CRAN Package Check Results for Package gyriq

Last updated on 2020-01-18 22:48:33 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0.2 7.52 55.08 62.60 ERROR
r-devel-linux-x86_64-debian-gcc 1.0.2 6.16 61.87 68.03 NOTE
r-devel-linux-x86_64-fedora-clang 1.0.2 106.75 NOTE
r-devel-linux-x86_64-fedora-gcc 1.0.2 102.43 NOTE
r-devel-windows-ix86+x86_64 1.0.2 22.00 132.00 154.00 OK
r-devel-windows-ix86+x86_64-gcc8 1.0.2 18.00 177.00 195.00 OK
r-patched-linux-x86_64 1.0.2 7.74 72.24 79.98 OK
r-patched-solaris-x86 1.0.2 164.90 OK
r-release-linux-x86_64 1.0.2 6.70 73.72 80.42 OK
r-release-windows-ix86+x86_64 1.0.2 22.00 124.00 146.00 OK
r-release-osx-x86_64 1.0.2 OK
r-oldrel-windows-ix86+x86_64 1.0.2 14.00 163.00 177.00 OK
r-oldrel-osx-x86_64 1.0.2 OK

Check Details

Version: 1.0.2
Check: examples
Result: ERROR
    Running examples in 'gyriq-Ex.R' failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: genComplResid
    > ### Title: genComplResid
    > ### Aliases: genComplResid
    >
    > ### ** Examples
    >
    > data(simGyriq)
    > for (i in seq_along(simGyriq)) assign(names(simGyriq)[i], simGyriq[[i]])
    >
    > cr <- genComplResid(U, Delta, Phi, blkID, m=50, X)
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    gyriq
     --- call from context ---
    genComplResid(U, Delta, Phi, blkID, m = 50, X)
     --- call from argument ---
    if (class(Phi) != "matrix") stop("Phi is not a matrix")
     --- R stacktrace ---
    where 1: genComplResid(U, Delta, Phi, blkID, m = 50, X)
    
     --- value of length: 2 type: logical ---
    [1] FALSE TRUE
     --- function from context ---
    function (U, Delta, Phi, blkID, m = 50, X = NULL)
    {
     if (class(Phi) != "matrix")
     stop("Phi is not a matrix")
     if (nrow(Phi) != ncol(Phi))
     stop("Phi is not a square matrix")
     if (sum(is.na(U)) != 0)
     stop("U cannot have any missing values")
     if (sum(is.na(Delta)) != 0)
     stop("Delta cannot have any missing values")
     if (sum(is.na(Phi)) != 0)
     stop("Phi cannot have any missing values")
     if (sum(is.na(blkID)) != 0)
     stop("blkID cannot have any missing values")
     if (length(U) != length(Delta))
     stop("Dimensions of U and Delta do not match")
     if (length(U) != nrow(Phi))
     stop("Dimensions of U and Phi do not match")
     if (length(U) != length(blkID))
     stop("Dimensions of U and blkID do not match")
     blkCens <- aggregate(x = 1 - Delta, by = list(blkID), FUN = sum)$x
     if (max(blkCens) > 1000)
     stop("The number of censored individuals in each correlated group of\n observations identified by the vector 'blkID' cannot exceed 1000.")
     if (is.null(X) == TRUE) {
     covPar <- NULL
     covTerm <- rep(0, length(U))
     }
     else {
     if (class(X) != "matrix")
     stop("X is not a matrix")
     if (length(U) != nrow(X))
     stop("Dimensions of U and X do not match")
     if (sum(apply(X, 2, chkVariation)) != ncol(X))
     stop("One of the covariates in X has no variation")
     fit <- survival::coxph(survival::Surv(U, Delta) ~ X)
     covPar <- fit$coef
     covTerm <- as.vector(X %*% covPar)
     }
     rawResid <- estimRawResid(U = U, Delta = Delta, covTerm = covTerm)
     herit <- estimHeritPar(rawResid = rawResid, Delta = Delta,
     Phi = Phi, blkID = blkID)
     Gam <- herit * Phi + (1 - herit) * diag(rep(1, dim(Phi)[1]))
     if (sum(Delta) == length(Delta)) {
     GamEig <- eigen(Gam)
     GamEigVal <- GamEig$values
     GamSqrt <- GamEig$vectors %*% diag(sqrt(GamEigVal)) %*%
     solve(GamEig$vectors)
     compResid <- as.vector(solve(GamSqrt) %*% rawResid)
     }
     else {
     compResid <- imputeResid(rawResid = rawResid, Delta = Delta,
     Gam = Gam, m = m, blkID = blkID)
     }
     return(list(compResid = compResid, herit = herit, covPar = covPar))
    }
    <bytecode: 0xa752618>
    <environment: namespace:gyriq>
     --- function search by body ---
    Function genComplResid in namespace gyriq has this body.
     ----------- END OF FAILURE REPORT --------------
    Error in if (class(Phi) != "matrix") stop("Phi is not a matrix") :
     the condition has length > 1
    Calls: genComplResid
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.0.2
Check: for non-standard things in the check directory
Result: NOTE
    Found the following files/directories:
     ‘outGyriq.out’
Flavors: r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 1.0.2
Check: compiled code
Result: NOTE
    File ‘gyriq/libs/gyriq.so’:
     Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’
    
    It is good practice to register native routines and to disable symbol
    search.
    
    See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc