CRAN Package Check Results for Package texmex

Last updated on 2020-01-24 05:47:29 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.4.2 35.15 101.55 136.70 ERROR
r-devel-linux-x86_64-debian-gcc 2.4.2 24.69 84.82 109.51 OK
r-devel-linux-x86_64-fedora-clang 2.4.2 184.79 OK
r-devel-linux-x86_64-fedora-gcc 2.4.2 176.14 OK
r-devel-windows-ix86+x86_64 2.4.2 76.00 231.00 307.00 NOTE
r-devel-windows-ix86+x86_64-gcc8 2.4.2 103.00 183.00 286.00 NOTE
r-patched-linux-x86_64 2.4.2 26.78 102.97 129.75 OK
r-patched-solaris-x86 2.4.2 200.60 OK
r-release-linux-x86_64 2.4.2 29.23 102.05 131.28 OK
r-release-windows-ix86+x86_64 2.4.2 67.00 209.00 276.00 NOTE
r-release-osx-x86_64 2.4.2 OK
r-oldrel-windows-ix86+x86_64 2.4.2 51.00 153.00 204.00 NOTE
r-oldrel-osx-x86_64 2.4.2 OK

Check Details

Version: 2.4.2
Check: examples
Result: ERROR
    Running examples in 'texmex-Ex.R' failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: ggplot.mex
    > ### Title: Conditional multivariate extreme values modelling
    > ### Aliases: ggplot.mex mex plot.mex print.mex predict.mex
    > ### summary.predict.mex plot.predict.mex mexAll print.mexList
    > ### print.summary.mex summary.mex ggplot.predict.mex
    > ### Keywords: models multivariate
    >
    > ### ** Examples
    >
    >
    > w <- mex(winter, mqu=.7)
    which not given. Conditioning onO3
    
    Warning in mexDependence(x = res1, which = which, dqu = dqu, margins = margins, :
     Assuming same quantile for dependence thesholding as was used
     to fit corresponding marginal model...
    
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    texmex
     --- call from context ---
    mexDependence(x = res1, which = which, dqu = dqu, margins = margins,
     constrain = constrain, v = v)
     --- call from argument ---
    if (class(z) %in% c("Error", "try-error")) {
     z <- matrix(nrow = 0, ncol = dim(x$data)[[2]] - 1)
    } else if (!is.array(z)) {
     z <- matrix(nrow = 0, ncol = dim(x$data)[[2]] - 1)
    }
     --- R stacktrace ---
    where 1: mexDependence(x = res1, which = which, dqu = dqu, margins = margins,
     constrain = constrain, v = v)
    where 2: mex(winter, mqu = 0.7)
    
     --- value of length: 2 type: logical ---
    [1] FALSE FALSE
     --- function from context ---
    function (x, which, dqu, margins = "laplace", constrain = TRUE,
     v = 10, maxit = 1e+06, start = c(0.01, 0.01), marTransform = "mixture",
     referenceMargin = NULL, nOptim = 1, PlotLikDo = FALSE, PlotLikRange = list(a = c(-1,
     1), b = c(-3, 1)), PlotLikTitle = NULL)
    {
     theCall <- match.call()
     if (class(x) != "migpd")
     stop("you need to use an object created by migpd")
     margins <- list(casefold(margins), p2q = switch(casefold(margins),
     gumbel = function(p) -log(-log(p)), laplace = function(p) ifelse(p <
     0.5, log(2 * p), -log(2 * (1 - p)))), q2p = switch(casefold(margins),
     gumbel = function(q) exp(-exp(-q)), laplace = function(q) ifelse(q <
     0, exp(q)/2, 1 - 0.5 * exp(-q))))
     x <- mexTransform(x, margins = margins, method = marTransform,
     r = referenceMargin)
     x$referenceMargin <- referenceMargin
     if (margins[[1]] == "gumbel" & constrain) {
     warning("With Gumbel margins, you can't constrain, setting constrain=FALSE")
     constrain <- FALSE
     }
     if (missing(which)) {
     message("Missing 'which'. Conditioning on", dimnames(x$transformed)[[2]][1],
     "\n")
     which <- 1
     }
     else if (length(which) > 1)
     stop("which must be of length 1")
     else if (is.character(which))
     which <- match(which, dimnames(x$transformed)[[2]])
     if (missing(dqu)) {
     warning("Assuming same quantile for dependence thesholding as was used\n to fit corresponding marginal model...\n")
     dqu <- x$mqu[which]
     }
     dth <- quantile(x$transformed[, which], dqu)
     dependent <- (1:(dim(x$data)[[2]]))[-which]
     if (length(dqu) < length(dependent))
     dqu <- rep(dqu, length = length(dependent))
     aLow <- ifelse(margins[[1]] == "gumbel", 10^(-10), -1 + 10^(-10))
     if (missing(start)) {
     start <- c(0.01, 0.01)
     }
     else if (class(start) == "mex") {
     start <- start$dependence$coefficients[1:2, ]
     }
     if (length(start) == 2) {
     start <- matrix(rep(start, length(dependent)), nrow = 2)
     }
     if (length(start) != 2 * length(dependent)) {
     stop("start should be of type 'mex' or be a vector of length 2, or be a matrix with 2 rows and ncol equal to the number of dependence models to be estimated")
     }
     if (!missing(PlotLikRange)) {
     PlotLikDo <- TRUE
     }
     qfun <- function(X, yex, wh, aLow, margins, constrain, v,
     maxit, start) {
     Qpos <- function(param, yex, ydep, constrain, v, aLow) {
     a <- param[1]
     b <- param[2]
     res <- PosGumb.Laplace.negProfileLogLik(yex, ydep,
     a, b, constrain, v, aLow)
     res$profLik
     }
     o <- try(optim(par = start, fn = Qpos, control = list(maxit = maxit),
     yex = yex[wh], ydep = X[wh], constrain = constrain,
     v = v, aLow = aLow), silent = TRUE)
     if (class(o) == "try-error") {
     warning("Error in optim call from mexDependence")
     o <- as.list(o)
     o$par <- rep(NA, 6)
     o$value <- NA
     }
     else if (o$convergence != 0) {
     warning("Non-convergence in mexDependence")
     o <- as.list(o)
     o$par <- rep(NA, 6)
     }
     else if (nOptim > 1) {
     for (i in 2:nOptim) {
     o <- try(optim(par = o$par, fn = Qpos, control = list(maxit = maxit),
     yex = yex[wh], ydep = X[wh], constrain = constrain,
     v = v, aLow = aLow), silent = TRUE)
     if (class(o) == "try-error") {
     warning("Error in optim call from mexDependence")
     o <- as.list(o)
     o$par <- rep(NA, 6)
     o$value <- NA
     (break)()
     }
     else if (o$convergence != 0) {
     warning("Non-convergence in mexDependence")
     o <- as.list(o)
     o$par <- rep(NA, 6)
     (break)()
     }
     }
     }
     if (PlotLikDo) {
     nGridPlotLik <- 50
     a.grid <- seq(PlotLikRange$a[1], PlotLikRange$a[2],
     length = nGridPlotLik)
     b.grid <- seq(PlotLikRange$b[1], PlotLikRange$b[2],
     length = nGridPlotLik)
     NegProfLik <- matrix(0, nrow = nGridPlotLik, ncol = nGridPlotLik)
     for (i in 1:nGridPlotLik) {
     for (j in 1:nGridPlotLik) {
     NegProfLik[i, j] <- PosGumb.Laplace.negProfileLogLik(yex = yex[wh],
     ydep = X[wh], a = a.grid[i], b = b.grid[j],
     constrain = constrain, v = v, aLow = aLow)$profLik
     }
     }
     NegProfLik[NegProfLik > 10^10] <- NA
     if (sum(!is.na(NegProfLik))) {
     filled.contour(a.grid, b.grid, -NegProfLik, main = paste("Profile likelihood",
     PlotLikTitle), color.palette = terrain.colors,
     xlab = "a", ylab = "b", plot.axes = {
     axis(1)
     axis(2)
     points(o$par[1], o$par[2])
     })
     }
     }
     if (!is.na(o$par[1])) {
     if (margins == "gumbel" & o$par[1] <= 10^(-5) & o$par[2] <
     0) {
     lo <- c(10^(-10), -Inf, -Inf, 10^(-10), -Inf,
     10^(-10))
     Qneg <- function(yex, ydep, param) {
     param <- param[-1]
     b <- param[1]
     cee <- param[2]
     d <- param[3]
     m <- param[4]
     s <- param[5]
     obj <- function(yex, ydep, b, cee, d, m, s) {
     mu <- cee - d * log(yex) + m * yex^b
     sig <- s * yex^b
     log(sig) + 0.5 * ((ydep - mu)/sig)^2
     }
     res <- sum(obj(yex, ydep, b, cee, d, m, s))
     res
     }
     o <- try(optim(c(0, 0, 0, 0, 0, 1), Qneg, method = "L-BFGS-B",
     lower = lo, upper = c(1, 1 - 10^(-10), Inf,
     1 - 10^(-10), Inf, Inf), yex = yex[wh], ydep = X[wh]),
     silent = TRUE)
     if (class(o) == "try-error" || o$convergence !=
     0) {
     warning("Non-convergence in mexDependence")
     o <- as.list(o)
     o$par <- rep(NA, 6)
     }
     }
     else {
     Z <- (X[wh] - yex[wh] * o$par[1])/(yex[wh]^o$par[2])
     o$par <- c(o$par[1:2], 0, 0, mean(Z), sd(Z))
     }
     }
     c(o$par[1:6], o$value)
     }
     yex <- c(x$transformed[, which])
     wh <- yex > unique(dth)
     res <- sapply(1:length(dependent), function(X, dat, yex,
     wh, aLow, margins, constrain, v, maxit, start) qfun(dat[,
     X], yex, wh, aLow, margins, constrain, v, maxit, start[,
     X]), dat = as.matrix(x$transformed[, dependent]), yex = yex,
     wh = wh, aLow = aLow, margins = margins[[1]], constrain = constrain,
     v = v, maxit = maxit, start = start)
     loglik <- -res[7, ]
     res <- matrix(res[1:6, ], nrow = 6)
     dimnames(res)[[1]] <- c(letters[1:4], "m", "s")
     dimnames(res)[[2]] <- dimnames(x$transformed)[[2]][dependent]
     gdata <- as.matrix(x$transformed[wh, -which])
     tfun <- function(i, data, yex, a, b, cee, d) {
     data <- data[, i]
     a <- a[i]
     b <- b[i]
     cee <- cee[i]
     d <- d[i]
     if (is.na(a))
     rep(NA, length(data))
     else {
     if (a < 10^(-5) & b < 0)
     a <- cee - d * log(yex)
     else a <- a * yex
     (data - a)/(yex^b)
     }
     }
     z <- try(sapply(1:(dim(gdata)[[2]]), tfun, data = gdata,
     yex = yex[wh], a = res[1, ], b = res[2, ], cee = res[3,
     ], d = res[4, ]))
     if (class(z) %in% c("Error", "try-error")) {
     z <- matrix(nrow = 0, ncol = dim(x$data)[[2]] - 1)
     }
     else if (!is.array(z)) {
     z <- matrix(nrow = 0, ncol = dim(x$data)[[2]] - 1)
     }
     dimnames(z) <- list(NULL, dimnames(x$transformed)[[2]][dependent])
     res2 <- list(coefficients = res, Z = z, dth = unique(dth),
     dqu = unique(dqu), which = which, conditioningVariable = colnames(x$data)[which],
     loglik = loglik, margins = margins, constrain = constrain,
     v = v)
     oldClass(res2) <- "mexDependence"
     output <- list(margins = x, dependence = res2, call = theCall)
     oldClass(output) <- "mex"
     output
    }
    <bytecode: 0x63605b8>
    <environment: namespace:texmex>
     --- function search by body ---
    Function mexDependence in namespace texmex has this body.
     ----------- END OF FAILURE REPORT --------------
    Error in if (class(z) %in% c("Error", "try-error")) { :
     the condition has length > 1
    Calls: mex -> mexDependence
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 2.4.2
Check: installed package size
Result: NOTE
     installed size is 5.5Mb
     sub-directories of 1Mb or more:
     doc 3.2Mb
     libs 1.5Mb
Flavors: r-devel-windows-ix86+x86_64, r-devel-windows-ix86+x86_64-gcc8, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64