CRAN Package Check Results for Package breakaway

Last updated on 2019-12-10 15:47:55 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 3.0 5.32 26.99 32.31 ERROR
r-devel-linux-x86_64-debian-gcc 3.0 3.90 26.77 30.67 OK
r-devel-linux-x86_64-fedora-clang 3.0 47.48 OK
r-devel-linux-x86_64-fedora-gcc 3.0 45.73 OK
r-devel-windows-ix86+x86_64 3.0 8.00 56.00 64.00 OK
r-devel-windows-ix86+x86_64-gcc8 3.0 9.00 39.00 48.00 OK
r-patched-linux-x86_64 3.0 4.29 31.54 35.83 OK
r-patched-solaris-x86 3.0 57.30 OK
r-release-linux-x86_64 3.0 4.65 31.85 36.50 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

Check Details

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: 0x32743b0>
    <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