Last updated on 2020-03-07 11:48:30 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.1.9.1 | 19.85 | 225.61 | 245.46 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.1.9.1 | 13.05 | 173.42 | 186.47 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.1.9.1 | 299.89 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 1.1.9.1 | 293.97 | ERROR | |||
| r-devel-windows-ix86+x86_64 | 1.1.9.1 | 54.00 | 186.00 | 240.00 | OK | --no-vignettes |
| r-devel-windows-ix86+x86_64-gcc8 | 1.1.9.1 | 30.00 | 188.00 | 218.00 | OK | --no-vignettes |
| r-patched-linux-x86_64 | 1.1.9.1 | 14.44 | 250.84 | 265.28 | OK | |
| r-patched-solaris-x86 | 1.1.9.1 | 644.40 | OK | |||
| r-release-linux-x86_64 | 1.1.9.1 | 15.65 | 253.45 | 269.10 | OK | |
| r-release-windows-ix86+x86_64 | 1.1.9.1 | 30.00 | 169.00 | 199.00 | OK | --no-vignettes |
| r-release-osx-x86_64 | 1.1.9.1 | OK | ||||
| r-oldrel-windows-ix86+x86_64 | 1.1.9.1 | 24.00 | 174.00 | 198.00 | OK | --no-vignettes |
| r-oldrel-osx-x86_64 | 1.1.9.1 | OK |
Version: 1.1.9.1
Check: examples
Result: ERROR
Running examples in 'SpatioTemporal-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: loglikeST
> ### Title: Compute the Log-likelihood for the Spatio-Temporal Model
> ### Aliases: loglikeST loglikeSTnaive
>
> ### ** Examples
>
> ##load the data
> data(mesa.model)
>
> ##Compute dimensions for the data structure
> dim <- loglikeSTdim(mesa.model)
>
> ##Find out in which order parameters should be given
> loglikeST(NULL, mesa.model)
[1] "log.range.const.exp" "log.sill.const.exp"
[3] "log.range.V1.exp" "log.sill.V1.exp"
[5] "log.range.V2.exp" "log.sill.V2.exp"
[7] "nu.log.range.exp" "nu.log.sill.exp"
[9] "nu.log.nugget.(Intercept).exp" "nu.log.nugget.typeFIXED.exp"
>
> ##Let's create random vectors of values
> x <- runif( dim$nparam.cov )
> x.all <- runif( dim$nparam )
>
> ##Evaluate the log-likelihood for these values
> loglikeST(x.all, mesa.model, "f")
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
SpatioTemporal
--- call from context ---
loglikeST(x.all, mesa.model, "f")
--- call from argument ---
if (class(sigma.B) == "try-error") {
return(-.Machine$double.xmax)
}
--- R stacktrace ---
where 1: loglikeST(x.all, mesa.model, "f")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (x = NULL, STmodel, type = "p", x.fixed = NULL)
{
stCheckClass(STmodel, "STmodel", name = "STmodel")
type <- tolower(type)
x <- stCheckLoglikeIn(x, x.fixed, type)
if (is.null(x) || any(is.na(x))) {
return(loglikeSTnames(STmodel, all = (type == "f")))
}
dimensions <- loglikeSTdim(STmodel)
if ((type == "f" && length(x) != dimensions$nparam) || (type !=
"f" && length(x) != dimensions$nparam.cov)) {
stop("Number of parameters, length(x), incorrect.")
}
tmp <- loglikeSTgetPars(x, STmodel)
if (type == "f") {
gamma <- tmp$gamma
alpha <- tmp$alpha
}
cov.pars.beta <- tmp$cov.beta
cov.pars.nu <- tmp$cov.nu
Y <- STmodel$obs$obs
F <- expandF(STmodel$F, STmodel$obs$idx, n.loc = dimensions$n.obs)
if (type == "f") {
mu.B <- matrix(calc.mu.B(STmodel$LUR, alpha), ncol = 1)
if (dimensions$L != 0) {
Y <- Y - STmodel$ST %*% gamma
}
}
sigma.B <- makeSigmaB(cov.pars.beta$pars, dist = STmodel$D.beta,
type = STmodel$cov.beta$covf, nugget = cov.pars.beta$nugget)
sigma.nu <- makeSigmaNu(cov.pars.nu$pars, dist = STmodel$D.nu,
type = STmodel$cov.nu$covf, nugget = cov.pars.nu$nugget,
random.effect = cov.pars.nu$random.effect, blocks1 = STmodel$nt,
ind1 = STmodel$obs$idx, sparse = TRUE)
sigma.B <- try(makeCholBlock(sigma.B, n.blocks = dimensions$m),
silent = TRUE)
if (class(sigma.B) == "try-error") {
return(-.Machine$double.xmax)
}
sigma.nu <- try(chol(sigma.nu), silent = TRUE)
if (class(sigma.nu) == "try-error") {
return(-.Machine$double.xmax)
}
l <- -sumLogDiag(sigma.B)
l <- l - sumLog(diag(sigma.nu))
sigma.B <- invCholBlock(sigma.B, n.blocks = dimensions$m)
sigma.nu <- chol2inv(sigma.nu)
i.sR.Y <- as.matrix(sigma.nu %*% Y)
if (type == "f") {
i.sB.mu.B <- blockMult(sigma.B, mu.B, n.blocks = dimensions$m)
l <- l - dotProd(i.sB.mu.B, mu.B)/2
l <- l - dotProd(i.sR.Y, Y)/2
}
else {
iS.X <- calc.iS.X(STmodel$LUR, sigma.B)
if (dimensions$L != 0) {
i.sR.M <- as.matrix(sigma.nu %*% STmodel$ST)
}
F.i.sR.Y <- calc.tFX(STmodel$F, i.sR.Y, STmodel$obs$idx,
n.loc = dimensions$n.obs)
if (dimensions$L != 0) {
F.i.sR.M <- calc.tFX(STmodel$F, i.sR.M, STmodel$obs$idx,
n.loc = dimensions$n.obs)
}
}
sigma.B.Y <- as.matrix(t(F) %*% sigma.nu %*% F) + sigma.B
sigma.B.Y <- try(chol(sigma.B.Y), silent = TRUE)
if (class(sigma.B.Y) == "try-error") {
return(-.Machine$double.xmax)
}
l <- l - sumLogDiag(sigma.B.Y)
if (type == "f") {
mu.B.Y <- i.sB.mu.B + calc.tFX(STmodel$F, i.sR.Y, STmodel$obs$idx,
n.loc = dimensions$n.obs)
mu.B.Y <- solveTriBlock(sigma.B.Y, mu.B.Y, transpose = TRUE)
l <- l + norm2(mu.B.Y)/2
}
else {
Y.hat <- solveTriBlock(sigma.B.Y, F.i.sR.Y, transpose = TRUE)
if (dimensions$L != 0) {
M.hat <- solveTriBlock(sigma.B.Y, F.i.sR.M, transpose = TRUE)
}
sigma.B.Y <- invCholBlock(sigma.B.Y)
sigma.B.Y.iS.X <- sigma.B.Y %*% iS.X
i.sigma.alpha.Y <- -t(iS.X) %*% sigma.B.Y.iS.X + calc.X.iS.X(STmodel$LUR,
iS.X)
i.sigma.alpha.Y <- try(chol(i.sigma.alpha.Y), silent = TRUE)
if (class(i.sigma.alpha.Y) == "try-error") {
return(-.Machine$double.xmax)
}
if (type == "r") {
l <- l - sumLogDiag(i.sigma.alpha.Y)
}
Y.hat.2 <- t(sigma.B.Y.iS.X) %*% F.i.sR.Y
Y.hat.2 <- solveTriBlock(i.sigma.alpha.Y, Y.hat.2, transpose = TRUE)
Y.sigma.hat.Y <- dotProd(Y, i.sR.Y) - norm2(Y.hat) -
norm2(Y.hat.2)
l <- l - Y.sigma.hat.Y/2
if (dimensions$L != 0) {
M.hat.2 <- t(sigma.B.Y.iS.X) %*% F.i.sR.M
M.hat.2 <- solveTriBlock(i.sigma.alpha.Y, M.hat.2,
transpose = TRUE)
Y.sigma.hat.M <- (t(Y) %*% i.sR.M - t(Y.hat) %*%
M.hat - t(Y.hat.2) %*% M.hat.2)
Y.sigma.hat.M <- t(Y.sigma.hat.M)
M.sigma.hat.M <- (t(STmodel$ST) %*% i.sR.M - t(M.hat) %*%
M.hat - t(M.hat.2) %*% M.hat.2)
M.sigma.hat.M <- try(chol(M.sigma.hat.M), silent = TRUE)
if (class(M.sigma.hat.M) == "try-error") {
return(-.Machine$double.xmax)
}
if (type == "r") {
l <- l - sumLogDiag(M.sigma.hat.M)
}
Y.sigma.hat.M <- solveTriBlock(M.sigma.hat.M, Y.sigma.hat.M,
transpose = TRUE)
l <- l + norm2(Y.sigma.hat.M)/2
}
}
l <- as.double(l)
if (!is.finite(l))
l <- -.Machine$double.xmax
return(l)
}
<bytecode: 0x239e118>
<environment: namespace:SpatioTemporal>
--- function search by body ---
Function loglikeST in namespace SpatioTemporal has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(sigma.B) == "try-error") { :
the condition has length > 1
Calls: loglikeST
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.1.9.1
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building 'ST_intro.Rnw' using Sweave
Loading required package: Matrix
Replacing existing trend.
Replacing existing trend.
Replacing existing trend.
--- finished re-building 'ST_intro.Rnw'
--- re-building 'ST_tutorial.Rnw' using Sweave
Loading required package: Matrix
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
SpatioTemporal
--- call from context ---
loglikeST(est.mesa.model$res.best$par, mesa.model)
--- call from argument ---
if (class(sigma.B) == "try-error") {
return(-.Machine$double.xmax)
}
--- R stacktrace ---
where 1: loglikeST(est.mesa.model$res.best$par, mesa.model)
where 2: eval(expr, .GlobalEnv)
where 3: eval(expr, .GlobalEnv)
where 4: withVisible(eval(expr, .GlobalEnv))
where 5: doTryCatch(return(expr), name, parentenv, handler)
where 6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 7: tryCatchList(expr, classes, parentenv, handlers)
where 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)[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 9: try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE)
where 10: evalFunc(ce, options)
where 11: tryCatchList(expr, classes, parentenv, handlers)
where 12: tryCatch(evalFunc(ce, options), finally = {
cat("\n")
sink()
})
where 13: driver$runcode(drobj, chunk, chunkopts)
where 14: utils::Sweave(...)
where 15: engine$weave(file, quiet = quiet, encoding = enc)
where 16: doTryCatch(return(expr), name, parentenv, handler)
where 17: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 18: tryCatchList(expr, classes, parentenv, handlers)
where 19: tryCatch({
engine$weave(file, quiet = quiet, encoding = enc)
setwd(startdir)
output <- find_vignette_product(name, by = "weave", engine = engine)
if (!have.makefile && vignette_is_tex(output)) {
texi2pdf(file = output, clean = FALSE, quiet = quiet)
output <- find_vignette_product(name, by = "texi2pdf",
engine = engine)
}
}, error = function(e) {
OK <<- FALSE
message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",
file, conditionMessage(e)))
})
where 20: tools:::.buildOneVignette("ST_tutorial.Rnw", "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/SpatioTemporal.Rcheck/vign_test/SpatioTemporal",
TRUE, FALSE, "ST_tutorial", "", "/tmp/RtmpQucNNk/file27926f9746e.rds")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (x = NULL, STmodel, type = "p", x.fixed = NULL)
{
stCheckClass(STmodel, "STmodel", name = "STmodel")
type <- tolower(type)
x <- stCheckLoglikeIn(x, x.fixed, type)
if (is.null(x) || any(is.na(x))) {
return(loglikeSTnames(STmodel, all = (type == "f")))
}
dimensions <- loglikeSTdim(STmodel)
if ((type == "f" && length(x) != dimensions$nparam) || (type !=
"f" && length(x) != dimensions$nparam.cov)) {
stop("Number of parameters, length(x), incorrect.")
}
tmp <- loglikeSTgetPars(x, STmodel)
if (type == "f") {
gamma <- tmp$gamma
alpha <- tmp$alpha
}
cov.pars.beta <- tmp$cov.beta
cov.pars.nu <- tmp$cov.nu
Y <- STmodel$obs$obs
F <- expandF(STmodel$F, STmodel$obs$idx, n.loc = dimensions$n.obs)
if (type == "f") {
mu.B <- matrix(calc.mu.B(STmodel$LUR, alpha), ncol = 1)
if (dimensions$L != 0) {
Y <- Y - STmodel$ST %*% gamma
}
}
sigma.B <- makeSigmaB(cov.pars.beta$pars, dist = STmodel$D.beta,
type = STmodel$cov.beta$covf, nugget = cov.pars.beta$nugget)
sigma.nu <- makeSigmaNu(cov.pars.nu$pars, dist = STmodel$D.nu,
type = STmodel$cov.nu$covf, nugget = cov.pars.nu$nugget,
random.effect = cov.pars.nu$random.effect, blocks1 = STmodel$nt,
ind1 = STmodel$obs$idx, sparse = TRUE)
sigma.B <- try(makeCholBlock(sigma.B, n.blocks = dimensions$m),
silent = TRUE)
if (class(sigma.B) == "try-error") {
return(-.Machine$double.xmax)
}
sigma.nu <- try(chol(sigma.nu), silent = TRUE)
if (class(sigma.nu) == "try-error") {
return(-.Machine$double.xmax)
}
l <- -sumLogDiag(sigma.B)
l <- l - sumLog(diag(sigma.nu))
sigma.B <- invCholBlock(sigma.B, n.blocks = dimensions$m)
sigma.nu <- chol2inv(sigma.nu)
i.sR.Y <- as.matrix(sigma.nu %*% Y)
if (type == "f") {
i.sB.mu.B <- blockMult(sigma.B, mu.B, n.blocks = dimensions$m)
l <- l - dotProd(i.sB.mu.B, mu.B)/2
l <- l - dotProd(i.sR.Y, Y)/2
}
else {
iS.X <- calc.iS.X(STmodel$LUR, sigma.B)
if (dimensions$L != 0) {
i.sR.M <- as.matrix(sigma.nu %*% STmodel$ST)
}
F.i.sR.Y <- calc.tFX(STmodel$F, i.sR.Y, STmodel$obs$idx,
n.loc = dimensions$n.obs)
if (dimensions$L != 0) {
F.i.sR.M <- calc.tFX(STmodel$F, i.sR.M, STmodel$obs$idx,
n.loc = dimensions$n.obs)
}
}
sigma.B.Y <- as.matrix(t(F) %*% sigma.nu %*% F) + sigma.B
sigma.B.Y <- try(chol(sigma.B.Y), silent = TRUE)
if (class(sigma.B.Y) == "try-error") {
return(-.Machine$double.xmax)
}
l <- l - sumLogDiag(sigma.B.Y)
if (type == "f") {
mu.B.Y <- i.sB.mu.B + calc.tFX(STmodel$F, i.sR.Y, STmodel$obs$idx,
n.loc = dimensions$n.obs)
mu.B.Y <- solveTriBlock(sigma.B.Y, mu.B.Y, transpose = TRUE)
l <- l + norm2(mu.B.Y)/2
}
else {
Y.hat <- solveTriBlock(sigma.B.Y, F.i.sR.Y, transpose = TRUE)
if (dimensions$L != 0) {
M.hat <- solveTriBlock(sigma.B.Y, F.i.sR.M, transpose = TRUE)
}
sigma.B.Y <- invCholBlock(sigma.B.Y)
sigma.B.Y.iS.X <- sigma.B.Y %*% iS.X
i.sigma.alpha.Y <- -t(iS.X) %*% sigma.B.Y.iS.X + calc.X.iS.X(STmodel$LUR,
iS.X)
i.sigma.alpha.Y <- try(chol(i.sigma.alpha.Y), silent = TRUE)
if (class(i.sigma.alpha.Y) == "try-error") {
return(-.Machine$double.xmax)
}
if (type == "r") {
l <- l - sumLogDiag(i.sigma.alpha.Y)
}
Y.hat.2 <- t(sigma.B.Y.iS.X) %*% F.i.sR.Y
Y.hat.2 <- solveTriBlock(i.sigma.alpha.Y, Y.hat.2, transpose = TRUE)
Y.sigma.hat.Y <- dotProd(Y, i.sR.Y) - norm2(Y.hat) -
norm2(Y.hat.2)
l <- l - Y.sigma.hat.Y/2
if (dimensions$L != 0) {
M.hat.2 <- t(sigma.B.Y.iS.X) %*% F.i.sR.M
M.hat.2 <- solveTriBlock(i.sigma.alpha.Y, M.hat.2,
transpose = TRUE)
Y.sigma.hat.M <- (t(Y) %*% i.sR.M - t(Y.hat) %*%
M.hat - t(Y.hat.2) %*% M.hat.2)
Y.sigma.hat.M <- t(Y.sigma.hat.M)
M.sigma.hat.M <- (t(STmodel$ST) %*% i.sR.M - t(M.hat) %*%
M.hat - t(M.hat.2) %*% M.hat.2)
M.sigma.hat.M <- try(chol(M.sigma.hat.M), silent = TRUE)
if (class(M.sigma.hat.M) == "try-error") {
return(-.Machine$double.xmax)
}
if (type == "r") {
l <- l - sumLogDiag(M.sigma.hat.M)
}
Y.sigma.hat.M <- solveTriBlock(M.sigma.hat.M, Y.sigma.hat.M,
transpose = TRUE)
l <- l + norm2(Y.sigma.hat.M)/2
}
}
l <- as.double(l)
if (!is.finite(l))
l <- -.Machine$double.xmax
return(l)
}
<bytecode: 0x7a74cb8>
<environment: namespace:SpatioTemporal>
--- function search by body ---
Function loglikeST in namespace SpatioTemporal has this body.
----------- END OF FAILURE REPORT --------------
Error: processing vignette 'ST_tutorial.Rnw' failed with diagnostics:
chunk 34
Error in if (class(sigma.B) == "try-error") { :
the condition has length > 1
--- failed re-building 'ST_tutorial.Rnw'
SUMMARY: processing the following file failed:
'ST_tutorial.Rnw'
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.1.9.1
Check: examples
Result: ERROR
Running examples in ‘SpatioTemporal-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: loglikeST
> ### Title: Compute the Log-likelihood for the Spatio-Temporal Model
> ### Aliases: loglikeST loglikeSTnaive
>
> ### ** Examples
>
> ##load the data
> data(mesa.model)
>
> ##Compute dimensions for the data structure
> dim <- loglikeSTdim(mesa.model)
>
> ##Find out in which order parameters should be given
> loglikeST(NULL, mesa.model)
[1] "log.range.const.exp" "log.sill.const.exp"
[3] "log.range.V1.exp" "log.sill.V1.exp"
[5] "log.range.V2.exp" "log.sill.V2.exp"
[7] "nu.log.range.exp" "nu.log.sill.exp"
[9] "nu.log.nugget.(Intercept).exp" "nu.log.nugget.typeFIXED.exp"
>
> ##Let's create random vectors of values
> x <- runif( dim$nparam.cov )
> x.all <- runif( dim$nparam )
>
> ##Evaluate the log-likelihood for these values
> loglikeST(x.all, mesa.model, "f")
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
SpatioTemporal
--- call from context ---
loglikeST(x.all, mesa.model, "f")
--- call from argument ---
if (class(sigma.B) == "try-error") {
return(-.Machine$double.xmax)
}
--- R stacktrace ---
where 1: loglikeST(x.all, mesa.model, "f")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (x = NULL, STmodel, type = "p", x.fixed = NULL)
{
stCheckClass(STmodel, "STmodel", name = "STmodel")
type <- tolower(type)
x <- stCheckLoglikeIn(x, x.fixed, type)
if (is.null(x) || any(is.na(x))) {
return(loglikeSTnames(STmodel, all = (type == "f")))
}
dimensions <- loglikeSTdim(STmodel)
if ((type == "f" && length(x) != dimensions$nparam) || (type !=
"f" && length(x) != dimensions$nparam.cov)) {
stop("Number of parameters, length(x), incorrect.")
}
tmp <- loglikeSTgetPars(x, STmodel)
if (type == "f") {
gamma <- tmp$gamma
alpha <- tmp$alpha
}
cov.pars.beta <- tmp$cov.beta
cov.pars.nu <- tmp$cov.nu
Y <- STmodel$obs$obs
F <- expandF(STmodel$F, STmodel$obs$idx, n.loc = dimensions$n.obs)
if (type == "f") {
mu.B <- matrix(calc.mu.B(STmodel$LUR, alpha), ncol = 1)
if (dimensions$L != 0) {
Y <- Y - STmodel$ST %*% gamma
}
}
sigma.B <- makeSigmaB(cov.pars.beta$pars, dist = STmodel$D.beta,
type = STmodel$cov.beta$covf, nugget = cov.pars.beta$nugget)
sigma.nu <- makeSigmaNu(cov.pars.nu$pars, dist = STmodel$D.nu,
type = STmodel$cov.nu$covf, nugget = cov.pars.nu$nugget,
random.effect = cov.pars.nu$random.effect, blocks1 = STmodel$nt,
ind1 = STmodel$obs$idx, sparse = TRUE)
sigma.B <- try(makeCholBlock(sigma.B, n.blocks = dimensions$m),
silent = TRUE)
if (class(sigma.B) == "try-error") {
return(-.Machine$double.xmax)
}
sigma.nu <- try(chol(sigma.nu), silent = TRUE)
if (class(sigma.nu) == "try-error") {
return(-.Machine$double.xmax)
}
l <- -sumLogDiag(sigma.B)
l <- l - sumLog(diag(sigma.nu))
sigma.B <- invCholBlock(sigma.B, n.blocks = dimensions$m)
sigma.nu <- chol2inv(sigma.nu)
i.sR.Y <- as.matrix(sigma.nu %*% Y)
if (type == "f") {
i.sB.mu.B <- blockMult(sigma.B, mu.B, n.blocks = dimensions$m)
l <- l - dotProd(i.sB.mu.B, mu.B)/2
l <- l - dotProd(i.sR.Y, Y)/2
}
else {
iS.X <- calc.iS.X(STmodel$LUR, sigma.B)
if (dimensions$L != 0) {
i.sR.M <- as.matrix(sigma.nu %*% STmodel$ST)
}
F.i.sR.Y <- calc.tFX(STmodel$F, i.sR.Y, STmodel$obs$idx,
n.loc = dimensions$n.obs)
if (dimensions$L != 0) {
F.i.sR.M <- calc.tFX(STmodel$F, i.sR.M, STmodel$obs$idx,
n.loc = dimensions$n.obs)
}
}
sigma.B.Y <- as.matrix(t(F) %*% sigma.nu %*% F) + sigma.B
sigma.B.Y <- try(chol(sigma.B.Y), silent = TRUE)
if (class(sigma.B.Y) == "try-error") {
return(-.Machine$double.xmax)
}
l <- l - sumLogDiag(sigma.B.Y)
if (type == "f") {
mu.B.Y <- i.sB.mu.B + calc.tFX(STmodel$F, i.sR.Y, STmodel$obs$idx,
n.loc = dimensions$n.obs)
mu.B.Y <- solveTriBlock(sigma.B.Y, mu.B.Y, transpose = TRUE)
l <- l + norm2(mu.B.Y)/2
}
else {
Y.hat <- solveTriBlock(sigma.B.Y, F.i.sR.Y, transpose = TRUE)
if (dimensions$L != 0) {
M.hat <- solveTriBlock(sigma.B.Y, F.i.sR.M, transpose = TRUE)
}
sigma.B.Y <- invCholBlock(sigma.B.Y)
sigma.B.Y.iS.X <- sigma.B.Y %*% iS.X
i.sigma.alpha.Y <- -t(iS.X) %*% sigma.B.Y.iS.X + calc.X.iS.X(STmodel$LUR,
iS.X)
i.sigma.alpha.Y <- try(chol(i.sigma.alpha.Y), silent = TRUE)
if (class(i.sigma.alpha.Y) == "try-error") {
return(-.Machine$double.xmax)
}
if (type == "r") {
l <- l - sumLogDiag(i.sigma.alpha.Y)
}
Y.hat.2 <- t(sigma.B.Y.iS.X) %*% F.i.sR.Y
Y.hat.2 <- solveTriBlock(i.sigma.alpha.Y, Y.hat.2, transpose = TRUE)
Y.sigma.hat.Y <- dotProd(Y, i.sR.Y) - norm2(Y.hat) -
norm2(Y.hat.2)
l <- l - Y.sigma.hat.Y/2
if (dimensions$L != 0) {
M.hat.2 <- t(sigma.B.Y.iS.X) %*% F.i.sR.M
M.hat.2 <- solveTriBlock(i.sigma.alpha.Y, M.hat.2,
transpose = TRUE)
Y.sigma.hat.M <- (t(Y) %*% i.sR.M - t(Y.hat) %*%
M.hat - t(Y.hat.2) %*% M.hat.2)
Y.sigma.hat.M <- t(Y.sigma.hat.M)
M.sigma.hat.M <- (t(STmodel$ST) %*% i.sR.M - t(M.hat) %*%
M.hat - t(M.hat.2) %*% M.hat.2)
M.sigma.hat.M <- try(chol(M.sigma.hat.M), silent = TRUE)
if (class(M.sigma.hat.M) == "try-error") {
return(-.Machine$double.xmax)
}
if (type == "r") {
l <- l - sumLogDiag(M.sigma.hat.M)
}
Y.sigma.hat.M <- solveTriBlock(M.sigma.hat.M, Y.sigma.hat.M,
transpose = TRUE)
l <- l + norm2(Y.sigma.hat.M)/2
}
}
l <- as.double(l)
if (!is.finite(l))
l <- -.Machine$double.xmax
return(l)
}
<bytecode: 0x55b2284e4f28>
<environment: namespace:SpatioTemporal>
--- function search by body ---
Function loglikeST in namespace SpatioTemporal has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(sigma.B) == "try-error") { :
the condition has length > 1
Calls: loglikeST
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.1.9.1
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building ‘ST_intro.Rnw’ using Sweave
Loading required package: Matrix
Replacing existing trend.
Replacing existing trend.
Replacing existing trend.
--- finished re-building ‘ST_intro.Rnw’
--- re-building ‘ST_tutorial.Rnw’ using Sweave
Loading required package: Matrix
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
SpatioTemporal
--- call from context ---
loglikeST(est.mesa.model$res.best$par, mesa.model)
--- call from argument ---
if (class(sigma.B) == "try-error") {
return(-.Machine$double.xmax)
}
--- R stacktrace ---
where 1: loglikeST(est.mesa.model$res.best$par, mesa.model)
where 2: eval(expr, .GlobalEnv)
where 3: eval(expr, .GlobalEnv)
where 4: withVisible(eval(expr, .GlobalEnv))
where 5: doTryCatch(return(expr), name, parentenv, handler)
where 6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 7: tryCatchList(expr, classes, parentenv, handlers)
where 8: tryCatch(expr, error = function(e) {
call <- conditionCall(e)
if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L)
dcall <- deparse(call)[1L]
prefix <- paste("Error in", dcall, ": ")
LONG <- 75L
sm <- strsplit(conditionMessage(e), "\n")[[1L]]
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
if (is.na(w))
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
type = "b")
if (w > LONG)
prefix <- paste0(prefix, "\n ")
}
else prefix <- "Error : "
msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L]))
if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile)
.Internal(printDeferredWarnings())
}
invisible(structure(msg, class = "try-error", condition = e))
})
where 9: try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE)
where 10: evalFunc(ce, options)
where 11: tryCatchList(expr, classes, parentenv, handlers)
where 12: tryCatch(evalFunc(ce, options), finally = {
cat("\n")
sink()
})
where 13: driver$runcode(drobj, chunk, chunkopts)
where 14: utils::Sweave(...)
where 15: engine$weave(file, quiet = quiet, encoding = enc)
where 16: doTryCatch(return(expr), name, parentenv, handler)
where 17: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 18: tryCatchList(expr, classes, parentenv, handlers)
where 19: tryCatch({
engine$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)
}
}, error = function(e) {
OK <<- FALSE
message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",
file, conditionMessage(e)))
})
where 20: tools:::.buildOneVignette("ST_tutorial.Rnw", "/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SpatioTemporal.Rcheck/vign_test/SpatioTemporal",
TRUE, FALSE, "ST_tutorial", "", "/home/hornik/tmp/scratch/RtmpVJ8RoN/file65070115541.rds")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (x = NULL, STmodel, type = "p", x.fixed = NULL)
{
stCheckClass(STmodel, "STmodel", name = "STmodel")
type <- tolower(type)
x <- stCheckLoglikeIn(x, x.fixed, type)
if (is.null(x) || any(is.na(x))) {
return(loglikeSTnames(STmodel, all = (type == "f")))
}
dimensions <- loglikeSTdim(STmodel)
if ((type == "f" && length(x) != dimensions$nparam) || (type !=
"f" && length(x) != dimensions$nparam.cov)) {
stop("Number of parameters, length(x), incorrect.")
}
tmp <- loglikeSTgetPars(x, STmodel)
if (type == "f") {
gamma <- tmp$gamma
alpha <- tmp$alpha
}
cov.pars.beta <- tmp$cov.beta
cov.pars.nu <- tmp$cov.nu
Y <- STmodel$obs$obs
F <- expandF(STmodel$F, STmodel$obs$idx, n.loc = dimensions$n.obs)
if (type == "f") {
mu.B <- matrix(calc.mu.B(STmodel$LUR, alpha), ncol = 1)
if (dimensions$L != 0) {
Y <- Y - STmodel$ST %*% gamma
}
}
sigma.B <- makeSigmaB(cov.pars.beta$pars, dist = STmodel$D.beta,
type = STmodel$cov.beta$covf, nugget = cov.pars.beta$nugget)
sigma.nu <- makeSigmaNu(cov.pars.nu$pars, dist = STmodel$D.nu,
type = STmodel$cov.nu$covf, nugget = cov.pars.nu$nugget,
random.effect = cov.pars.nu$random.effect, blocks1 = STmodel$nt,
ind1 = STmodel$obs$idx, sparse = TRUE)
sigma.B <- try(makeCholBlock(sigma.B, n.blocks = dimensions$m),
silent = TRUE)
if (class(sigma.B) == "try-error") {
return(-.Machine$double.xmax)
}
sigma.nu <- try(chol(sigma.nu), silent = TRUE)
if (class(sigma.nu) == "try-error") {
return(-.Machine$double.xmax)
}
l <- -sumLogDiag(sigma.B)
l <- l - sumLog(diag(sigma.nu))
sigma.B <- invCholBlock(sigma.B, n.blocks = dimensions$m)
sigma.nu <- chol2inv(sigma.nu)
i.sR.Y <- as.matrix(sigma.nu %*% Y)
if (type == "f") {
i.sB.mu.B <- blockMult(sigma.B, mu.B, n.blocks = dimensions$m)
l <- l - dotProd(i.sB.mu.B, mu.B)/2
l <- l - dotProd(i.sR.Y, Y)/2
}
else {
iS.X <- calc.iS.X(STmodel$LUR, sigma.B)
if (dimensions$L != 0) {
i.sR.M <- as.matrix(sigma.nu %*% STmodel$ST)
}
F.i.sR.Y <- calc.tFX(STmodel$F, i.sR.Y, STmodel$obs$idx,
n.loc = dimensions$n.obs)
if (dimensions$L != 0) {
F.i.sR.M <- calc.tFX(STmodel$F, i.sR.M, STmodel$obs$idx,
n.loc = dimensions$n.obs)
}
}
sigma.B.Y <- as.matrix(t(F) %*% sigma.nu %*% F) + sigma.B
sigma.B.Y <- try(chol(sigma.B.Y), silent = TRUE)
if (class(sigma.B.Y) == "try-error") {
return(-.Machine$double.xmax)
}
l <- l - sumLogDiag(sigma.B.Y)
if (type == "f") {
mu.B.Y <- i.sB.mu.B + calc.tFX(STmodel$F, i.sR.Y, STmodel$obs$idx,
n.loc = dimensions$n.obs)
mu.B.Y <- solveTriBlock(sigma.B.Y, mu.B.Y, transpose = TRUE)
l <- l + norm2(mu.B.Y)/2
}
else {
Y.hat <- solveTriBlock(sigma.B.Y, F.i.sR.Y, transpose = TRUE)
if (dimensions$L != 0) {
M.hat <- solveTriBlock(sigma.B.Y, F.i.sR.M, transpose = TRUE)
}
sigma.B.Y <- invCholBlock(sigma.B.Y)
sigma.B.Y.iS.X <- sigma.B.Y %*% iS.X
i.sigma.alpha.Y <- -t(iS.X) %*% sigma.B.Y.iS.X + calc.X.iS.X(STmodel$LUR,
iS.X)
i.sigma.alpha.Y <- try(chol(i.sigma.alpha.Y), silent = TRUE)
if (class(i.sigma.alpha.Y) == "try-error") {
return(-.Machine$double.xmax)
}
if (type == "r") {
l <- l - sumLogDiag(i.sigma.alpha.Y)
}
Y.hat.2 <- t(sigma.B.Y.iS.X) %*% F.i.sR.Y
Y.hat.2 <- solveTriBlock(i.sigma.alpha.Y, Y.hat.2, transpose = TRUE)
Y.sigma.hat.Y <- dotProd(Y, i.sR.Y) - norm2(Y.hat) -
norm2(Y.hat.2)
l <- l - Y.sigma.hat.Y/2
if (dimensions$L != 0) {
M.hat.2 <- t(sigma.B.Y.iS.X) %*% F.i.sR.M
M.hat.2 <- solveTriBlock(i.sigma.alpha.Y, M.hat.2,
transpose = TRUE)
Y.sigma.hat.M <- (t(Y) %*% i.sR.M - t(Y.hat) %*%
M.hat - t(Y.hat.2) %*% M.hat.2)
Y.sigma.hat.M <- t(Y.sigma.hat.M)
M.sigma.hat.M <- (t(STmodel$ST) %*% i.sR.M - t(M.hat) %*%
M.hat - t(M.hat.2) %*% M.hat.2)
M.sigma.hat.M <- try(chol(M.sigma.hat.M), silent = TRUE)
if (class(M.sigma.hat.M) == "try-error") {
return(-.Machine$double.xmax)
}
if (type == "r") {
l <- l - sumLogDiag(M.sigma.hat.M)
}
Y.sigma.hat.M <- solveTriBlock(M.sigma.hat.M, Y.sigma.hat.M,
transpose = TRUE)
l <- l + norm2(Y.sigma.hat.M)/2
}
}
l <- as.double(l)
if (!is.finite(l))
l <- -.Machine$double.xmax
return(l)
}
<bytecode: 0x5646a3124f48>
<environment: namespace:SpatioTemporal>
--- function search by body ---
Function loglikeST in namespace SpatioTemporal has this body.
----------- END OF FAILURE REPORT --------------
Error: processing vignette 'ST_tutorial.Rnw' failed with diagnostics:
chunk 34
Error in if (class(sigma.B) == "try-error") { :
the condition has length > 1
--- failed re-building ‘ST_tutorial.Rnw’
SUMMARY: processing the following file failed:
‘ST_tutorial.Rnw’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.1.9.1
Check: examples
Result: ERROR
Running examples in ‘SpatioTemporal-Ex.R’ failed
The error most likely occurred in:
> ### Name: loglikeST
> ### Title: Compute the Log-likelihood for the Spatio-Temporal Model
> ### Aliases: loglikeST loglikeSTnaive
>
> ### ** Examples
>
> ##load the data
> data(mesa.model)
>
> ##Compute dimensions for the data structure
> dim <- loglikeSTdim(mesa.model)
>
> ##Find out in which order parameters should be given
> loglikeST(NULL, mesa.model)
[1] "log.range.const.exp" "log.sill.const.exp"
[3] "log.range.V1.exp" "log.sill.V1.exp"
[5] "log.range.V2.exp" "log.sill.V2.exp"
[7] "nu.log.range.exp" "nu.log.sill.exp"
[9] "nu.log.nugget.(Intercept).exp" "nu.log.nugget.typeFIXED.exp"
>
> ##Let's create random vectors of values
> x <- runif( dim$nparam.cov )
> x.all <- runif( dim$nparam )
>
> ##Evaluate the log-likelihood for these values
> loglikeST(x.all, mesa.model, "f")
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
SpatioTemporal
--- call from context ---
loglikeST(x.all, mesa.model, "f")
--- call from argument ---
if (class(sigma.B) == "try-error") {
return(-.Machine$double.xmax)
}
--- R stacktrace ---
where 1: loglikeST(x.all, mesa.model, "f")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (x = NULL, STmodel, type = "p", x.fixed = NULL)
{
stCheckClass(STmodel, "STmodel", name = "STmodel")
type <- tolower(type)
x <- stCheckLoglikeIn(x, x.fixed, type)
if (is.null(x) || any(is.na(x))) {
return(loglikeSTnames(STmodel, all = (type == "f")))
}
dimensions <- loglikeSTdim(STmodel)
if ((type == "f" && length(x) != dimensions$nparam) || (type !=
"f" && length(x) != dimensions$nparam.cov)) {
stop("Number of parameters, length(x), incorrect.")
}
tmp <- loglikeSTgetPars(x, STmodel)
if (type == "f") {
gamma <- tmp$gamma
alpha <- tmp$alpha
}
cov.pars.beta <- tmp$cov.beta
cov.pars.nu <- tmp$cov.nu
Y <- STmodel$obs$obs
F <- expandF(STmodel$F, STmodel$obs$idx, n.loc = dimensions$n.obs)
if (type == "f") {
mu.B <- matrix(calc.mu.B(STmodel$LUR, alpha), ncol = 1)
if (dimensions$L != 0) {
Y <- Y - STmodel$ST %*% gamma
}
}
sigma.B <- makeSigmaB(cov.pars.beta$pars, dist = STmodel$D.beta,
type = STmodel$cov.beta$covf, nugget = cov.pars.beta$nugget)
sigma.nu <- makeSigmaNu(cov.pars.nu$pars, dist = STmodel$D.nu,
type = STmodel$cov.nu$covf, nugget = cov.pars.nu$nugget,
random.effect = cov.pars.nu$random.effect, blocks1 = STmodel$nt,
ind1 = STmodel$obs$idx, sparse = TRUE)
sigma.B <- try(makeCholBlock(sigma.B, n.blocks = dimensions$m),
silent = TRUE)
if (class(sigma.B) == "try-error") {
return(-.Machine$double.xmax)
}
sigma.nu <- try(chol(sigma.nu), silent = TRUE)
if (class(sigma.nu) == "try-error") {
return(-.Machine$double.xmax)
}
l <- -sumLogDiag(sigma.B)
l <- l - sumLog(diag(sigma.nu))
sigma.B <- invCholBlock(sigma.B, n.blocks = dimensions$m)
sigma.nu <- chol2inv(sigma.nu)
i.sR.Y <- as.matrix(sigma.nu %*% Y)
if (type == "f") {
i.sB.mu.B <- blockMult(sigma.B, mu.B, n.blocks = dimensions$m)
l <- l - dotProd(i.sB.mu.B, mu.B)/2
l <- l - dotProd(i.sR.Y, Y)/2
}
else {
iS.X <- calc.iS.X(STmodel$LUR, sigma.B)
if (dimensions$L != 0) {
i.sR.M <- as.matrix(sigma.nu %*% STmodel$ST)
}
F.i.sR.Y <- calc.tFX(STmodel$F, i.sR.Y, STmodel$obs$idx,
n.loc = dimensions$n.obs)
if (dimensions$L != 0) {
F.i.sR.M <- calc.tFX(STmodel$F, i.sR.M, STmodel$obs$idx,
n.loc = dimensions$n.obs)
}
}
sigma.B.Y <- as.matrix(t(F) %*% sigma.nu %*% F) + sigma.B
sigma.B.Y <- try(chol(sigma.B.Y), silent = TRUE)
if (class(sigma.B.Y) == "try-error") {
return(-.Machine$double.xmax)
}
l <- l - sumLogDiag(sigma.B.Y)
if (type == "f") {
mu.B.Y <- i.sB.mu.B + calc.tFX(STmodel$F, i.sR.Y, STmodel$obs$idx,
n.loc = dimensions$n.obs)
mu.B.Y <- solveTriBlock(sigma.B.Y, mu.B.Y, transpose = TRUE)
l <- l + norm2(mu.B.Y)/2
}
else {
Y.hat <- solveTriBlock(sigma.B.Y, F.i.sR.Y, transpose = TRUE)
if (dimensions$L != 0) {
M.hat <- solveTriBlock(sigma.B.Y, F.i.sR.M, transpose = TRUE)
}
sigma.B.Y <- invCholBlock(sigma.B.Y)
sigma.B.Y.iS.X <- sigma.B.Y %*% iS.X
i.sigma.alpha.Y <- -t(iS.X) %*% sigma.B.Y.iS.X + calc.X.iS.X(STmodel$LUR,
iS.X)
i.sigma.alpha.Y <- try(chol(i.sigma.alpha.Y), silent = TRUE)
if (class(i.sigma.alpha.Y) == "try-error") {
return(-.Machine$double.xmax)
}
if (type == "r") {
l <- l - sumLogDiag(i.sigma.alpha.Y)
}
Y.hat.2 <- t(sigma.B.Y.iS.X) %*% F.i.sR.Y
Y.hat.2 <- solveTriBlock(i.sigma.alpha.Y, Y.hat.2, transpose = TRUE)
Y.sigma.hat.Y <- dotProd(Y, i.sR.Y) - norm2(Y.hat) -
norm2(Y.hat.2)
l <- l - Y.sigma.hat.Y/2
if (dimensions$L != 0) {
M.hat.2 <- t(sigma.B.Y.iS.X) %*% F.i.sR.M
M.hat.2 <- solveTriBlock(i.sigma.alpha.Y, M.hat.2,
transpose = TRUE)
Y.sigma.hat.M <- (t(Y) %*% i.sR.M - t(Y.hat) %*%
M.hat - t(Y.hat.2) %*% M.hat.2)
Y.sigma.hat.M <- t(Y.sigma.hat.M)
M.sigma.hat.M <- (t(STmodel$ST) %*% i.sR.M - t(M.hat) %*%
M.hat - t(M.hat.2) %*% M.hat.2)
M.sigma.hat.M <- try(chol(M.sigma.hat.M), silent = TRUE)
if (class(M.sigma.hat.M) == "try-error") {
return(-.Machine$double.xmax)
}
if (type == "r") {
l <- l - sumLogDiag(M.sigma.hat.M)
}
Y.sigma.hat.M <- solveTriBlock(M.sigma.hat.M, Y.sigma.hat.M,
transpose = TRUE)
l <- l + norm2(Y.sigma.hat.M)/2
}
}
l <- as.double(l)
if (!is.finite(l))
l <- -.Machine$double.xmax
return(l)
}
<bytecode: 0x45a7350>
<environment: namespace:SpatioTemporal>
--- function search by body ---
Function loglikeST in namespace SpatioTemporal has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(sigma.B) == "try-error") { :
the condition has length > 1
Calls: loglikeST
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.1.9.1
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building ‘ST_intro.Rnw’ using Sweave
Loading required package: Matrix
Replacing existing trend.
Replacing existing trend.
Replacing existing trend.
--- finished re-building ‘ST_intro.Rnw’
--- re-building ‘ST_tutorial.Rnw’ using Sweave
Loading required package: Matrix
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
SpatioTemporal
--- call from context ---
loglikeST(est.mesa.model$res.best$par, mesa.model)
--- call from argument ---
if (class(sigma.B) == "try-error") {
return(-.Machine$double.xmax)
}
--- R stacktrace ---
where 1: loglikeST(est.mesa.model$res.best$par, mesa.model)
where 2: eval(expr, .GlobalEnv)
where 3: eval(expr, .GlobalEnv)
where 4: withVisible(eval(expr, .GlobalEnv))
where 5: doTryCatch(return(expr), name, parentenv, handler)
where 6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 7: tryCatchList(expr, classes, parentenv, handlers)
where 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)[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 9: try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE)
where 10: evalFunc(ce, options)
where 11: tryCatchList(expr, classes, parentenv, handlers)
where 12: tryCatch(evalFunc(ce, options), finally = {
cat("\n")
sink()
})
where 13: driver$runcode(drobj, chunk, chunkopts)
where 14: utils::Sweave(...)
where 15: engine$weave(file, quiet = quiet, encoding = enc)
where 16: doTryCatch(return(expr), name, parentenv, handler)
where 17: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 18: tryCatchList(expr, classes, parentenv, handlers)
where 19: tryCatch({
engine$weave(file, quiet = quiet, encoding = enc)
setwd(startdir)
output <- find_vignette_product(name, by = "weave", engine = engine)
if (!have.makefile && vignette_is_tex(output)) {
texi2pdf(file = output, clean = FALSE, quiet = quiet)
output <- find_vignette_product(name, by = "texi2pdf",
engine = engine)
}
}, error = function(e) {
OK <<- FALSE
message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",
file, conditionMessage(e)))
})
where 20: tools:::.buildOneVignette("ST_tutorial.Rnw", "/data/gannet/ripley/R/packages/tests-clang/SpatioTemporal.Rcheck/vign_test/SpatioTemporal",
TRUE, FALSE, "ST_tutorial", "", "/tmp/RtmppF5fxJ/working_dir/RtmpzzI0IQ/file961553153cab.rds")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (x = NULL, STmodel, type = "p", x.fixed = NULL)
{
stCheckClass(STmodel, "STmodel", name = "STmodel")
type <- tolower(type)
x <- stCheckLoglikeIn(x, x.fixed, type)
if (is.null(x) || any(is.na(x))) {
return(loglikeSTnames(STmodel, all = (type == "f")))
}
dimensions <- loglikeSTdim(STmodel)
if ((type == "f" && length(x) != dimensions$nparam) || (type !=
"f" && length(x) != dimensions$nparam.cov)) {
stop("Number of parameters, length(x), incorrect.")
}
tmp <- loglikeSTgetPars(x, STmodel)
if (type == "f") {
gamma <- tmp$gamma
alpha <- tmp$alpha
}
cov.pars.beta <- tmp$cov.beta
cov.pars.nu <- tmp$cov.nu
Y <- STmodel$obs$obs
F <- expandF(STmodel$F, STmodel$obs$idx, n.loc = dimensions$n.obs)
if (type == "f") {
mu.B <- matrix(calc.mu.B(STmodel$LUR, alpha), ncol = 1)
if (dimensions$L != 0) {
Y <- Y - STmodel$ST %*% gamma
}
}
sigma.B <- makeSigmaB(cov.pars.beta$pars, dist = STmodel$D.beta,
type = STmodel$cov.beta$covf, nugget = cov.pars.beta$nugget)
sigma.nu <- makeSigmaNu(cov.pars.nu$pars, dist = STmodel$D.nu,
type = STmodel$cov.nu$covf, nugget = cov.pars.nu$nugget,
random.effect = cov.pars.nu$random.effect, blocks1 = STmodel$nt,
ind1 = STmodel$obs$idx, sparse = TRUE)
sigma.B <- try(makeCholBlock(sigma.B, n.blocks = dimensions$m),
silent = TRUE)
if (class(sigma.B) == "try-error") {
return(-.Machine$double.xmax)
}
sigma.nu <- try(chol(sigma.nu), silent = TRUE)
if (class(sigma.nu) == "try-error") {
return(-.Machine$double.xmax)
}
l <- -sumLogDiag(sigma.B)
l <- l - sumLog(diag(sigma.nu))
sigma.B <- invCholBlock(sigma.B, n.blocks = dimensions$m)
sigma.nu <- chol2inv(sigma.nu)
i.sR.Y <- as.matrix(sigma.nu %*% Y)
if (type == "f") {
i.sB.mu.B <- blockMult(sigma.B, mu.B, n.blocks = dimensions$m)
l <- l - dotProd(i.sB.mu.B, mu.B)/2
l <- l - dotProd(i.sR.Y, Y)/2
}
else {
iS.X <- calc.iS.X(STmodel$LUR, sigma.B)
if (dimensions$L != 0) {
i.sR.M <- as.matrix(sigma.nu %*% STmodel$ST)
}
F.i.sR.Y <- calc.tFX(STmodel$F, i.sR.Y, STmodel$obs$idx,
n.loc = dimensions$n.obs)
if (dimensions$L != 0) {
F.i.sR.M <- calc.tFX(STmodel$F, i.sR.M, STmodel$obs$idx,
n.loc = dimensions$n.obs)
}
}
sigma.B.Y <- as.matrix(t(F) %*% sigma.nu %*% F) + sigma.B
sigma.B.Y <- try(chol(sigma.B.Y), silent = TRUE)
if (class(sigma.B.Y) == "try-error") {
return(-.Machine$double.xmax)
}
l <- l - sumLogDiag(sigma.B.Y)
if (type == "f") {
mu.B.Y <- i.sB.mu.B + calc.tFX(STmodel$F, i.sR.Y, STmodel$obs$idx,
n.loc = dimensions$n.obs)
mu.B.Y <- solveTriBlock(sigma.B.Y, mu.B.Y, transpose = TRUE)
l <- l + norm2(mu.B.Y)/2
}
else {
Y.hat <- solveTriBlock(sigma.B.Y, F.i.sR.Y, transpose = TRUE)
if (dimensions$L != 0) {
M.hat <- solveTriBlock(sigma.B.Y, F.i.sR.M, transpose = TRUE)
}
sigma.B.Y <- invCholBlock(sigma.B.Y)
sigma.B.Y.iS.X <- sigma.B.Y %*% iS.X
i.sigma.alpha.Y <- -t(iS.X) %*% sigma.B.Y.iS.X + calc.X.iS.X(STmodel$LUR,
iS.X)
i.sigma.alpha.Y <- try(chol(i.sigma.alpha.Y), silent = TRUE)
if (class(i.sigma.alpha.Y) == "try-error") {
return(-.Machine$double.xmax)
}
if (type == "r") {
l <- l - sumLogDiag(i.sigma.alpha.Y)
}
Y.hat.2 <- t(sigma.B.Y.iS.X) %*% F.i.sR.Y
Y.hat.2 <- solveTriBlock(i.sigma.alpha.Y, Y.hat.2, transpose = TRUE)
Y.sigma.hat.Y <- dotProd(Y, i.sR.Y) - norm2(Y.hat) -
norm2(Y.hat.2)
l <- l - Y.sigma.hat.Y/2
if (dimensions$L != 0) {
M.hat.2 <- t(sigma.B.Y.iS.X) %*% F.i.sR.M
M.hat.2 <- solveTriBlock(i.sigma.alpha.Y, M.hat.2,
transpose = TRUE)
Y.sigma.hat.M <- (t(Y) %*% i.sR.M - t(Y.hat) %*%
M.hat - t(Y.hat.2) %*% M.hat.2)
Y.sigma.hat.M <- t(Y.sigma.hat.M)
M.sigma.hat.M <- (t(STmodel$ST) %*% i.sR.M - t(M.hat) %*%
M.hat - t(M.hat.2) %*% M.hat.2)
M.sigma.hat.M <- try(chol(M.sigma.hat.M), silent = TRUE)
if (class(M.sigma.hat.M) == "try-error") {
return(-.Machine$double.xmax)
}
if (type == "r") {
l <- l - sumLogDiag(M.sigma.hat.M)
}
Y.sigma.hat.M <- solveTriBlock(M.sigma.hat.M, Y.sigma.hat.M,
transpose = TRUE)
l <- l + norm2(Y.sigma.hat.M)/2
}
}
l <- as.double(l)
if (!is.finite(l))
l <- -.Machine$double.xmax
return(l)
}
<bytecode: 0x988ab08>
<environment: namespace:SpatioTemporal>
--- function search by body ---
Function loglikeST in namespace SpatioTemporal has this body.
----------- END OF FAILURE REPORT --------------
Error: processing vignette 'ST_tutorial.Rnw' failed with diagnostics:
chunk 34
Error in if (class(sigma.B) == "try-error") { :
the condition has length > 1
--- failed re-building ‘ST_tutorial.Rnw’
SUMMARY: processing the following file failed:
‘ST_tutorial.Rnw’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.1.9.1
Check: examples
Result: ERROR
Running examples in ‘SpatioTemporal-Ex.R’ failed
The error most likely occurred in:
> ### Name: loglikeST
> ### Title: Compute the Log-likelihood for the Spatio-Temporal Model
> ### Aliases: loglikeST loglikeSTnaive
>
> ### ** Examples
>
> ##load the data
> data(mesa.model)
>
> ##Compute dimensions for the data structure
> dim <- loglikeSTdim(mesa.model)
>
> ##Find out in which order parameters should be given
> loglikeST(NULL, mesa.model)
[1] "log.range.const.exp" "log.sill.const.exp"
[3] "log.range.V1.exp" "log.sill.V1.exp"
[5] "log.range.V2.exp" "log.sill.V2.exp"
[7] "nu.log.range.exp" "nu.log.sill.exp"
[9] "nu.log.nugget.(Intercept).exp" "nu.log.nugget.typeFIXED.exp"
>
> ##Let's create random vectors of values
> x <- runif( dim$nparam.cov )
> x.all <- runif( dim$nparam )
>
> ##Evaluate the log-likelihood for these values
> loglikeST(x.all, mesa.model, "f")
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
SpatioTemporal
--- call from context ---
loglikeST(x.all, mesa.model, "f")
--- call from argument ---
if (class(sigma.B) == "try-error") {
return(-.Machine$double.xmax)
}
--- R stacktrace ---
where 1: loglikeST(x.all, mesa.model, "f")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (x = NULL, STmodel, type = "p", x.fixed = NULL)
{
stCheckClass(STmodel, "STmodel", name = "STmodel")
type <- tolower(type)
x <- stCheckLoglikeIn(x, x.fixed, type)
if (is.null(x) || any(is.na(x))) {
return(loglikeSTnames(STmodel, all = (type == "f")))
}
dimensions <- loglikeSTdim(STmodel)
if ((type == "f" && length(x) != dimensions$nparam) || (type !=
"f" && length(x) != dimensions$nparam.cov)) {
stop("Number of parameters, length(x), incorrect.")
}
tmp <- loglikeSTgetPars(x, STmodel)
if (type == "f") {
gamma <- tmp$gamma
alpha <- tmp$alpha
}
cov.pars.beta <- tmp$cov.beta
cov.pars.nu <- tmp$cov.nu
Y <- STmodel$obs$obs
F <- expandF(STmodel$F, STmodel$obs$idx, n.loc = dimensions$n.obs)
if (type == "f") {
mu.B <- matrix(calc.mu.B(STmodel$LUR, alpha), ncol = 1)
if (dimensions$L != 0) {
Y <- Y - STmodel$ST %*% gamma
}
}
sigma.B <- makeSigmaB(cov.pars.beta$pars, dist = STmodel$D.beta,
type = STmodel$cov.beta$covf, nugget = cov.pars.beta$nugget)
sigma.nu <- makeSigmaNu(cov.pars.nu$pars, dist = STmodel$D.nu,
type = STmodel$cov.nu$covf, nugget = cov.pars.nu$nugget,
random.effect = cov.pars.nu$random.effect, blocks1 = STmodel$nt,
ind1 = STmodel$obs$idx, sparse = TRUE)
sigma.B <- try(makeCholBlock(sigma.B, n.blocks = dimensions$m),
silent = TRUE)
if (class(sigma.B) == "try-error") {
return(-.Machine$double.xmax)
}
sigma.nu <- try(chol(sigma.nu), silent = TRUE)
if (class(sigma.nu) == "try-error") {
return(-.Machine$double.xmax)
}
l <- -sumLogDiag(sigma.B)
l <- l - sumLog(diag(sigma.nu))
sigma.B <- invCholBlock(sigma.B, n.blocks = dimensions$m)
sigma.nu <- chol2inv(sigma.nu)
i.sR.Y <- as.matrix(sigma.nu %*% Y)
if (type == "f") {
i.sB.mu.B <- blockMult(sigma.B, mu.B, n.blocks = dimensions$m)
l <- l - dotProd(i.sB.mu.B, mu.B)/2
l <- l - dotProd(i.sR.Y, Y)/2
}
else {
iS.X <- calc.iS.X(STmodel$LUR, sigma.B)
if (dimensions$L != 0) {
i.sR.M <- as.matrix(sigma.nu %*% STmodel$ST)
}
F.i.sR.Y <- calc.tFX(STmodel$F, i.sR.Y, STmodel$obs$idx,
n.loc = dimensions$n.obs)
if (dimensions$L != 0) {
F.i.sR.M <- calc.tFX(STmodel$F, i.sR.M, STmodel$obs$idx,
n.loc = dimensions$n.obs)
}
}
sigma.B.Y <- as.matrix(t(F) %*% sigma.nu %*% F) + sigma.B
sigma.B.Y <- try(chol(sigma.B.Y), silent = TRUE)
if (class(sigma.B.Y) == "try-error") {
return(-.Machine$double.xmax)
}
l <- l - sumLogDiag(sigma.B.Y)
if (type == "f") {
mu.B.Y <- i.sB.mu.B + calc.tFX(STmodel$F, i.sR.Y, STmodel$obs$idx,
n.loc = dimensions$n.obs)
mu.B.Y <- solveTriBlock(sigma.B.Y, mu.B.Y, transpose = TRUE)
l <- l + norm2(mu.B.Y)/2
}
else {
Y.hat <- solveTriBlock(sigma.B.Y, F.i.sR.Y, transpose = TRUE)
if (dimensions$L != 0) {
M.hat <- solveTriBlock(sigma.B.Y, F.i.sR.M, transpose = TRUE)
}
sigma.B.Y <- invCholBlock(sigma.B.Y)
sigma.B.Y.iS.X <- sigma.B.Y %*% iS.X
i.sigma.alpha.Y <- -t(iS.X) %*% sigma.B.Y.iS.X + calc.X.iS.X(STmodel$LUR,
iS.X)
i.sigma.alpha.Y <- try(chol(i.sigma.alpha.Y), silent = TRUE)
if (class(i.sigma.alpha.Y) == "try-error") {
return(-.Machine$double.xmax)
}
if (type == "r") {
l <- l - sumLogDiag(i.sigma.alpha.Y)
}
Y.hat.2 <- t(sigma.B.Y.iS.X) %*% F.i.sR.Y
Y.hat.2 <- solveTriBlock(i.sigma.alpha.Y, Y.hat.2, transpose = TRUE)
Y.sigma.hat.Y <- dotProd(Y, i.sR.Y) - norm2(Y.hat) -
norm2(Y.hat.2)
l <- l - Y.sigma.hat.Y/2
if (dimensions$L != 0) {
M.hat.2 <- t(sigma.B.Y.iS.X) %*% F.i.sR.M
M.hat.2 <- solveTriBlock(i.sigma.alpha.Y, M.hat.2,
transpose = TRUE)
Y.sigma.hat.M <- (t(Y) %*% i.sR.M - t(Y.hat) %*%
M.hat - t(Y.hat.2) %*% M.hat.2)
Y.sigma.hat.M <- t(Y.sigma.hat.M)
M.sigma.hat.M <- (t(STmodel$ST) %*% i.sR.M - t(M.hat) %*%
M.hat - t(M.hat.2) %*% M.hat.2)
M.sigma.hat.M <- try(chol(M.sigma.hat.M), silent = TRUE)
if (class(M.sigma.hat.M) == "try-error") {
return(-.Machine$double.xmax)
}
if (type == "r") {
l <- l - sumLogDiag(M.sigma.hat.M)
}
Y.sigma.hat.M <- solveTriBlock(M.sigma.hat.M, Y.sigma.hat.M,
transpose = TRUE)
l <- l + norm2(Y.sigma.hat.M)/2
}
}
l <- as.double(l)
if (!is.finite(l))
l <- -.Machine$double.xmax
return(l)
}
<bytecode: 0x2a8ff40>
<environment: namespace:SpatioTemporal>
--- function search by body ---
Function loglikeST in namespace SpatioTemporal has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(sigma.B) == "try-error") { :
the condition has length > 1
Calls: loglikeST
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 1.1.9.1
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building ‘ST_intro.Rnw’ using Sweave
Loading required package: Matrix
Replacing existing trend.
Replacing existing trend.
Replacing existing trend.
--- finished re-building ‘ST_intro.Rnw’
--- re-building ‘ST_tutorial.Rnw’ using Sweave
Loading required package: Matrix
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
SpatioTemporal
--- call from context ---
loglikeST(est.mesa.model$res.best$par, mesa.model)
--- call from argument ---
if (class(sigma.B) == "try-error") {
return(-.Machine$double.xmax)
}
--- R stacktrace ---
where 1: loglikeST(est.mesa.model$res.best$par, mesa.model)
where 2: eval(expr, .GlobalEnv)
where 3: eval(expr, .GlobalEnv)
where 4: withVisible(eval(expr, .GlobalEnv))
where 5: doTryCatch(return(expr), name, parentenv, handler)
where 6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 7: tryCatchList(expr, classes, parentenv, handlers)
where 8: tryCatch(expr, error = function(e) {
call <- conditionCall(e)
if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L)
dcall <- deparse(call)[1L]
prefix <- paste("Error in", dcall, ": ")
LONG <- 75L
sm <- strsplit(conditionMessage(e), "\n")[[1L]]
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
if (is.na(w))
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
type = "b")
if (w > LONG)
prefix <- paste0(prefix, "\n ")
}
else prefix <- "Error : "
msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L]))
if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile)
.Internal(printDeferredWarnings())
}
invisible(structure(msg, class = "try-error", condition = e))
})
where 9: try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE)
where 10: evalFunc(ce, options)
where 11: tryCatchList(expr, classes, parentenv, handlers)
where 12: tryCatch(evalFunc(ce, options), finally = {
cat("\n")
sink()
})
where 13: driver$runcode(drobj, chunk, chunkopts)
where 14: utils::Sweave(...)
where 15: engine$weave(file, quiet = quiet, encoding = enc)
where 16: doTryCatch(return(expr), name, parentenv, handler)
where 17: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 18: tryCatchList(expr, classes, parentenv, handlers)
where 19: tryCatch({
engine$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)
}
}, error = function(e) {
OK <<- FALSE
message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",
file, conditionMessage(e)))
})
where 20: tools:::.buildOneVignette("ST_tutorial.Rnw", "/data/gannet/ripley/R/packages/tests-devel/SpatioTemporal.Rcheck/vign_test/SpatioTemporal",
TRUE, FALSE, "ST_tutorial", "", "/tmp/RtmptwmPr1/working_dir/RtmprNoxMQ/file37524abe2c59.rds")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (x = NULL, STmodel, type = "p", x.fixed = NULL)
{
stCheckClass(STmodel, "STmodel", name = "STmodel")
type <- tolower(type)
x <- stCheckLoglikeIn(x, x.fixed, type)
if (is.null(x) || any(is.na(x))) {
return(loglikeSTnames(STmodel, all = (type == "f")))
}
dimensions <- loglikeSTdim(STmodel)
if ((type == "f" && length(x) != dimensions$nparam) || (type !=
"f" && length(x) != dimensions$nparam.cov)) {
stop("Number of parameters, length(x), incorrect.")
}
tmp <- loglikeSTgetPars(x, STmodel)
if (type == "f") {
gamma <- tmp$gamma
alpha <- tmp$alpha
}
cov.pars.beta <- tmp$cov.beta
cov.pars.nu <- tmp$cov.nu
Y <- STmodel$obs$obs
F <- expandF(STmodel$F, STmodel$obs$idx, n.loc = dimensions$n.obs)
if (type == "f") {
mu.B <- matrix(calc.mu.B(STmodel$LUR, alpha), ncol = 1)
if (dimensions$L != 0) {
Y <- Y - STmodel$ST %*% gamma
}
}
sigma.B <- makeSigmaB(cov.pars.beta$pars, dist = STmodel$D.beta,
type = STmodel$cov.beta$covf, nugget = cov.pars.beta$nugget)
sigma.nu <- makeSigmaNu(cov.pars.nu$pars, dist = STmodel$D.nu,
type = STmodel$cov.nu$covf, nugget = cov.pars.nu$nugget,
random.effect = cov.pars.nu$random.effect, blocks1 = STmodel$nt,
ind1 = STmodel$obs$idx, sparse = TRUE)
sigma.B <- try(makeCholBlock(sigma.B, n.blocks = dimensions$m),
silent = TRUE)
if (class(sigma.B) == "try-error") {
return(-.Machine$double.xmax)
}
sigma.nu <- try(chol(sigma.nu), silent = TRUE)
if (class(sigma.nu) == "try-error") {
return(-.Machine$double.xmax)
}
l <- -sumLogDiag(sigma.B)
l <- l - sumLog(diag(sigma.nu))
sigma.B <- invCholBlock(sigma.B, n.blocks = dimensions$m)
sigma.nu <- chol2inv(sigma.nu)
i.sR.Y <- as.matrix(sigma.nu %*% Y)
if (type == "f") {
i.sB.mu.B <- blockMult(sigma.B, mu.B, n.blocks = dimensions$m)
l <- l - dotProd(i.sB.mu.B, mu.B)/2
l <- l - dotProd(i.sR.Y, Y)/2
}
else {
iS.X <- calc.iS.X(STmodel$LUR, sigma.B)
if (dimensions$L != 0) {
i.sR.M <- as.matrix(sigma.nu %*% STmodel$ST)
}
F.i.sR.Y <- calc.tFX(STmodel$F, i.sR.Y, STmodel$obs$idx,
n.loc = dimensions$n.obs)
if (dimensions$L != 0) {
F.i.sR.M <- calc.tFX(STmodel$F, i.sR.M, STmodel$obs$idx,
n.loc = dimensions$n.obs)
}
}
sigma.B.Y <- as.matrix(t(F) %*% sigma.nu %*% F) + sigma.B
sigma.B.Y <- try(chol(sigma.B.Y), silent = TRUE)
if (class(sigma.B.Y) == "try-error") {
return(-.Machine$double.xmax)
}
l <- l - sumLogDiag(sigma.B.Y)
if (type == "f") {
mu.B.Y <- i.sB.mu.B + calc.tFX(STmodel$F, i.sR.Y, STmodel$obs$idx,
n.loc = dimensions$n.obs)
mu.B.Y <- solveTriBlock(sigma.B.Y, mu.B.Y, transpose = TRUE)
l <- l + norm2(mu.B.Y)/2
}
else {
Y.hat <- solveTriBlock(sigma.B.Y, F.i.sR.Y, transpose = TRUE)
if (dimensions$L != 0) {
M.hat <- solveTriBlock(sigma.B.Y, F.i.sR.M, transpose = TRUE)
}
sigma.B.Y <- invCholBlock(sigma.B.Y)
sigma.B.Y.iS.X <- sigma.B.Y %*% iS.X
i.sigma.alpha.Y <- -t(iS.X) %*% sigma.B.Y.iS.X + calc.X.iS.X(STmodel$LUR,
iS.X)
i.sigma.alpha.Y <- try(chol(i.sigma.alpha.Y), silent = TRUE)
if (class(i.sigma.alpha.Y) == "try-error") {
return(-.Machine$double.xmax)
}
if (type == "r") {
l <- l - sumLogDiag(i.sigma.alpha.Y)
}
Y.hat.2 <- t(sigma.B.Y.iS.X) %*% F.i.sR.Y
Y.hat.2 <- solveTriBlock(i.sigma.alpha.Y, Y.hat.2, transpose = TRUE)
Y.sigma.hat.Y <- dotProd(Y, i.sR.Y) - norm2(Y.hat) -
norm2(Y.hat.2)
l <- l - Y.sigma.hat.Y/2
if (dimensions$L != 0) {
M.hat.2 <- t(sigma.B.Y.iS.X) %*% F.i.sR.M
M.hat.2 <- solveTriBlock(i.sigma.alpha.Y, M.hat.2,
transpose = TRUE)
Y.sigma.hat.M <- (t(Y) %*% i.sR.M - t(Y.hat) %*%
M.hat - t(Y.hat.2) %*% M.hat.2)
Y.sigma.hat.M <- t(Y.sigma.hat.M)
M.sigma.hat.M <- (t(STmodel$ST) %*% i.sR.M - t(M.hat) %*%
M.hat - t(M.hat.2) %*% M.hat.2)
M.sigma.hat.M <- try(chol(M.sigma.hat.M), silent = TRUE)
if (class(M.sigma.hat.M) == "try-error") {
return(-.Machine$double.xmax)
}
if (type == "r") {
l <- l - sumLogDiag(M.sigma.hat.M)
}
Y.sigma.hat.M <- solveTriBlock(M.sigma.hat.M, Y.sigma.hat.M,
transpose = TRUE)
l <- l + norm2(Y.sigma.hat.M)/2
}
}
l <- as.double(l)
if (!is.finite(l))
l <- -.Machine$double.xmax
return(l)
}
<bytecode: 0x9a928b8>
<environment: namespace:SpatioTemporal>
--- function search by body ---
Function loglikeST in namespace SpatioTemporal has this body.
----------- END OF FAILURE REPORT --------------
Error: processing vignette 'ST_tutorial.Rnw' failed with diagnostics:
chunk 34
Error in if (class(sigma.B) == "try-error") { :
the condition has length > 1
--- failed re-building ‘ST_tutorial.Rnw’
SUMMARY: processing the following file failed:
‘ST_tutorial.Rnw’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc