: utils::Sweave(...)
where 22: engine$weave(file, quiet = quiet, encoding = enc)
where 23: doTryCatch(return(expr), name, parentenv, handler)
where 24: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 25: tryCatchList(expr, classes, parentenv, handlers)
where 26: tryCatch({
    engine$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)))
})
where 27: tools:::buildVignettes(dir = "/data/gannet/ripley/R/packages/tests-devel/spikeSlabGAM.Rcheck/vign_test/spikeSlabGAM", 
    ser_elibs = "/tmp/RtmpnjGGsc/fileaef839a61c1c.rds")

 --- value of length: 2 type: logical ---
[1] FALSE FALSE
 --- function from context --- 
function (label, model, newdata = NULL, aggregate = mean, quantiles = c(0.1, 
    0.9), returnData = TRUE) 
{
    stopifnot(is.null(aggregate) | is.function(aggregate), is.null(quantiles) | 
        all(quantiles >= 0 & quantiles <= 1), class(model) == 
        "spikeSlabGAM")
    trms <- strsplit(label, ":")[[1]]
    vars <- sapply(trms, function(x) gsub("\\)", "", gsub("([[:graph:]]+\\()", 
        "", x)))
    betaInd <- which(names(model$model$groupIndicatorsOrig) == 
        label)
    fhat <- getPosteriorTerm(label, model, betaInd)
    if (!is.null(newdata)) {
        newX <- vector(length(trms), mode = "list")
        names(newX) <- trms
        for (trm in trms) {
            newX[[trm]] <- do.call(model$predvars[[trm]]$makeNewX, 
                list(xnew = newdata[, vars[trm]]))
        }
        if (length(newX) > 1) {
            X <- matrix(1, nrow = nrow(newX[[1]]))
            for (i in 1:length(newX)) {
                X <- matrix(apply(X, 2, function(x) {
                  x * newX[[i]]
                }), nrow = nrow(X), ncol = NCOL(X) * NCOL(newX[[i]]))
            }
        }
        else {
            X <- newX[[1]]
        }
        coef <- if (!is.null(model$predvars[[label]]$qrB)) {
            tmp <- try(qr.coef(model$predvars[[label]]$qrB, fhat), 
                silent = TRUE)
            if (class(tmp) == "try-error") {
                tmp <- (ginv(qr.R(model$predvars[[label]]$qrB)) %*% 
                  t(qr.Q(model$predvars[[label]]$qrB))) %*% fhat
            }
            tmp
        }
        else {
            attr(fhat, "coef")
        }
        if (any(is.na(coef))) {
            warning("Recalculating original coefficients for ", 
                label, " seems to be problematic. Predictions may be unstable.")
            rm <- is.na(coef[, 1])
            coef[rm, ] <- 0
        }
        fhat <- X %*% coef
        data <- newdata[, vars, drop = F]
    }
    else {
        data <- model$data[, vars, drop = F]
    }
    pred <- summarizeF(fhat, aggregate, quantiles)
    if (returnData) {
        return(cbind(data, pred))
    }
    else {
        return(pred)
    }
}
<bytecode: 0xbcbbc50>
<environment: namespace:spikeSlabGAM>
 --- function search by body ---
Function evalTerm in namespace spikeSlabGAM has this body.
 ----------- END OF FAILURE REPORT -------------- 

Error: processing vignette 'UsingSpikeSlabGAM.Rnw' failed with diagnostics:
 chunk 11 (label = plotm1prep) 
Error in if (class(tmp) == "try-error") { : the condition has length > 1

--- failed re-building 'UsingSpikeSlabGAM.Rnw'

SUMMARY: processing the following file failed:
  'UsingSpikeSlabGAM.Rnw'

Error: Vignette re-building failed.
Execution halted