Last updated on 2020-02-19 10:48:55 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.2 | 7.95 | 57.36 | 65.31 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.0.2 | 6.55 | 45.19 | 51.74 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.0.2 | 81.09 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 1.0.2 | 79.39 | ERROR | |||
| r-devel-windows-ix86+x86_64 | 1.0.2 | 13.00 | 130.00 | 143.00 | OK | |
| r-devel-windows-ix86+x86_64-gcc8 | 1.0.2 | 23.00 | 179.00 | 202.00 | OK | |
| r-patched-linux-x86_64 | 1.0.2 | 6.69 | 72.65 | 79.34 | OK | |
| r-patched-solaris-x86 | 1.0.2 | 171.00 | OK | |||
| r-release-linux-x86_64 | 1.0.2 | 6.51 | 72.67 | 79.18 | OK | |
| r-release-windows-ix86+x86_64 | 1.0.2 | 15.00 | 126.00 | 141.00 | OK | |
| r-release-osx-x86_64 | 1.0.2 | OK | ||||
| r-oldrel-windows-ix86+x86_64 | 1.0.2 | 9.00 | 123.00 | 132.00 | OK | |
| r-oldrel-osx-x86_64 | 1.0.2 | OK |
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: 0xa30ee38>
<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: 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: 0x557ff0e452c0>
<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-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
Version: 1.0.2
Check: examples
Result: ERROR
Running examples in ‘gyriq-Ex.R’ failed
The error most likely occurred in:
> ### 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: 0xbf5e2e8>
<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-fedora-clang
Version: 1.0.2
Check: examples
Result: ERROR
Running examples in ‘gyriq-Ex.R’ failed
The error most likely occurred in:
> ### 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: 0xbe4e828>
<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-fedora-gcc