Last updated on 2020-01-20 01:50:22 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.5.7 | 9.63 | 56.16 | 65.79 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.5.7 | 8.26 | 59.65 | 67.91 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.5.7 | 110.80 | WARN | |||
| r-devel-linux-x86_64-fedora-gcc | 1.5.7 | 106.69 | NOTE | |||
| r-devel-windows-ix86+x86_64 | 1.5.7 | 29.00 | 175.00 | 204.00 | OK | |
| r-devel-windows-ix86+x86_64-gcc8 | 1.5.7 | 17.00 | 173.00 | 190.00 | OK | |
| r-patched-linux-x86_64 | 1.5.7 | 7.57 | 73.15 | 80.72 | OK | |
| r-patched-solaris-x86 | 1.5.7 | 131.30 | OK | |||
| r-release-linux-x86_64 | 1.5.7 | 7.47 | 73.33 | 80.80 | OK | |
| r-release-windows-ix86+x86_64 | 1.5.7 | 23.00 | 119.00 | 142.00 | OK | |
| r-release-osx-x86_64 | 1.5.7 | OK | ||||
| r-oldrel-windows-ix86+x86_64 | 1.5.7 | 10.00 | 149.00 | 159.00 | OK | |
| r-oldrel-osx-x86_64 | 1.5.7 | OK |
Version: 1.5.7
Check: examples
Result: ERROR
Running examples in 'ghyp-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: fit.ghypuv
> ### Title: Fitting generalized hyperbolic distributions to univariate data
> ### Aliases: fit.ghypuv fit.hypuv fit.NIGuv fit.VGuv fit.tuv fit.gaussuv
> ### Keywords: iteration optimize distribution models
>
> ### ** Examples
>
> data(smi.stocks)
>
> nig.fit <- fit.NIGuv(smi.stocks[,"SMI"], opt.pars = c(alpha.bar = FALSE),
+ alpha.bar = 1, control = list(abstol = 1e-8))
[1] "Llh: 5.43442381858987E+03; Pars: 5.626297E-04, 8.875123E-03, 0.000000E+00"
[1] "Llh: -9.63118912675987E+04; Pars: 4.730129E-01, 8.875123E-03, 0.000000E+00"
[1] "Llh: 5.44117035692981E+03; Pars: 5.626297E-04, 1.423498E-02, 0.000000E+00"
[1] "Llh: -1.33159421324728E+05; Pars: 5.626297E-04, 8.875123E-03, 4.724503E-01"
[1] "Llh: 5.40585124384195E+03; Pars: 2.562630E-03, 1.423498E-02, 0.000000E+00"
[1] "Llh: 5.44117035692981E+03; Pars: 5.626297E-04, 1.423498E-02, 0.000000E+00"
[1] "Llh: 5.42996237953101E+03; Pars: 1.562630E-03, 1.424923E-02, 0.000000E+00"
[1] "Llh: 5.43079814576067E+03; Pars: 1.562630E-03, 1.422076E-02, 0.000000E+00"
[1] "Llh: 5.41369364563650E+03; Pars: 1.562630E-03, 1.423498E-02, 1.000000E-03"
[1] "Llh: 5.43906676328363E+03; Pars: 1.562630E-03, 1.423498E-02, -1.000000E-03"
[1] "Llh: 5.44117035692981E+03; Pars: 5.626297E-04, 1.423498E-02, 0.000000E+00"
[1] "Llh: 5.42137059007665E+03; Pars: -1.437370E-03, 1.423498E-02, 0.000000E+00"
[1] "Llh: 5.43772029929769E+03; Pars: -4.373703E-04, 1.424923E-02, 0.000000E+00"
[1] "Llh: 5.43857178038201E+03; Pars: -4.373703E-04, 1.422076E-02, 0.000000E+00"
[1] "Llh: 5.43892892734741E+03; Pars: -4.373703E-04, 1.423498E-02, 1.000000E-03"
[1] "Llh: 5.42938207221730E+03; Pars: -4.373703E-04, 1.423498E-02, -1.000000E-03"
[1] "Llh: 5.42996237953101E+03; Pars: 1.562630E-03, 1.424923E-02, 0.000000E+00"
[1] "Llh: 5.43772029929769E+03; Pars: -4.373703E-04, 1.424923E-02, 0.000000E+00"
[1] "Llh: 5.44030385848315E+03; Pars: 5.626297E-04, 1.426348E-02, 0.000000E+00"
[1] "Llh: 5.44117035692981E+03; Pars: 5.626297E-04, 1.423498E-02, 0.000000E+00"
[1] "Llh: 5.43280955921200E+03; Pars: 5.626297E-04, 1.424923E-02, 1.000000E-03"
[1] "Llh: 5.44070688002371E+03; Pars: 5.626297E-04, 1.424923E-02, -1.000000E-03"
[1] "Llh: 5.43079814576067E+03; Pars: 1.562630E-03, 1.422076E-02, 0.000000E+00"
[1] "Llh: 5.43857178038201E+03; Pars: -4.373703E-04, 1.422076E-02, 0.000000E+00"
[1] "Llh: 5.44117035692981E+03; Pars: 5.626297E-04, 1.423498E-02, 0.000000E+00"
[1] "Llh: 5.44203031551468E+03; Pars: 5.626297E-04, 1.420654E-02, 0.000000E+00"
[1] "Llh: 5.43363797827799E+03; Pars: 5.626297E-04, 1.422076E-02, 1.000000E-03"
[1] "Llh: 5.44156695163584E+03; Pars: 5.626297E-04, 1.422076E-02, -1.000000E-03"
[1] "Llh: 5.41369364563650E+03; Pars: 1.562630E-03, 1.423498E-02, 1.000000E-03"
[1] "Llh: 5.43892892734741E+03; Pars: -4.373703E-04, 1.423498E-02, 1.000000E-03"
[1] "Llh: 5.43280955921200E+03; Pars: 5.626297E-04, 1.424923E-02, 1.000000E-03"
[1] "Llh: 5.43363797827799E+03; Pars: 5.626297E-04, 1.422076E-02, 1.000000E-03"
[1] "Llh: 5.41734544414001E+03; Pars: 5.626297E-04, 1.423498E-02, 2.000000E-03"
[1] "Llh: 5.44117035692981E+03; Pars: 5.626297E-04, 1.423498E-02, 0.000000E+00"
[1] "Llh: 5.43906676328363E+03; Pars: 1.562630E-03, 1.423498E-02, -1.000000E-03"
[1] "Llh: 5.42938207221730E+03; Pars: -4.373703E-04, 1.423498E-02, -1.000000E-03"
[1] "Llh: 5.44070688002371E+03; Pars: 5.626297E-04, 1.424923E-02, -1.000000E-03"
[1] "Llh: 5.44156695163584E+03; Pars: 5.626297E-04, 1.422076E-02, -1.000000E-03"
[1] "Llh: 5.44117035692981E+03; Pars: 5.626297E-04, 1.423498E-02, 0.000000E+00"
[1] "Llh: 5.43317170665703E+03; Pars: 5.626297E-04, 1.423498E-02, -2.000000E-03"
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
ghyp
--- call from context ---
.mle.default(data = data, pdf = ".dghypuv", vars = vars, opt.pars = opt.pars,
transform = transform, se = T, silent = silent, ...)
--- call from argument ---
if (class(inv.hess) == "try-error") {
warning("Hessian matrix is singular!")
inv.hess <- matrix(NA, ncol(hess), ncol(hess), dimnames = dimnames(hess))
}
--- R stacktrace ---
where 1: .mle.default(data = data, pdf = ".dghypuv", vars = vars, opt.pars = opt.pars,
transform = transform, se = T, silent = silent, ...)
where 2: fit.ghypuv(data = data, lambda = -0.5, opt.pars = c(lambda = F,
opt.pars), symmetric = symmetric, ...)
where 3: fit.NIGuv(smi.stocks[, "SMI"], opt.pars = c(alpha.bar = FALSE),
alpha.bar = 1, control = list(abstol = 1e-08))
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (data, pdf, vars, opt.pars = rep(TRUE, length(vars)),
transform = NULL, se = FALSE, na.rm = FALSE, silent = FALSE,
...)
{
if (na.rm) {
data <- data[!is.na(data)]
}
else {
if (any(is.na(data))) {
stop(".mle.default: The sample contains NAs!\n",
"Set na.rm = TRUE to remove the rows which contain NAs.\n")
}
}
opt.pars <- opt.pars[match(names(vars), names(opt.pars))]
theta <- vars[opt.pars]
theta.backup <- theta
trace.pars <- NULL
negloglik <- function(theta, pdf, tmp.data, transf, const.pars,
silent, par.names) {
theta.backup <<- theta
for (nam in intersect(names(theta), names(transf))) {
theta[nam] = do.call(transf[nam], list(theta[nam]))
}
pars <- c(theta, const.pars)
trace.pars <<- rbind(trace.pars, pars[match(par.names,
names(pars))])
pdf.args = c(list(x = tmp.data, logvalue = TRUE), as.list(pars))
llh <- -sum(do.call(pdf, pdf.args))
if (!silent) {
print(paste("Llh: ", sprintf("% .14E", -llh), "; Pars: ",
paste(sprintf("% .6E", theta), collapse = ", "),
sep = ""))
}
return(llh)
}
fit <- try(optim(theta, negloglik, hessian = se, pdf = pdf,
tmp.data = data, transf = transform, const.pars = vars[!opt.pars],
silent = silent, par.names = names(vars), ...))
if (class(fit) == "try-error") {
convergence <- 100
hess <- as.numeric(NA)
n.iter <- as.numeric(NA)
inv.hess <- matrix(NA)
message <- fit
par.ests <- theta.backup
for (nam in intersect(names(par.ests), names(transform))) {
par.ests[nam] <- do.call(transform[nam], list(par.ests[nam]))
}
vars[opt.pars] <- par.ests
pdf.args <- c(list(x = data, logvalue = TRUE), as.list(vars))
ll.max <- -sum(do.call(".dghypuv", pdf.args))
}
else {
par.ests <- fit$par
names(par.ests) <- names(theta)
for (nam in intersect(names(par.ests), names(transform))) {
par.ests[nam] <- do.call(transform[nam], list(par.ests[nam]))
}
vars[opt.pars] <- par.ests
convergence <- fit$convergence
n.iter <- fit$counts[1]
ll.max <- -fit$value
message <- NULL
if (se) {
hess <- fit$hessian
par.ses <- suppressWarnings(sqrt(diag(hess)))
inv.hess <- try(solve(hess))
if (class(inv.hess) == "try-error") {
warning("Hessian matrix is singular!")
inv.hess <- matrix(NA, ncol(hess), ncol(hess),
dimnames = dimnames(hess))
}
names(par.ses) <- names(par.ests)
dimnames(hess) <- list(names(par.ests), names(par.ests))
}
else {
par.ses <- NA
hess <- NA
inv.hess <- NA
}
}
list(convergence = convergence, par.ests = vars, parameter.variance = inv.hess,
ll.max = ll.max, n.iter = n.iter, message = message,
trace.pars = trace.pars)
}
<bytecode: 0x2473940>
<environment: namespace:ghyp>
--- function search by body ---
Function .mle.default in namespace ghyp has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(inv.hess) == "try-error") { :
the condition has length > 1
Calls: fit.NIGuv -> fit.ghypuv -> .mle.default
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.5.7
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building 'Generalized_Hyperbolic_Distribution.Rnw' using Sweave
Loading required package: numDeriv
Loading required package: gplots
Attaching package: 'gplots'
The following object is masked from 'package:stats':
lowess
Warning in (psi + skewness.norm) * (chi + Q) :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in (psi + skewness.norm) * (chi + Q) :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in log.const.top + log.top :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in (psi + skewness.norm) * (chi + Q) :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in (psi + skewness.norm) * (chi + Q) :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in log.const.top + log.top :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in (psi + skewness.norm) * (chi + Q) :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in (psi + skewness.norm) * (chi + Q) :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in log.const.top + log.top :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in (psi + skewness.norm) * (chi + Q) :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in (psi + skewness.norm) * (chi + Q) :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in log.const.top + log.top :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in (psi + skewness.norm) * (chi + Q) :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in (psi + skewness.norm) * (chi + Q) :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in log.const.top + log.top :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in (psi + skewness.norm) * (chi + Q) :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in (psi + skewness.norm) * (chi + Q) :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in log.const.top + log.top :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in (psi + skewness.norm) * (chi + Q) :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in (psi + skewness.norm) * (chi + Q) :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in log.const.top + log.top :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in (psi + skewness.norm) * (chi + Q) :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in (psi + skewness.norm) * (chi + Q) :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in log.const.top + log.top :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in (psi + skewness.norm) * (chi + Q) :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in (psi + skewness.norm) * (chi + Q) :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in log.const.top + log.top :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in (psi + skewness.norm) * (chi + Q) :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in (psi + skewness.norm) * (chi + Q) :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in log.const.top + log.top :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in (psi + skewness.norm) * (chi + Q) :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in (psi + skewness.norm) * (chi + Q) :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in log.const.top + log.top :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in (psi + skewness.norm) * (chi + Q) :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in (psi + skewness.norm) * (chi + Q) :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in log.const.top + log.top :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in (psi + skewness.norm) * (chi + Q) :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in (psi + skewness.norm) * (chi + Q) :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in log.const.top + log.top :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in (psi + skewness.norm) * (chi + Q) :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in (psi + skewness.norm) * (chi + Q) :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in log.const.top + log.top :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in (psi + skewness.norm) * (chi + Q) :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in (psi + skewness.norm) * (chi + Q) :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in log.const.top + log.top :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in (psi + skewness.norm) * (chi + Q) :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in (psi + skewness.norm) * (chi + Q) :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in log.const.top + log.top :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in (psi + skewness.norm) * (chi + Q) :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in (psi + skewness.norm) * (chi + Q) :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in log.const.top + log.top :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in (psi + skewness.norm) * (chi + Q) :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in (psi + skewness.norm) * (chi + Q) :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in log.const.top + log.top :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in (psi + skewness.norm) * (chi + Q) :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in (psi + skewness.norm) * (chi + Q) :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in log.const.top + log.top :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in (psi + skewness.norm) * (chi + Q) :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in (psi + skewness.norm) * (chi + Q) :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in log.const.top + log.top :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in (psi + skewness.norm) * (chi + Q) :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in (psi + skewness.norm) * (chi + Q) :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in log.const.top + log.top :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in (psi + skewness.norm) * (chi + Q) :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in (psi + skewness.norm) * (chi + Q) :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in log.const.top + log.top :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in (psi + skewness.norm) * (chi + Q) :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in (psi + skewness.norm) * (chi + Q) :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in log.const.top + log.top :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in (psi + skewness.norm) * (chi + Q) :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in (psi + skewness.norm) * (chi + Q) :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in log.const.top + log.top :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in (psi + skewness.norm) * (chi + Q) :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in (psi + skewness.norm) * (chi + Q) :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in log.const.top + log.top :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in (psi + skewness.norm) * (chi + Q) :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in (psi + skewness.norm) * (chi + Q) :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in log.const.top + log.top :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in (psi + skewness.norm) * (chi + Q) :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in (psi + skewness.norm) * (chi + Q) :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in log.const.top + log.top :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in (psi + skewness.norm) * (chi + Q) :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in (psi + skewness.norm) * (chi + Q) :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in log.const.top + log.top :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in (psi + skewness.norm) * (chi + Q) :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in (psi + skewness.norm) * (chi + Q) :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Warning in log.const.top + log.top :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
ghyp
--- call from context ---
.mle.default(data = data, pdf = ".dghypuv", vars = vars, opt.pars = opt.pars,
transform = transform, se = T, silent = silent, ...)
--- call from argument ---
if (class(inv.hess) == "try-error") {
warning("Hessian matrix is singular!")
inv.hess <- matrix(NA, ncol(hess), ncol(hess), dimnames = dimnames(hess))
}
--- R stacktrace ---
where 1: .mle.default(data = data, pdf = ".dghypuv", vars = vars, opt.pars = opt.pars,
transform = transform, se = T, silent = silent, ...)
where 2: fit.ghypuv(data = data, lambda = 1, opt.pars = c(lambda = F,
opt.pars), symmetric = symmetric, ...)
where 3: fit.hypuv(data = smi.stocks[, c("SMI")], silent = TRUE)
where 4: eval(expr, .GlobalEnv)
where 5: eval(expr, .GlobalEnv)
where 6: withVisible(eval(expr, .GlobalEnv))
where 7: doTryCatch(return(expr), name, parentenv, handler)
where 8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 9: tryCatchList(expr, classes, parentenv, handlers)
where 10: 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 11: try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE)
where 12: evalFunc(ce, options)
where 13: tryCatchList(expr, classes, parentenv, handlers)
where 14: tryCatch(evalFunc(ce, options), finally = {
cat("\n")
sink()
})
where 15: driver$runcode(drobj, chunk, chunkopts)
where 16: utils::Sweave(...)
where 17: engine$weave(file, quiet = quiet, encoding = enc)
where 18: doTryCatch(return(expr), name, parentenv, handler)
where 19: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 20: tryCatchList(expr, classes, parentenv, handlers)
where 21: tryCatch({
engine$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 22: tools:::buildVignettes(dir = "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/ghyp.Rcheck/vign_test/ghyp",
ser_elibs = "/tmp/RtmpItg1Gb/file2cd08a3f299.rds")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (data, pdf, vars, opt.pars = rep(TRUE, length(vars)),
transform = NULL, se = FALSE, na.rm = FALSE, silent = FALSE,
...)
{
if (na.rm) {
data <- data[!is.na(data)]
}
else {
if (any(is.na(data))) {
stop(".mle.default: The sample contains NAs!\n",
"Set na.rm = TRUE to remove the rows which contain NAs.\n")
}
}
opt.pars <- opt.pars[match(names(vars), names(opt.pars))]
theta <- vars[opt.pars]
theta.backup <- theta
trace.pars <- NULL
negloglik <- function(theta, pdf, tmp.data, transf, const.pars,
silent, par.names) {
theta.backup <<- theta
for (nam in intersect(names(theta), names(transf))) {
theta[nam] = do.call(transf[nam], list(theta[nam]))
}
pars <- c(theta, const.pars)
trace.pars <<- rbind(trace.pars, pars[match(par.names,
names(pars))])
pdf.args = c(list(x = tmp.data, logvalue = TRUE), as.list(pars))
llh <- -sum(do.call(pdf, pdf.args))
if (!silent) {
print(paste("Llh: ", sprintf("% .14E", -llh), "; Pars: ",
paste(sprintf("% .6E", theta), collapse = ", "),
sep = ""))
}
return(llh)
}
fit <- try(optim(theta, negloglik, hessian = se, pdf = pdf,
tmp.data = data, transf = transform, const.pars = vars[!opt.pars],
silent = silent, par.names = names(vars), ...))
if (class(fit) == "try-error") {
convergence <- 100
hess <- as.numeric(NA)
n.iter <- as.numeric(NA)
inv.hess <- matrix(NA)
message <- fit
par.ests <- theta.backup
for (nam in intersect(names(par.ests), names(transform))) {
par.ests[nam] <- do.call(transform[nam], list(par.ests[nam]))
}
vars[opt.pars] <- par.ests
pdf.args <- c(list(x = data, logvalue = TRUE), as.list(vars))
ll.max <- -sum(do.call(".dghypuv", pdf.args))
}
else {
par.ests <- fit$par
names(par.ests) <- names(theta)
for (nam in intersect(names(par.ests), names(transform))) {
par.ests[nam] <- do.call(transform[nam], list(par.ests[nam]))
}
vars[opt.pars] <- par.ests
convergence <- fit$convergence
n.iter <- fit$counts[1]
ll.max <- -fit$value
message <- NULL
if (se) {
hess <- fit$hessian
par.ses <- suppressWarnings(sqrt(diag(hess)))
inv.hess <- try(solve(hess))
if (class(inv.hess) == "try-error") {
warning("Hessian matrix is singular!")
inv.hess <- matrix(NA, ncol(hess), ncol(hess),
dimnames = dimnames(hess))
}
names(par.ses) <- names(par.ests)
dimnames(hess) <- list(names(par.ests), names(par.ests))
}
else {
par.ses <- NA
hess <- NA
inv.hess <- NA
}
}
list(convergence = convergence, par.ests = vars, parameter.variance = inv.hess,
ll.max = ll.max, n.iter = n.iter, message = message,
trace.pars = trace.pars)
}
<bytecode: 0x7a343b8>
<environment: namespace:ghyp>
--- function search by body ---
Function .mle.default in namespace ghyp has this body.
----------- END OF FAILURE REPORT --------------
Error: processing vignette 'Generalized_Hyperbolic_Distribution.Rnw' failed with diagnostics:
chunk 7
Error in if (class(inv.hess) == "try-error") { :
the condition has length > 1
--- failed re-building 'Generalized_Hyperbolic_Distribution.Rnw'
SUMMARY: processing the following file failed:
'Generalized_Hyperbolic_Distribution.Rnw'
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.5.7
Check: package dependencies
Result: WARN
Requires orphaned package: ‘gplots’
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.5.7
Check: compiled code
Result: NOTE
File ‘ghyp/libs/ghyp.so’:
Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’
It is good practice to register native routines and to disable symbol
search.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc