Last updated on 2020-03-07 11:48:09 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 3.0 | 5.41 | 27.18 | 32.59 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 3.0 | 3.88 | 21.61 | 25.49 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 3.0 | 38.68 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 3.0 | 37.50 | ERROR | |||
| r-devel-windows-ix86+x86_64 | 3.0 | 9.00 | 36.00 | 45.00 | OK | |
| r-devel-windows-ix86+x86_64-gcc8 | 3.0 | 7.00 | 41.00 | 48.00 | OK | |
| r-patched-linux-x86_64 | 3.0 | 4.26 | 31.62 | 35.88 | OK | |
| r-patched-solaris-x86 | 3.0 | 60.70 | OK | |||
| r-release-linux-x86_64 | 3.0 | 4.21 | 31.62 | 35.83 | OK | |
| r-release-windows-ix86+x86_64 | 3.0 | 8.00 | 66.00 | 74.00 | OK | |
| r-release-osx-x86_64 | 3.0 | OK | ||||
| r-oldrel-windows-ix86+x86_64 | 3.0 | 6.00 | 34.00 | 40.00 | OK | |
| r-oldrel-osx-x86_64 | 3.0 | OK |
Version: 3.0
Check: examples
Result: ERROR
Running examples in 'breakaway-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: betta
> ### Title: modelling total diversity
> ### Aliases: betta
> ### Keywords: diversity
>
> ### ** Examples
> betta(c(2000, 3000, 4000, 3000), c(100, 200, 150, 180), cbind(1, c(100, 150, 100, 50)))
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
breakaway
--- call from context ---
betta(c(2000, 3000, 4000, 3000), c(100, 200, 150, 180), cbind(1,
c(100, 150, 100, 50)))
--- call from argument ---
if (class(try(getvar(), silent = T)) != "try-error") {
C <- getvar()
blupvars <- rep(NA, length(chats))
blupvars[consider] <- c(sqrt(diag(cbind(X_effective, diag(1,
n)) %*% C %*% t(cbind(X_effective, diag(1, n))))))
mytable$blupses <- blupvars
}
--- R stacktrace ---
where 1: betta(c(2000, 3000, 4000, 3000), c(100, 200, 150, 180), cbind(1,
c(100, 150, 100, 50)))
--- value of length: 2 type: logical ---
[1] TRUE TRUE
--- function from context ---
function (chats, ses, X = NA)
{
if (isTRUE(is.na(X))) {
X <- matrix(rep(1, length(chats)), ncol = 1)
}
consider <- !(is.na(chats) | is.na(ses) | apply(is.na(X),
1, sum))
chats_effective <- chats[consider]
ses_effective <- ses[consider]
X_effective <- as.matrix(X[consider, ])
n <- dim(X_effective)[1]
p <- dim(X_effective)[2]
likelihood <- function(input) {
ssq_u <- input[1]
beta <- input[2:length(input)]
W <- diag(1/(ssq_u + ses_effective^2))
-0.5 * (sum(log(ssq_u + ses_effective^2) + (chats_effective -
X_effective %*% beta)^2/(ssq_u + ses_effective^2)) +
log(det(t(X_effective) %*% W %*% X_effective)))
}
mystart <- c(var(chats_effective), solve(t(X_effective) %*%
X_effective) %*% t(X_effective) %*% chats_effective)
output <- optim(mystart, likelihood, hessian = FALSE, control = list(fnscale = -1),
lower = c(0, -Inf), method = "L-BFGS-B")
ssq_u <- output$par[1]
beta <- output$par[2:length(output$par)]
W <- diag(1/(ssq_u + ses_effective^2))
vars <- 1/diag(t(X_effective) %*% W %*% X_effective)
global <- t(beta) %*% (t(X_effective) %*% W %*% X_effective) %*%
beta
Q <- sum((chats_effective - X_effective %*% beta)^2/ses_effective^2)
R <- diag(ses_effective^2)
G <- diag(ssq_u, n)
getvar <- function() {
C <- matrix(NA, nrow = n + p, ncol = n + p)
C[1:p, 1:p] <- t(X_effective) %*% solve(R) %*% X_effective
C[(p + 1):(n + p), (p + 1):(n + p)] <- solve(R) + solve(G)
C[1:p, (p + 1):(n + p)] <- t(X_effective) %*% solve(R)
C[(p + 1):(n + p), 1:p] <- solve(R) %*% X_effective
return(solve(C))
}
mytable <- list()
mytable$table <- cbind(Estimates = beta, `Standard Errors` = sqrt(vars),
`p-values` = round(2 * (1 - pnorm(abs(beta/sqrt(vars)))),
3))
mytable$cov <- solve(t(X_effective) %*% W %*% X_effective)
mytable$ssq_u <- ssq_u
mytable$homogeneity <- c(Q, 1 - pchisq(Q, n - p))
mytable$global <- c(global, 1 - pchisq(global, p - 1))
us <- c(ssq_u * W %*% (chats_effective - X_effective %*%
beta))
blups <- rep(NA, length(chats))
blups[consider] <- c(X_effective %*% beta + us)
mytable$blups <- blups
if (class(try(getvar(), silent = T)) != "try-error") {
C <- getvar()
blupvars <- rep(NA, length(chats))
blupvars[consider] <- c(sqrt(diag(cbind(X_effective,
diag(1, n)) %*% C %*% t(cbind(X_effective, diag(1,
n))))))
mytable$blupses <- blupvars
}
return(mytable)
}
<bytecode: 0x2093220>
<environment: namespace:breakaway>
--- function search by body ---
Function betta in namespace breakaway has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(try(getvar(), silent = T)) != "try-error") { :
the condition has length > 1
Calls: betta
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 3.0
Check: examples
Result: ERROR
Running examples in ‘breakaway-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: betta
> ### Title: modelling total diversity
> ### Aliases: betta
> ### Keywords: diversity
>
> ### ** Examples
> betta(c(2000, 3000, 4000, 3000), c(100, 200, 150, 180), cbind(1, c(100, 150, 100, 50)))
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
breakaway
--- call from context ---
betta(c(2000, 3000, 4000, 3000), c(100, 200, 150, 180), cbind(1,
c(100, 150, 100, 50)))
--- call from argument ---
if (class(try(getvar(), silent = T)) != "try-error") {
C <- getvar()
blupvars <- rep(NA, length(chats))
blupvars[consider] <- c(sqrt(diag(cbind(X_effective, diag(1,
n)) %*% C %*% t(cbind(X_effective, diag(1, n))))))
mytable$blupses <- blupvars
}
--- R stacktrace ---
where 1: betta(c(2000, 3000, 4000, 3000), c(100, 200, 150, 180), cbind(1,
c(100, 150, 100, 50)))
--- value of length: 2 type: logical ---
[1] TRUE TRUE
--- function from context ---
function (chats, ses, X = NA)
{
if (isTRUE(is.na(X))) {
X <- matrix(rep(1, length(chats)), ncol = 1)
}
consider <- !(is.na(chats) | is.na(ses) | apply(is.na(X),
1, sum))
chats_effective <- chats[consider]
ses_effective <- ses[consider]
X_effective <- as.matrix(X[consider, ])
n <- dim(X_effective)[1]
p <- dim(X_effective)[2]
likelihood <- function(input) {
ssq_u <- input[1]
beta <- input[2:length(input)]
W <- diag(1/(ssq_u + ses_effective^2))
-0.5 * (sum(log(ssq_u + ses_effective^2) + (chats_effective -
X_effective %*% beta)^2/(ssq_u + ses_effective^2)) +
log(det(t(X_effective) %*% W %*% X_effective)))
}
mystart <- c(var(chats_effective), solve(t(X_effective) %*%
X_effective) %*% t(X_effective) %*% chats_effective)
output <- optim(mystart, likelihood, hessian = FALSE, control = list(fnscale = -1),
lower = c(0, -Inf), method = "L-BFGS-B")
ssq_u <- output$par[1]
beta <- output$par[2:length(output$par)]
W <- diag(1/(ssq_u + ses_effective^2))
vars <- 1/diag(t(X_effective) %*% W %*% X_effective)
global <- t(beta) %*% (t(X_effective) %*% W %*% X_effective) %*%
beta
Q <- sum((chats_effective - X_effective %*% beta)^2/ses_effective^2)
R <- diag(ses_effective^2)
G <- diag(ssq_u, n)
getvar <- function() {
C <- matrix(NA, nrow = n + p, ncol = n + p)
C[1:p, 1:p] <- t(X_effective) %*% solve(R) %*% X_effective
C[(p + 1):(n + p), (p + 1):(n + p)] <- solve(R) + solve(G)
C[1:p, (p + 1):(n + p)] <- t(X_effective) %*% solve(R)
C[(p + 1):(n + p), 1:p] <- solve(R) %*% X_effective
return(solve(C))
}
mytable <- list()
mytable$table <- cbind(Estimates = beta, `Standard Errors` = sqrt(vars),
`p-values` = round(2 * (1 - pnorm(abs(beta/sqrt(vars)))),
3))
mytable$cov <- solve(t(X_effective) %*% W %*% X_effective)
mytable$ssq_u <- ssq_u
mytable$homogeneity <- c(Q, 1 - pchisq(Q, n - p))
mytable$global <- c(global, 1 - pchisq(global, p - 1))
us <- c(ssq_u * W %*% (chats_effective - X_effective %*%
beta))
blups <- rep(NA, length(chats))
blups[consider] <- c(X_effective %*% beta + us)
mytable$blups <- blups
if (class(try(getvar(), silent = T)) != "try-error") {
C <- getvar()
blupvars <- rep(NA, length(chats))
blupvars[consider] <- c(sqrt(diag(cbind(X_effective,
diag(1, n)) %*% C %*% t(cbind(X_effective, diag(1,
n))))))
mytable$blupses <- blupvars
}
return(mytable)
}
<bytecode: 0x5636e369a678>
<environment: namespace:breakaway>
--- function search by body ---
Function betta in namespace breakaway has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(try(getvar(), silent = T)) != "try-error") { :
the condition has length > 1
Calls: betta
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 3.0
Check: examples
Result: ERROR
Running examples in ‘breakaway-Ex.R’ failed
The error most likely occurred in:
> ### Name: betta
> ### Title: modelling total diversity
> ### Aliases: betta
> ### Keywords: diversity
>
> ### ** Examples
> betta(c(2000, 3000, 4000, 3000), c(100, 200, 150, 180), cbind(1, c(100, 150, 100, 50)))
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
breakaway
--- call from context ---
betta(c(2000, 3000, 4000, 3000), c(100, 200, 150, 180), cbind(1,
c(100, 150, 100, 50)))
--- call from argument ---
if (class(try(getvar(), silent = T)) != "try-error") {
C <- getvar()
blupvars <- rep(NA, length(chats))
blupvars[consider] <- c(sqrt(diag(cbind(X_effective, diag(1,
n)) %*% C %*% t(cbind(X_effective, diag(1, n))))))
mytable$blupses <- blupvars
}
--- R stacktrace ---
where 1: betta(c(2000, 3000, 4000, 3000), c(100, 200, 150, 180), cbind(1,
c(100, 150, 100, 50)))
--- value of length: 2 type: logical ---
[1] TRUE TRUE
--- function from context ---
function (chats, ses, X = NA)
{
if (isTRUE(is.na(X))) {
X <- matrix(rep(1, length(chats)), ncol = 1)
}
consider <- !(is.na(chats) | is.na(ses) | apply(is.na(X),
1, sum))
chats_effective <- chats[consider]
ses_effective <- ses[consider]
X_effective <- as.matrix(X[consider, ])
n <- dim(X_effective)[1]
p <- dim(X_effective)[2]
likelihood <- function(input) {
ssq_u <- input[1]
beta <- input[2:length(input)]
W <- diag(1/(ssq_u + ses_effective^2))
-0.5 * (sum(log(ssq_u + ses_effective^2) + (chats_effective -
X_effective %*% beta)^2/(ssq_u + ses_effective^2)) +
log(det(t(X_effective) %*% W %*% X_effective)))
}
mystart <- c(var(chats_effective), solve(t(X_effective) %*%
X_effective) %*% t(X_effective) %*% chats_effective)
output <- optim(mystart, likelihood, hessian = FALSE, control = list(fnscale = -1),
lower = c(0, -Inf), method = "L-BFGS-B")
ssq_u <- output$par[1]
beta <- output$par[2:length(output$par)]
W <- diag(1/(ssq_u + ses_effective^2))
vars <- 1/diag(t(X_effective) %*% W %*% X_effective)
global <- t(beta) %*% (t(X_effective) %*% W %*% X_effective) %*%
beta
Q <- sum((chats_effective - X_effective %*% beta)^2/ses_effective^2)
R <- diag(ses_effective^2)
G <- diag(ssq_u, n)
getvar <- function() {
C <- matrix(NA, nrow = n + p, ncol = n + p)
C[1:p, 1:p] <- t(X_effective) %*% solve(R) %*% X_effective
C[(p + 1):(n + p), (p + 1):(n + p)] <- solve(R) + solve(G)
C[1:p, (p + 1):(n + p)] <- t(X_effective) %*% solve(R)
C[(p + 1):(n + p), 1:p] <- solve(R) %*% X_effective
return(solve(C))
}
mytable <- list()
mytable$table <- cbind(Estimates = beta, `Standard Errors` = sqrt(vars),
`p-values` = round(2 * (1 - pnorm(abs(beta/sqrt(vars)))),
3))
mytable$cov <- solve(t(X_effective) %*% W %*% X_effective)
mytable$ssq_u <- ssq_u
mytable$homogeneity <- c(Q, 1 - pchisq(Q, n - p))
mytable$global <- c(global, 1 - pchisq(global, p - 1))
us <- c(ssq_u * W %*% (chats_effective - X_effective %*%
beta))
blups <- rep(NA, length(chats))
blups[consider] <- c(X_effective %*% beta + us)
mytable$blups <- blups
if (class(try(getvar(), silent = T)) != "try-error") {
C <- getvar()
blupvars <- rep(NA, length(chats))
blupvars[consider] <- c(sqrt(diag(cbind(X_effective,
diag(1, n)) %*% C %*% t(cbind(X_effective, diag(1,
n))))))
mytable$blupses <- blupvars
}
return(mytable)
}
<bytecode: 0x186aff0>
<environment: namespace:breakaway>
--- function search by body ---
Function betta in namespace breakaway has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(try(getvar(), silent = T)) != "try-error") { :
the condition has length > 1
Calls: betta
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 3.0
Check: examples
Result: ERROR
Running examples in ‘breakaway-Ex.R’ failed
The error most likely occurred in:
> ### Name: betta
> ### Title: modelling total diversity
> ### Aliases: betta
> ### Keywords: diversity
>
> ### ** Examples
> betta(c(2000, 3000, 4000, 3000), c(100, 200, 150, 180), cbind(1, c(100, 150, 100, 50)))
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
breakaway
--- call from context ---
betta(c(2000, 3000, 4000, 3000), c(100, 200, 150, 180), cbind(1,
c(100, 150, 100, 50)))
--- call from argument ---
if (class(try(getvar(), silent = T)) != "try-error") {
C <- getvar()
blupvars <- rep(NA, length(chats))
blupvars[consider] <- c(sqrt(diag(cbind(X_effective, diag(1,
n)) %*% C %*% t(cbind(X_effective, diag(1, n))))))
mytable$blupses <- blupvars
}
--- R stacktrace ---
where 1: betta(c(2000, 3000, 4000, 3000), c(100, 200, 150, 180), cbind(1,
c(100, 150, 100, 50)))
--- value of length: 2 type: logical ---
[1] TRUE TRUE
--- function from context ---
function (chats, ses, X = NA)
{
if (isTRUE(is.na(X))) {
X <- matrix(rep(1, length(chats)), ncol = 1)
}
consider <- !(is.na(chats) | is.na(ses) | apply(is.na(X),
1, sum))
chats_effective <- chats[consider]
ses_effective <- ses[consider]
X_effective <- as.matrix(X[consider, ])
n <- dim(X_effective)[1]
p <- dim(X_effective)[2]
likelihood <- function(input) {
ssq_u <- input[1]
beta <- input[2:length(input)]
W <- diag(1/(ssq_u + ses_effective^2))
-0.5 * (sum(log(ssq_u + ses_effective^2) + (chats_effective -
X_effective %*% beta)^2/(ssq_u + ses_effective^2)) +
log(det(t(X_effective) %*% W %*% X_effective)))
}
mystart <- c(var(chats_effective), solve(t(X_effective) %*%
X_effective) %*% t(X_effective) %*% chats_effective)
output <- optim(mystart, likelihood, hessian = FALSE, control = list(fnscale = -1),
lower = c(0, -Inf), method = "L-BFGS-B")
ssq_u <- output$par[1]
beta <- output$par[2:length(output$par)]
W <- diag(1/(ssq_u + ses_effective^2))
vars <- 1/diag(t(X_effective) %*% W %*% X_effective)
global <- t(beta) %*% (t(X_effective) %*% W %*% X_effective) %*%
beta
Q <- sum((chats_effective - X_effective %*% beta)^2/ses_effective^2)
R <- diag(ses_effective^2)
G <- diag(ssq_u, n)
getvar <- function() {
C <- matrix(NA, nrow = n + p, ncol = n + p)
C[1:p, 1:p] <- t(X_effective) %*% solve(R) %*% X_effective
C[(p + 1):(n + p), (p + 1):(n + p)] <- solve(R) + solve(G)
C[1:p, (p + 1):(n + p)] <- t(X_effective) %*% solve(R)
C[(p + 1):(n + p), 1:p] <- solve(R) %*% X_effective
return(solve(C))
}
mytable <- list()
mytable$table <- cbind(Estimates = beta, `Standard Errors` = sqrt(vars),
`p-values` = round(2 * (1 - pnorm(abs(beta/sqrt(vars)))),
3))
mytable$cov <- solve(t(X_effective) %*% W %*% X_effective)
mytable$ssq_u <- ssq_u
mytable$homogeneity <- c(Q, 1 - pchisq(Q, n - p))
mytable$global <- c(global, 1 - pchisq(global, p - 1))
us <- c(ssq_u * W %*% (chats_effective - X_effective %*%
beta))
blups <- rep(NA, length(chats))
blups[consider] <- c(X_effective %*% beta + us)
mytable$blups <- blups
if (class(try(getvar(), silent = T)) != "try-error") {
C <- getvar()
blupvars <- rep(NA, length(chats))
blupvars[consider] <- c(sqrt(diag(cbind(X_effective,
diag(1, n)) %*% C %*% t(cbind(X_effective, diag(1,
n))))))
mytable$blupses <- blupvars
}
return(mytable)
}
<bytecode: 0x13e2328>
<environment: namespace:breakaway>
--- function search by body ---
Function betta in namespace breakaway has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(try(getvar(), silent = T)) != "try-error") { :
the condition has length > 1
Calls: betta
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc