Last updated on 2020-02-26 18:47:21 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0 | 6.54 | 47.23 | 53.77 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.0 | ERROR | ||||
| r-devel-linux-x86_64-fedora-clang | 1.0 | 65.77 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 1.0 | 65.46 | ERROR | |||
| r-devel-windows-ix86+x86_64 | 1.0 | 12.00 | 64.00 | 76.00 | OK | |
| r-devel-windows-ix86+x86_64-gcc8 | 1.0 | 13.00 | 68.00 | 81.00 | OK | |
| r-patched-linux-x86_64 | 1.0 | 5.23 | 49.55 | 54.78 | OK | |
| r-patched-solaris-x86 | 1.0 | 100.80 | OK | |||
| r-release-linux-x86_64 | 1.0 | 4.96 | 49.39 | 54.35 | OK | |
| r-release-windows-ix86+x86_64 | 1.0 | 10.00 | 63.00 | 73.00 | OK | |
| r-release-osx-x86_64 | 1.0 | OK | ||||
| r-oldrel-windows-ix86+x86_64 | 1.0 | 9.00 | 62.00 | 71.00 | OK | |
| r-oldrel-osx-x86_64 | 1.0 | OK |
Version: 1.0
Check: examples
Result: ERROR
Running examples in 'jmdem-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: anova.jmdem
> ### Title: Analysis of Deviance for Joint Mean and Dispersion Effect Models
> ### Fits
> ### Aliases: anova.jmdem
>
> ### ** Examples
>
> ## Example in jmdem(...)
> MyData <- simdata.jmdem.sim(mformula = y ~ x, dformula = ~ z,
+ mfamily = poisson(),
+ dfamily = Gamma(link = "log"),
+ beta.true = c(0.5, 4),
+ lambda.true = c(2.5, 3), n = 100)
>
> fit <- jmdem(mformula = y ~ x, dformula = ~ z, data = MyData,
+ mfamily = poisson, dfamily = Gamma(link = "log"),
+ dev.type = "deviance", method = "CG")
>
> ## Run a partial analysis (type 3) with Wald test
> anova(fit, test = "Wald", type = 3)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
jmdem
--- call from context ---
minv(object2$info.matrix)
--- call from argument ---
if (!class(ans) == "try-error") {
not.ok <- any(diag(ans) < 0) | any(eigen(ans)$values < 0)
} else {
not.ok <- TRUE
}
--- R stacktrace ---
where 1: minv(object2$info.matrix)
where 2: solve(m)
where 3: doTryCatch(return(expr), name, parentenv, handler)
where 4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 5: tryCatchList(expr, classes, parentenv, handlers)
where 6: tryCatch(expr, error = function(e) {
call <- conditionCall(e)
if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L)
dcall <- deparse(call)[1L]
prefix <- paste("Error in", dcall, ": ")
LONG <- 75L
sm <- strsplit(conditionMessage(e), "\n")[[1L]]
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
if (is.na(w))
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
type = "b")
if (w > LONG)
prefix <- paste0(prefix, "\n ")
}
else prefix <- "Error : "
msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L]))
if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile)
.Internal(printDeferredWarnings())
}
invisible(structure(msg, class = "try-error", condition = e))
})
where 7: try(solve(m), silent = TRUE)
where 8: minv(t(par0) %*% minv(object2$info.matrix)$inv %*% par0)
where 9: wald.jmdem(test.list)
where 10: anova.jmdem(fit, test = "Wald", type = 3)
where 11: anova(fit, test = "Wald", type = 3)
--- value of length: 2 type: logical ---
[1] TRUE TRUE
--- function from context ---
function (m, minv.method = NULL, tol = sqrt(.Machine$double.eps))
{
if (!is.null(minv.method)) {
ans <- try(do.call(minv.method, list(m)), silent = TRUE)
if (minv.method == "solve") {
ansnam <- "inverse"
}
else if (minv.method == "chol2inv") {
ansnam <- "inverse from Choleski decomposition"
}
else {
ansnam <- "generalised inverse"
}
}
else {
ans <- try(solve(m), silent = TRUE)
ansnam <- "inverse"
if (!class(ans) == "try-error") {
not.ok <- any(diag(ans) < 0) | any(eigen(ans)$values <
0)
}
else {
not.ok <- TRUE
}
if (not.ok) {
ans <- try(chol2inv(m), silent = TRUE)
ansnam <- "inverse from Choleski decomposition"
if (!class(ans) == "try-error") {
not.ok <- any(diag(ans) < 0) | any(eigen(ans)$values <
0)
}
else {
not.ok <- TRUE
}
if (not.ok) {
ans <- try(ginv(m), silent = TRUE)
ansnam <- "generalised inverse"
}
}
}
return(list(inv = ans, inv.nam = ansnam))
}
<bytecode: 0x6fa5780>
<environment: namespace:jmdem>
--- function search by body ---
Function minv in namespace jmdem has this body.
----------- END OF FAILURE REPORT --------------
Warning in chol2inv(m) : restarting interrupted promise evaluation
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
jmdem
--- call from context ---
minv(object2$info.matrix)
--- call from argument ---
if (!class(ans) == "try-error") {
not.ok <- any(diag(ans) < 0) | any(eigen(ans)$values < 0)
} else {
not.ok <- TRUE
}
--- R stacktrace ---
where 1: minv(object2$info.matrix)
where 2: chol2inv(m)
where 3: doTryCatch(return(expr), name, parentenv, handler)
where 4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 5: tryCatchList(expr, classes, parentenv, handlers)
where 6: tryCatch(expr, error = function(e) {
call <- conditionCall(e)
if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L)
dcall <- deparse(call)[1L]
prefix <- paste("Error in", dcall, ": ")
LONG <- 75L
sm <- strsplit(conditionMessage(e), "\n")[[1L]]
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
if (is.na(w))
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
type = "b")
if (w > LONG)
prefix <- paste0(prefix, "\n ")
}
else prefix <- "Error : "
msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L]))
if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile)
.Internal(printDeferredWarnings())
}
invisible(structure(msg, class = "try-error", condition = e))
})
where 7: try(chol2inv(m), silent = TRUE)
where 8: minv(t(par0) %*% minv(object2$info.matrix)$inv %*% par0)
where 9: wald.jmdem(test.list)
where 10: anova.jmdem(fit, test = "Wald", type = 3)
where 11: anova(fit, test = "Wald", type = 3)
--- value of length: 2 type: logical ---
[1] TRUE TRUE
--- function from context ---
function (m, minv.method = NULL, tol = sqrt(.Machine$double.eps))
{
if (!is.null(minv.method)) {
ans <- try(do.call(minv.method, list(m)), silent = TRUE)
if (minv.method == "solve") {
ansnam <- "inverse"
}
else if (minv.method == "chol2inv") {
ansnam <- "inverse from Choleski decomposition"
}
else {
ansnam <- "generalised inverse"
}
}
else {
ans <- try(solve(m), silent = TRUE)
ansnam <- "inverse"
if (!class(ans) == "try-error") {
not.ok <- any(diag(ans) < 0) | any(eigen(ans)$values <
0)
}
else {
not.ok <- TRUE
}
if (not.ok) {
ans <- try(chol2inv(m), silent = TRUE)
ansnam <- "inverse from Choleski decomposition"
if (!class(ans) == "try-error") {
not.ok <- any(diag(ans) < 0) | any(eigen(ans)$values <
0)
}
else {
not.ok <- TRUE
}
if (not.ok) {
ans <- try(ginv(m), silent = TRUE)
ansnam <- "generalised inverse"
}
}
}
return(list(inv = ans, inv.nam = ansnam))
}
<bytecode: 0x6fa5780>
<environment: namespace:jmdem>
--- function search by body ---
Function minv in namespace jmdem has this body.
----------- END OF FAILURE REPORT --------------
Warning in ginv(m) : restarting interrupted promise evaluation
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
jmdem
--- call from context ---
minv(object2$info.matrix)
--- call from argument ---
if (!class(ans) == "try-error") {
not.ok <- any(diag(ans) < 0) | any(eigen(ans)$values < 0)
} else {
not.ok <- TRUE
}
--- R stacktrace ---
where 1: minv(object2$info.matrix)
where 2: ginv(m)
where 3: doTryCatch(return(expr), name, parentenv, handler)
where 4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 5: tryCatchList(expr, classes, parentenv, handlers)
where 6: tryCatch(expr, error = function(e) {
call <- conditionCall(e)
if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L)
dcall <- deparse(call)[1L]
prefix <- paste("Error in", dcall, ": ")
LONG <- 75L
sm <- strsplit(conditionMessage(e), "\n")[[1L]]
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
if (is.na(w))
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
type = "b")
if (w > LONG)
prefix <- paste0(prefix, "\n ")
}
else prefix <- "Error : "
msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L]))
if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile)
.Internal(printDeferredWarnings())
}
invisible(structure(msg, class = "try-error", condition = e))
})
where 7: try(ginv(m), silent = TRUE)
where 8: minv(t(par0) %*% minv(object2$info.matrix)$inv %*% par0)
where 9: wald.jmdem(test.list)
where 10: anova.jmdem(fit, test = "Wald", type = 3)
where 11: anova(fit, test = "Wald", type = 3)
--- value of length: 2 type: logical ---
[1] TRUE TRUE
--- function from context ---
function (m, minv.method = NULL, tol = sqrt(.Machine$double.eps))
{
if (!is.null(minv.method)) {
ans <- try(do.call(minv.method, list(m)), silent = TRUE)
if (minv.method == "solve") {
ansnam <- "inverse"
}
else if (minv.method == "chol2inv") {
ansnam <- "inverse from Choleski decomposition"
}
else {
ansnam <- "generalised inverse"
}
}
else {
ans <- try(solve(m), silent = TRUE)
ansnam <- "inverse"
if (!class(ans) == "try-error") {
not.ok <- any(diag(ans) < 0) | any(eigen(ans)$values <
0)
}
else {
not.ok <- TRUE
}
if (not.ok) {
ans <- try(chol2inv(m), silent = TRUE)
ansnam <- "inverse from Choleski decomposition"
if (!class(ans) == "try-error") {
not.ok <- any(diag(ans) < 0) | any(eigen(ans)$values <
0)
}
else {
not.ok <- TRUE
}
if (not.ok) {
ans <- try(ginv(m), silent = TRUE)
ansnam <- "generalised inverse"
}
}
}
return(list(inv = ans, inv.nam = ansnam))
}
<bytecode: 0x6fa5780>
<environment: namespace:jmdem>
--- function search by body ---
Function minv in namespace jmdem has this body.
----------- END OF FAILURE REPORT --------------
Error in t(g0) %*% i0 : requires numeric/complex matrix/vector arguments
Calls: anova -> anova.jmdem -> wald.jmdem
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.0
Check: examples
Result: ERROR
Running examples in ‘jmdem-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: anova.jmdem
> ### Title: Analysis of Deviance for Joint Mean and Dispersion Effect Models
> ### Fits
> ### Aliases: anova.jmdem
>
> ### ** Examples
>
> ## Example in jmdem(...)
> MyData <- simdata.jmdem.sim(mformula = y ~ x, dformula = ~ z,
+ mfamily = poisson(),
+ dfamily = Gamma(link = "log"),
+ beta.true = c(0.5, 4),
+ lambda.true = c(2.5, 3), n = 100)
>
> fit <- jmdem(mformula = y ~ x, dformula = ~ z, data = MyData,
+ mfamily = poisson, dfamily = Gamma(link = "log"),
+ dev.type = "deviance", method = "CG")
>
> ## Run a partial analysis (type 3) with Wald test
> anova(fit, test = "Wald", type = 3)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
jmdem
--- call from context ---
minv(object2$info.matrix)
--- call from argument ---
if (!class(ans) == "try-error") {
not.ok <- any(diag(ans) < 0) | any(eigen(ans)$values < 0)
} else {
not.ok <- TRUE
}
--- R stacktrace ---
where 1: minv(object2$info.matrix)
where 2: solve(m)
where 3: doTryCatch(return(expr), name, parentenv, handler)
where 4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 5: tryCatchList(expr, classes, parentenv, handlers)
where 6: tryCatch(expr, error = function(e) {
call <- conditionCall(e)
if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L)
dcall <- deparse(call)[1L]
prefix <- paste("Error in", dcall, ": ")
LONG <- 75L
sm <- strsplit(conditionMessage(e), "\n")[[1L]]
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
if (is.na(w))
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
type = "b")
if (w > LONG)
prefix <- paste0(prefix, "\n ")
}
else prefix <- "Error : "
msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L]))
if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile)
.Internal(printDeferredWarnings())
}
invisible(structure(msg, class = "try-error", condition = e))
})
where 7: try(solve(m), silent = TRUE)
where 8: minv(t(par0) %*% minv(object2$info.matrix)$inv %*% par0)
where 9: wald.jmdem(test.list)
where 10: anova.jmdem(fit, test = "Wald", type = 3)
where 11: anova(fit, test = "Wald", type = 3)
--- value of length: 2 type: logical ---
[1] TRUE TRUE
--- function from context ---
function (m, minv.method = NULL, tol = sqrt(.Machine$double.eps))
{
if (!is.null(minv.method)) {
ans <- try(do.call(minv.method, list(m)), silent = TRUE)
if (minv.method == "solve") {
ansnam <- "inverse"
}
else if (minv.method == "chol2inv") {
ansnam <- "inverse from Choleski decomposition"
}
else {
ansnam <- "generalised inverse"
}
}
else {
ans <- try(solve(m), silent = TRUE)
ansnam <- "inverse"
if (!class(ans) == "try-error") {
not.ok <- any(diag(ans) < 0) | any(eigen(ans)$values <
0)
}
else {
not.ok <- TRUE
}
if (not.ok) {
ans <- try(chol2inv(m), silent = TRUE)
ansnam <- "inverse from Choleski decomposition"
if (!class(ans) == "try-error") {
not.ok <- any(diag(ans) < 0) | any(eigen(ans)$values <
0)
}
else {
not.ok <- TRUE
}
if (not.ok) {
ans <- try(ginv(m), silent = TRUE)
ansnam <- "generalised inverse"
}
}
}
return(list(inv = ans, inv.nam = ansnam))
}
<bytecode: 0x563767d8ef40>
<environment: namespace:jmdem>
--- function search by body ---
Function minv in namespace jmdem has this body.
----------- END OF FAILURE REPORT --------------
Warning in chol2inv(m) : restarting interrupted promise evaluation
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
jmdem
--- call from context ---
minv(object2$info.matrix)
--- call from argument ---
if (!class(ans) == "try-error") {
not.ok <- any(diag(ans) < 0) | any(eigen(ans)$values < 0)
} else {
not.ok <- TRUE
}
--- R stacktrace ---
where 1: minv(object2$info.matrix)
where 2: chol2inv(m)
where 3: doTryCatch(return(expr), name, parentenv, handler)
where 4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 5: tryCatchList(expr, classes, parentenv, handlers)
where 6: tryCatch(expr, error = function(e) {
call <- conditionCall(e)
if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L)
dcall <- deparse(call)[1L]
prefix <- paste("Error in", dcall, ": ")
LONG <- 75L
sm <- strsplit(conditionMessage(e), "\n")[[1L]]
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
if (is.na(w))
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
type = "b")
if (w > LONG)
prefix <- paste0(prefix, "\n ")
}
else prefix <- "Error : "
msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L]))
if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile)
.Internal(printDeferredWarnings())
}
invisible(structure(msg, class = "try-error", condition = e))
})
where 7: try(chol2inv(m), silent = TRUE)
where 8: minv(t(par0) %*% minv(object2$info.matrix)$inv %*% par0)
where 9: wald.jmdem(test.list)
where 10: anova.jmdem(fit, test = "Wald", type = 3)
where 11: anova(fit, test = "Wald", type = 3)
--- value of length: 2 type: logical ---
[1] TRUE TRUE
--- function from context ---
function (m, minv.method = NULL, tol = sqrt(.Machine$double.eps))
{
if (!is.null(minv.method)) {
ans <- try(do.call(minv.method, list(m)), silent = TRUE)
if (minv.method == "solve") {
ansnam <- "inverse"
}
else if (minv.method == "chol2inv") {
ansnam <- "inverse from Choleski decomposition"
}
else {
ansnam <- "generalised inverse"
}
}
else {
ans <- try(solve(m), silent = TRUE)
ansnam <- "inverse"
if (!class(ans) == "try-error") {
not.ok <- any(diag(ans) < 0) | any(eigen(ans)$values <
0)
}
else {
not.ok <- TRUE
}
if (not.ok) {
ans <- try(chol2inv(m), silent = TRUE)
ansnam <- "inverse from Choleski decomposition"
if (!class(ans) == "try-error") {
not.ok <- any(diag(ans) < 0) | any(eigen(ans)$values <
0)
}
else {
not.ok <- TRUE
}
if (not.ok) {
ans <- try(ginv(m), silent = TRUE)
ansnam <- "generalised inverse"
}
}
}
return(list(inv = ans, inv.nam = ansnam))
}
<bytecode: 0x563767d8ef40>
<environment: namespace:jmdem>
--- function search by body ---
Function minv in namespace jmdem has this body.
----------- END OF FAILURE REPORT --------------
Warning in ginv(m) : restarting interrupted promise evaluation
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
jmdem
--- call from context ---
minv(object2$info.matrix)
--- call from argument ---
if (!class(ans) == "try-error") {
not.ok <- any(diag(ans) < 0) | any(eigen(ans)$values < 0)
} else {
not.ok <- TRUE
}
--- R stacktrace ---
where 1: minv(object2$info.matrix)
where 2: ginv(m)
where 3: doTryCatch(return(expr), name, parentenv, handler)
where 4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 5: tryCatchList(expr, classes, parentenv, handlers)
where 6: tryCatch(expr, error = function(e) {
call <- conditionCall(e)
if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L)
dcall <- deparse(call)[1L]
prefix <- paste("Error in", dcall, ": ")
LONG <- 75L
sm <- strsplit(conditionMessage(e), "\n")[[1L]]
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
if (is.na(w))
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
type = "b")
if (w > LONG)
prefix <- paste0(prefix, "\n ")
}
else prefix <- "Error : "
msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L]))
if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile)
.Internal(printDeferredWarnings())
}
invisible(structure(msg, class = "try-error", condition = e))
})
where 7: try(ginv(m), silent = TRUE)
where 8: minv(t(par0) %*% minv(object2$info.matrix)$inv %*% par0)
where 9: wald.jmdem(test.list)
where 10: anova.jmdem(fit, test = "Wald", type = 3)
where 11: anova(fit, test = "Wald", type = 3)
--- value of length: 2 type: logical ---
[1] TRUE TRUE
--- function from context ---
function (m, minv.method = NULL, tol = sqrt(.Machine$double.eps))
{
if (!is.null(minv.method)) {
ans <- try(do.call(minv.method, list(m)), silent = TRUE)
if (minv.method == "solve") {
ansnam <- "inverse"
}
else if (minv.method == "chol2inv") {
ansnam <- "inverse from Choleski decomposition"
}
else {
ansnam <- "generalised inverse"
}
}
else {
ans <- try(solve(m), silent = TRUE)
ansnam <- "inverse"
if (!class(ans) == "try-error") {
not.ok <- any(diag(ans) < 0) | any(eigen(ans)$values <
0)
}
else {
not.ok <- TRUE
}
if (not.ok) {
ans <- try(chol2inv(m), silent = TRUE)
ansnam <- "inverse from Choleski decomposition"
if (!class(ans) == "try-error") {
not.ok <- any(diag(ans) < 0) | any(eigen(ans)$values <
0)
}
else {
not.ok <- TRUE
}
if (not.ok) {
ans <- try(ginv(m), silent = TRUE)
ansnam <- "generalised inverse"
}
}
}
return(list(inv = ans, inv.nam = ansnam))
}
<bytecode: 0x563767d8ef40>
<environment: namespace:jmdem>
--- function search by body ---
Function minv in namespace jmdem has this body.
----------- END OF FAILURE REPORT --------------
Error in t(g0) %*% i0 : requires numeric/complex matrix/vector arguments
Calls: anova -> anova.jmdem -> wald.jmdem
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.0
Check: examples
Result: ERROR
Running examples in ‘jmdem-Ex.R’ failed
The error most likely occurred in:
> ### Name: anova.jmdem
> ### Title: Analysis of Deviance for Joint Mean and Dispersion Effect Models
> ### Fits
> ### Aliases: anova.jmdem
>
> ### ** Examples
>
> ## Example in jmdem(...)
> MyData <- simdata.jmdem.sim(mformula = y ~ x, dformula = ~ z,
+ mfamily = poisson(),
+ dfamily = Gamma(link = "log"),
+ beta.true = c(0.5, 4),
+ lambda.true = c(2.5, 3), n = 100)
>
> fit <- jmdem(mformula = y ~ x, dformula = ~ z, data = MyData,
+ mfamily = poisson, dfamily = Gamma(link = "log"),
+ dev.type = "deviance", method = "CG")
>
> ## Run a partial analysis (type 3) with Wald test
> anova(fit, test = "Wald", type = 3)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
jmdem
--- call from context ---
minv(object2$info.matrix)
--- call from argument ---
if (!class(ans) == "try-error") {
not.ok <- any(diag(ans) < 0) | any(eigen(ans)$values < 0)
} else {
not.ok <- TRUE
}
--- R stacktrace ---
where 1: minv(object2$info.matrix)
where 2: solve(m)
where 3: doTryCatch(return(expr), name, parentenv, handler)
where 4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 5: tryCatchList(expr, classes, parentenv, handlers)
where 6: tryCatch(expr, error = function(e) {
call <- conditionCall(e)
if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L)
dcall <- deparse(call)[1L]
prefix <- paste("Error in", dcall, ": ")
LONG <- 75L
sm <- strsplit(conditionMessage(e), "\n")[[1L]]
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
if (is.na(w))
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
type = "b")
if (w > LONG)
prefix <- paste0(prefix, "\n ")
}
else prefix <- "Error : "
msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L]))
if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile)
.Internal(printDeferredWarnings())
}
invisible(structure(msg, class = "try-error", condition = e))
})
where 7: try(solve(m), silent = TRUE)
where 8: minv(t(par0) %*% minv(object2$info.matrix)$inv %*% par0)
where 9: wald.jmdem(test.list)
where 10: anova.jmdem(fit, test = "Wald", type = 3)
where 11: anova(fit, test = "Wald", type = 3)
--- value of length: 2 type: logical ---
[1] TRUE TRUE
--- function from context ---
function (m, minv.method = NULL, tol = sqrt(.Machine$double.eps))
{
if (!is.null(minv.method)) {
ans <- try(do.call(minv.method, list(m)), silent = TRUE)
if (minv.method == "solve") {
ansnam <- "inverse"
}
else if (minv.method == "chol2inv") {
ansnam <- "inverse from Choleski decomposition"
}
else {
ansnam <- "generalised inverse"
}
}
else {
ans <- try(solve(m), silent = TRUE)
ansnam <- "inverse"
if (!class(ans) == "try-error") {
not.ok <- any(diag(ans) < 0) | any(eigen(ans)$values <
0)
}
else {
not.ok <- TRUE
}
if (not.ok) {
ans <- try(chol2inv(m), silent = TRUE)
ansnam <- "inverse from Choleski decomposition"
if (!class(ans) == "try-error") {
not.ok <- any(diag(ans) < 0) | any(eigen(ans)$values <
0)
}
else {
not.ok <- TRUE
}
if (not.ok) {
ans <- try(ginv(m), silent = TRUE)
ansnam <- "generalised inverse"
}
}
}
return(list(inv = ans, inv.nam = ansnam))
}
<bytecode: 0x7b94590>
<environment: namespace:jmdem>
--- function search by body ---
Function minv in namespace jmdem has this body.
----------- END OF FAILURE REPORT --------------
Warning in chol2inv(m) : restarting interrupted promise evaluation
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
jmdem
--- call from context ---
minv(object2$info.matrix)
--- call from argument ---
if (!class(ans) == "try-error") {
not.ok <- any(diag(ans) < 0) | any(eigen(ans)$values < 0)
} else {
not.ok <- TRUE
}
--- R stacktrace ---
where 1: minv(object2$info.matrix)
where 2: chol2inv(m)
where 3: doTryCatch(return(expr), name, parentenv, handler)
where 4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 5: tryCatchList(expr, classes, parentenv, handlers)
where 6: tryCatch(expr, error = function(e) {
call <- conditionCall(e)
if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L)
dcall <- deparse(call)[1L]
prefix <- paste("Error in", dcall, ": ")
LONG <- 75L
sm <- strsplit(conditionMessage(e), "\n")[[1L]]
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
if (is.na(w))
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
type = "b")
if (w > LONG)
prefix <- paste0(prefix, "\n ")
}
else prefix <- "Error : "
msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L]))
if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile)
.Internal(printDeferredWarnings())
}
invisible(structure(msg, class = "try-error", condition = e))
})
where 7: try(chol2inv(m), silent = TRUE)
where 8: minv(t(par0) %*% minv(object2$info.matrix)$inv %*% par0)
where 9: wald.jmdem(test.list)
where 10: anova.jmdem(fit, test = "Wald", type = 3)
where 11: anova(fit, test = "Wald", type = 3)
--- value of length: 2 type: logical ---
[1] TRUE TRUE
--- function from context ---
function (m, minv.method = NULL, tol = sqrt(.Machine$double.eps))
{
if (!is.null(minv.method)) {
ans <- try(do.call(minv.method, list(m)), silent = TRUE)
if (minv.method == "solve") {
ansnam <- "inverse"
}
else if (minv.method == "chol2inv") {
ansnam <- "inverse from Choleski decomposition"
}
else {
ansnam <- "generalised inverse"
}
}
else {
ans <- try(solve(m), silent = TRUE)
ansnam <- "inverse"
if (!class(ans) == "try-error") {
not.ok <- any(diag(ans) < 0) | any(eigen(ans)$values <
0)
}
else {
not.ok <- TRUE
}
if (not.ok) {
ans <- try(chol2inv(m), silent = TRUE)
ansnam <- "inverse from Choleski decomposition"
if (!class(ans) == "try-error") {
not.ok <- any(diag(ans) < 0) | any(eigen(ans)$values <
0)
}
else {
not.ok <- TRUE
}
if (not.ok) {
ans <- try(ginv(m), silent = TRUE)
ansnam <- "generalised inverse"
}
}
}
return(list(inv = ans, inv.nam = ansnam))
}
<bytecode: 0x7b94590>
<environment: namespace:jmdem>
--- function search by body ---
Function minv in namespace jmdem has this body.
----------- END OF FAILURE REPORT --------------
Warning in ginv(m) : restarting interrupted promise evaluation
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
jmdem
--- call from context ---
minv(object2$info.matrix)
--- call from argument ---
if (!class(ans) == "try-error") {
not.ok <- any(diag(ans) < 0) | any(eigen(ans)$values < 0)
} else {
not.ok <- TRUE
}
--- R stacktrace ---
where 1: minv(object2$info.matrix)
where 2: ginv(m)
where 3: doTryCatch(return(expr), name, parentenv, handler)
where 4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 5: tryCatchList(expr, classes, parentenv, handlers)
where 6: tryCatch(expr, error = function(e) {
call <- conditionCall(e)
if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L)
dcall <- deparse(call)[1L]
prefix <- paste("Error in", dcall, ": ")
LONG <- 75L
sm <- strsplit(conditionMessage(e), "\n")[[1L]]
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
if (is.na(w))
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
type = "b")
if (w > LONG)
prefix <- paste0(prefix, "\n ")
}
else prefix <- "Error : "
msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L]))
if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile)
.Internal(printDeferredWarnings())
}
invisible(structure(msg, class = "try-error", condition = e))
})
where 7: try(ginv(m), silent = TRUE)
where 8: minv(t(par0) %*% minv(object2$info.matrix)$inv %*% par0)
where 9: wald.jmdem(test.list)
where 10: anova.jmdem(fit, test = "Wald", type = 3)
where 11: anova(fit, test = "Wald", type = 3)
--- value of length: 2 type: logical ---
[1] TRUE TRUE
--- function from context ---
function (m, minv.method = NULL, tol = sqrt(.Machine$double.eps))
{
if (!is.null(minv.method)) {
ans <- try(do.call(minv.method, list(m)), silent = TRUE)
if (minv.method == "solve") {
ansnam <- "inverse"
}
else if (minv.method == "chol2inv") {
ansnam <- "inverse from Choleski decomposition"
}
else {
ansnam <- "generalised inverse"
}
}
else {
ans <- try(solve(m), silent = TRUE)
ansnam <- "inverse"
if (!class(ans) == "try-error") {
not.ok <- any(diag(ans) < 0) | any(eigen(ans)$values <
0)
}
else {
not.ok <- TRUE
}
if (not.ok) {
ans <- try(chol2inv(m), silent = TRUE)
ansnam <- "inverse from Choleski decomposition"
if (!class(ans) == "try-error") {
not.ok <- any(diag(ans) < 0) | any(eigen(ans)$values <
0)
}
else {
not.ok <- TRUE
}
if (not.ok) {
ans <- try(ginv(m), silent = TRUE)
ansnam <- "generalised inverse"
}
}
}
return(list(inv = ans, inv.nam = ansnam))
}
<bytecode: 0x7b94590>
<environment: namespace:jmdem>
--- function search by body ---
Function minv in namespace jmdem has this body.
----------- END OF FAILURE REPORT --------------
Error in t(g0) %*% i0 : requires numeric/complex matrix/vector arguments
Calls: anova -> anova.jmdem -> wald.jmdem
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.0
Check: examples
Result: ERROR
Running examples in ‘jmdem-Ex.R’ failed
The error most likely occurred in:
> ### Name: anova.jmdem
> ### Title: Analysis of Deviance for Joint Mean and Dispersion Effect Models
> ### Fits
> ### Aliases: anova.jmdem
>
> ### ** Examples
>
> ## Example in jmdem(...)
> MyData <- simdata.jmdem.sim(mformula = y ~ x, dformula = ~ z,
+ mfamily = poisson(),
+ dfamily = Gamma(link = "log"),
+ beta.true = c(0.5, 4),
+ lambda.true = c(2.5, 3), n = 100)
>
> fit <- jmdem(mformula = y ~ x, dformula = ~ z, data = MyData,
+ mfamily = poisson, dfamily = Gamma(link = "log"),
+ dev.type = "deviance", method = "CG")
>
> ## Run a partial analysis (type 3) with Wald test
> anova(fit, test = "Wald", type = 3)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
jmdem
--- call from context ---
minv(object2$info.matrix)
--- call from argument ---
if (!class(ans) == "try-error") {
not.ok <- any(diag(ans) < 0) | any(eigen(ans)$values < 0)
} else {
not.ok <- TRUE
}
--- R stacktrace ---
where 1: minv(object2$info.matrix)
where 2: solve(m)
where 3: doTryCatch(return(expr), name, parentenv, handler)
where 4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 5: tryCatchList(expr, classes, parentenv, handlers)
where 6: tryCatch(expr, error = function(e) {
call <- conditionCall(e)
if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L)
dcall <- deparse(call)[1L]
prefix <- paste("Error in", dcall, ": ")
LONG <- 75L
sm <- strsplit(conditionMessage(e), "\n")[[1L]]
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
if (is.na(w))
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
type = "b")
if (w > LONG)
prefix <- paste0(prefix, "\n ")
}
else prefix <- "Error : "
msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L]))
if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile)
.Internal(printDeferredWarnings())
}
invisible(structure(msg, class = "try-error", condition = e))
})
where 7: try(solve(m), silent = TRUE)
where 8: minv(t(par0) %*% minv(object2$info.matrix)$inv %*% par0)
where 9: wald.jmdem(test.list)
where 10: anova.jmdem(fit, test = "Wald", type = 3)
where 11: anova(fit, test = "Wald", type = 3)
--- value of length: 2 type: logical ---
[1] TRUE TRUE
--- function from context ---
function (m, minv.method = NULL, tol = sqrt(.Machine$double.eps))
{
if (!is.null(minv.method)) {
ans <- try(do.call(minv.method, list(m)), silent = TRUE)
if (minv.method == "solve") {
ansnam <- "inverse"
}
else if (minv.method == "chol2inv") {
ansnam <- "inverse from Choleski decomposition"
}
else {
ansnam <- "generalised inverse"
}
}
else {
ans <- try(solve(m), silent = TRUE)
ansnam <- "inverse"
if (!class(ans) == "try-error") {
not.ok <- any(diag(ans) < 0) | any(eigen(ans)$values <
0)
}
else {
not.ok <- TRUE
}
if (not.ok) {
ans <- try(chol2inv(m), silent = TRUE)
ansnam <- "inverse from Choleski decomposition"
if (!class(ans) == "try-error") {
not.ok <- any(diag(ans) < 0) | any(eigen(ans)$values <
0)
}
else {
not.ok <- TRUE
}
if (not.ok) {
ans <- try(ginv(m), silent = TRUE)
ansnam <- "generalised inverse"
}
}
}
return(list(inv = ans, inv.nam = ansnam))
}
<bytecode: 0x7c87f90>
<environment: namespace:jmdem>
--- function search by body ---
Function minv in namespace jmdem has this body.
----------- END OF FAILURE REPORT --------------
Warning in chol2inv(m) : restarting interrupted promise evaluation
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
jmdem
--- call from context ---
minv(object2$info.matrix)
--- call from argument ---
if (!class(ans) == "try-error") {
not.ok <- any(diag(ans) < 0) | any(eigen(ans)$values < 0)
} else {
not.ok <- TRUE
}
--- R stacktrace ---
where 1: minv(object2$info.matrix)
where 2: chol2inv(m)
where 3: doTryCatch(return(expr), name, parentenv, handler)
where 4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 5: tryCatchList(expr, classes, parentenv, handlers)
where 6: tryCatch(expr, error = function(e) {
call <- conditionCall(e)
if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L)
dcall <- deparse(call)[1L]
prefix <- paste("Error in", dcall, ": ")
LONG <- 75L
sm <- strsplit(conditionMessage(e), "\n")[[1L]]
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
if (is.na(w))
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
type = "b")
if (w > LONG)
prefix <- paste0(prefix, "\n ")
}
else prefix <- "Error : "
msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L]))
if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile)
.Internal(printDeferredWarnings())
}
invisible(structure(msg, class = "try-error", condition = e))
})
where 7: try(chol2inv(m), silent = TRUE)
where 8: minv(t(par0) %*% minv(object2$info.matrix)$inv %*% par0)
where 9: wald.jmdem(test.list)
where 10: anova.jmdem(fit, test = "Wald", type = 3)
where 11: anova(fit, test = "Wald", type = 3)
--- value of length: 2 type: logical ---
[1] TRUE TRUE
--- function from context ---
function (m, minv.method = NULL, tol = sqrt(.Machine$double.eps))
{
if (!is.null(minv.method)) {
ans <- try(do.call(minv.method, list(m)), silent = TRUE)
if (minv.method == "solve") {
ansnam <- "inverse"
}
else if (minv.method == "chol2inv") {
ansnam <- "inverse from Choleski decomposition"
}
else {
ansnam <- "generalised inverse"
}
}
else {
ans <- try(solve(m), silent = TRUE)
ansnam <- "inverse"
if (!class(ans) == "try-error") {
not.ok <- any(diag(ans) < 0) | any(eigen(ans)$values <
0)
}
else {
not.ok <- TRUE
}
if (not.ok) {
ans <- try(chol2inv(m), silent = TRUE)
ansnam <- "inverse from Choleski decomposition"
if (!class(ans) == "try-error") {
not.ok <- any(diag(ans) < 0) | any(eigen(ans)$values <
0)
}
else {
not.ok <- TRUE
}
if (not.ok) {
ans <- try(ginv(m), silent = TRUE)
ansnam <- "generalised inverse"
}
}
}
return(list(inv = ans, inv.nam = ansnam))
}
<bytecode: 0x7c87f90>
<environment: namespace:jmdem>
--- function search by body ---
Function minv in namespace jmdem has this body.
----------- END OF FAILURE REPORT --------------
Warning in ginv(m) : restarting interrupted promise evaluation
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
jmdem
--- call from context ---
minv(object2$info.matrix)
--- call from argument ---
if (!class(ans) == "try-error") {
not.ok <- any(diag(ans) < 0) | any(eigen(ans)$values < 0)
} else {
not.ok <- TRUE
}
--- R stacktrace ---
where 1: minv(object2$info.matrix)
where 2: ginv(m)
where 3: doTryCatch(return(expr), name, parentenv, handler)
where 4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 5: tryCatchList(expr, classes, parentenv, handlers)
where 6: tryCatch(expr, error = function(e) {
call <- conditionCall(e)
if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L)
dcall <- deparse(call)[1L]
prefix <- paste("Error in", dcall, ": ")
LONG <- 75L
sm <- strsplit(conditionMessage(e), "\n")[[1L]]
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
if (is.na(w))
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
type = "b")
if (w > LONG)
prefix <- paste0(prefix, "\n ")
}
else prefix <- "Error : "
msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L]))
if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile)
.Internal(printDeferredWarnings())
}
invisible(structure(msg, class = "try-error", condition = e))
})
where 7: try(ginv(m), silent = TRUE)
where 8: minv(t(par0) %*% minv(object2$info.matrix)$inv %*% par0)
where 9: wald.jmdem(test.list)
where 10: anova.jmdem(fit, test = "Wald", type = 3)
where 11: anova(fit, test = "Wald", type = 3)
--- value of length: 2 type: logical ---
[1] TRUE TRUE
--- function from context ---
function (m, minv.method = NULL, tol = sqrt(.Machine$double.eps))
{
if (!is.null(minv.method)) {
ans <- try(do.call(minv.method, list(m)), silent = TRUE)
if (minv.method == "solve") {
ansnam <- "inverse"
}
else if (minv.method == "chol2inv") {
ansnam <- "inverse from Choleski decomposition"
}
else {
ansnam <- "generalised inverse"
}
}
else {
ans <- try(solve(m), silent = TRUE)
ansnam <- "inverse"
if (!class(ans) == "try-error") {
not.ok <- any(diag(ans) < 0) | any(eigen(ans)$values <
0)
}
else {
not.ok <- TRUE
}
if (not.ok) {
ans <- try(chol2inv(m), silent = TRUE)
ansnam <- "inverse from Choleski decomposition"
if (!class(ans) == "try-error") {
not.ok <- any(diag(ans) < 0) | any(eigen(ans)$values <
0)
}
else {
not.ok <- TRUE
}
if (not.ok) {
ans <- try(ginv(m), silent = TRUE)
ansnam <- "generalised inverse"
}
}
}
return(list(inv = ans, inv.nam = ansnam))
}
<bytecode: 0x7c87f90>
<environment: namespace:jmdem>
--- function search by body ---
Function minv in namespace jmdem has this body.
----------- END OF FAILURE REPORT --------------
Error in t(g0) %*% i0 : requires numeric/complex matrix/vector arguments
Calls: anova -> anova.jmdem -> wald.jmdem
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc