Last updated on 2020-02-19 10:48:55 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.2-0 | 7.29 | 59.61 | 66.90 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 2.2-0 | 6.37 | 46.89 | 53.26 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 2.2-0 | 83.63 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 2.2-0 | 84.01 | ERROR | |||
| r-devel-windows-ix86+x86_64 | 2.2-0 | 14.00 | 82.00 | 96.00 | OK | |
| r-devel-windows-ix86+x86_64-gcc8 | 2.2-0 | 20.00 | 108.00 | 128.00 | OK | |
| r-patched-linux-x86_64 | 2.2-0 | 7.32 | 74.25 | 81.57 | OK | |
| r-patched-solaris-x86 | 2.2-0 | 140.90 | OK | |||
| r-release-linux-x86_64 | 2.2-0 | 5.93 | 75.06 | 80.99 | OK | |
| r-release-windows-ix86+x86_64 | 2.2-0 | 13.00 | 72.00 | 85.00 | OK | |
| r-release-osx-x86_64 | 2.2-0 | OK | ||||
| r-oldrel-windows-ix86+x86_64 | 2.2-0 | 8.00 | 78.00 | 86.00 | OK | |
| r-oldrel-osx-x86_64 | 2.2-0 | OK |
Version: 2.2-0
Check: examples
Result: ERROR
Running examples in 'grpregOverlap-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cv.grpregOverlap
> ### Title: Cross-validation for choosing regularization parameter lambda
> ### Aliases: cv.grpregOverlap
>
> ### ** Examples
>
> ## linear regression, a simulation demo.
> set.seed(123)
> group <- list(gr1 = c(1, 2, 3),
+ gr2 = c(1, 4),
+ gr3 = c(2, 4, 5),
+ gr4 = c(3, 5),
+ gr5 = c(6))
> beta.latent.T <- c(5, 5, 5, 0, 0, 0, 0, 0, 5, 5, 0) # true latent coefficients.
> # beta.T <- c(5, 5, 10, 0, 5, 0), true variables: 1, 2, 3, 5; true groups: 1, 4.
> X <- matrix(rnorm(n = 6*100), ncol = 6)
> X.latent <- expandX(X, group)
> y <- X.latent %*% beta.latent.T + rnorm(100)
>
> cvfit <- cv.grpregOverlap(X, y, group, penalty = 'grMCP')
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
grpregOverlap
--- call from context ---
grpregOverlap(X = X, y = y, group = group, returnX = TRUE, ...)
--- call from argument ---
if (class(X) != "matrix") {
tmp <- try(X <- as.matrix(X), silent = TRUE)
if (class(tmp)[1] == "try-error") {
stop("X must be a matrix or able to be coerced to a matrix")
}
}
--- R stacktrace ---
where 1: grpregOverlap(X = X, y = y, group = group, returnX = TRUE, ...)
where 2: cv.grpregOverlap(X, y, group, penalty = "grMCP")
--- value of length: 2 type: logical ---
[1] FALSE TRUE
--- function from context ---
function (X, y, group, penalty = c("grLasso", "grMCP", "grSCAD",
"gel", "cMCP", "gLasso", "gMCP"), family = c("gaussian",
"binomial", "poisson", "cox"), nlambda = 100, lambda, lambda.min = {
if (nrow(X) > ncol(X))
1e-04
else 0.05
}, alpha = 1, eps = 0.001, max.iter = 1000, dfmax = ncol(X),
gmax = length(group), gamma = ifelse(penalty == "grSCAD",
4, 3), tau = 1/3, group.multiplier, returnX = FALSE,
returnOverlap = FALSE, warn = TRUE, ...)
{
if (class(X) != "matrix") {
tmp <- try(X <- as.matrix(X), silent = TRUE)
if (class(tmp)[1] == "try-error") {
stop("X must be a matrix or able to be coerced to a matrix")
}
}
if (storage.mode(X) == "integer")
X <- 1 * X
incid.mat <- incidenceMatrix(X, group)
over.mat <- over.temp <- Matrix(incid.mat %*% t(incid.mat))
grp.vec <- rep(1:nrow(over.mat), times = diag(over.mat))
X.latent <- expandX(X, group)
diag(over.temp) <- 0
if (all(over.temp == 0)) {
cat("Note: There are NO overlaps between groups at all!",
"\n")
cat(" Now conducting non-overlapping group selection ...")
}
gs <- diag(over.mat)
gs <- gs[gs != 0]
penalty <- match.arg(penalty)
if (missing(group.multiplier)) {
if (strtrim(penalty, 2) == "gr") {
group.multiplier <- sqrt(gs)
}
else {
group.multiplier <- rep(1, length(group))
}
}
family <- match.arg(family)
if (family != "cox") {
fit <- grpreg(X = X.latent, y = y, group = grp.vec, penalty = penalty,
family = family, nlambda = nlambda, lambda = lambda,
lambda.min = lambda.min, alpha = alpha, eps = eps,
max.iter = max.iter, dfmax = dfmax, gmax = gmax,
gamma = gamma, tau = tau, group.multiplier = group.multiplier,
warn = warn, ...)
}
else {
fit <- grpsurv(X = X.latent, y = y, group = grp.vec,
penalty = penalty, gamma = gamma, alpha = alpha,
nlambda = nlambda, lambda = lambda, lambda.min = lambda.min,
eps = eps, max.iter = max.iter, dfmax = dfmax, gmax = gmax,
tau = tau, group.multiplier = group.multiplier, warn = warn,
...)
}
fit$beta.latent <- fit$beta
fit$beta <- gamma2beta(gamma = fit$beta, incid.mat, grp.vec,
family = family)
fit$incidence.mat <- incid.mat
fit$group <- group
fit$grp.vec <- grp.vec
fit$family <- family
if (returnX) {
fit$X.latent <- X.latent
}
if (returnOverlap) {
fit$overlap.mat <- over.mat
}
if (family != "cox") {
val <- structure(fit, class = c("grpregOverlap", "grpreg"))
}
else {
val <- structure(fit, class = c("grpsurvOverlap", "grpregOverlap"))
}
val
}
<bytecode: 0xc197688>
<environment: namespace:grpregOverlap>
--- function search by body ---
Function grpregOverlap in namespace grpregOverlap has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(X) != "matrix") { : the condition has length > 1
Calls: cv.grpregOverlap -> grpregOverlap
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 2.2-0
Check: examples
Result: ERROR
Running examples in ‘grpregOverlap-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cv.grpregOverlap
> ### Title: Cross-validation for choosing regularization parameter lambda
> ### Aliases: cv.grpregOverlap
>
> ### ** Examples
>
> ## linear regression, a simulation demo.
> set.seed(123)
> group <- list(gr1 = c(1, 2, 3),
+ gr2 = c(1, 4),
+ gr3 = c(2, 4, 5),
+ gr4 = c(3, 5),
+ gr5 = c(6))
> beta.latent.T <- c(5, 5, 5, 0, 0, 0, 0, 0, 5, 5, 0) # true latent coefficients.
> # beta.T <- c(5, 5, 10, 0, 5, 0), true variables: 1, 2, 3, 5; true groups: 1, 4.
> X <- matrix(rnorm(n = 6*100), ncol = 6)
> X.latent <- expandX(X, group)
> y <- X.latent %*% beta.latent.T + rnorm(100)
>
> cvfit <- cv.grpregOverlap(X, y, group, penalty = 'grMCP')
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
grpregOverlap
--- call from context ---
grpregOverlap(X = X, y = y, group = group, returnX = TRUE, ...)
--- call from argument ---
if (class(X) != "matrix") {
tmp <- try(X <- as.matrix(X), silent = TRUE)
if (class(tmp)[1] == "try-error") {
stop("X must be a matrix or able to be coerced to a matrix")
}
}
--- R stacktrace ---
where 1: grpregOverlap(X = X, y = y, group = group, returnX = TRUE, ...)
where 2: cv.grpregOverlap(X, y, group, penalty = "grMCP")
--- value of length: 2 type: logical ---
[1] FALSE TRUE
--- function from context ---
function (X, y, group, penalty = c("grLasso", "grMCP", "grSCAD",
"gel", "cMCP", "gLasso", "gMCP"), family = c("gaussian",
"binomial", "poisson", "cox"), nlambda = 100, lambda, lambda.min = {
if (nrow(X) > ncol(X))
1e-04
else 0.05
}, alpha = 1, eps = 0.001, max.iter = 1000, dfmax = ncol(X),
gmax = length(group), gamma = ifelse(penalty == "grSCAD",
4, 3), tau = 1/3, group.multiplier, returnX = FALSE,
returnOverlap = FALSE, warn = TRUE, ...)
{
if (class(X) != "matrix") {
tmp <- try(X <- as.matrix(X), silent = TRUE)
if (class(tmp)[1] == "try-error") {
stop("X must be a matrix or able to be coerced to a matrix")
}
}
if (storage.mode(X) == "integer")
X <- 1 * X
incid.mat <- incidenceMatrix(X, group)
over.mat <- over.temp <- Matrix(incid.mat %*% t(incid.mat))
grp.vec <- rep(1:nrow(over.mat), times = diag(over.mat))
X.latent <- expandX(X, group)
diag(over.temp) <- 0
if (all(over.temp == 0)) {
cat("Note: There are NO overlaps between groups at all!",
"\n")
cat(" Now conducting non-overlapping group selection ...")
}
gs <- diag(over.mat)
gs <- gs[gs != 0]
penalty <- match.arg(penalty)
if (missing(group.multiplier)) {
if (strtrim(penalty, 2) == "gr") {
group.multiplier <- sqrt(gs)
}
else {
group.multiplier <- rep(1, length(group))
}
}
family <- match.arg(family)
if (family != "cox") {
fit <- grpreg(X = X.latent, y = y, group = grp.vec, penalty = penalty,
family = family, nlambda = nlambda, lambda = lambda,
lambda.min = lambda.min, alpha = alpha, eps = eps,
max.iter = max.iter, dfmax = dfmax, gmax = gmax,
gamma = gamma, tau = tau, group.multiplier = group.multiplier,
warn = warn, ...)
}
else {
fit <- grpsurv(X = X.latent, y = y, group = grp.vec,
penalty = penalty, gamma = gamma, alpha = alpha,
nlambda = nlambda, lambda = lambda, lambda.min = lambda.min,
eps = eps, max.iter = max.iter, dfmax = dfmax, gmax = gmax,
tau = tau, group.multiplier = group.multiplier, warn = warn,
...)
}
fit$beta.latent <- fit$beta
fit$beta <- gamma2beta(gamma = fit$beta, incid.mat, grp.vec,
family = family)
fit$incidence.mat <- incid.mat
fit$group <- group
fit$grp.vec <- grp.vec
fit$family <- family
if (returnX) {
fit$X.latent <- X.latent
}
if (returnOverlap) {
fit$overlap.mat <- over.mat
}
if (family != "cox") {
val <- structure(fit, class = c("grpregOverlap", "grpreg"))
}
else {
val <- structure(fit, class = c("grpsurvOverlap", "grpregOverlap"))
}
val
}
<bytecode: 0x55a041504478>
<environment: namespace:grpregOverlap>
--- function search by body ---
Function grpregOverlap in namespace grpregOverlap has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(X) != "matrix") { : the condition has length > 1
Calls: cv.grpregOverlap -> grpregOverlap
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2.2-0
Check: examples
Result: ERROR
Running examples in ‘grpregOverlap-Ex.R’ failed
The error most likely occurred in:
> ### Name: cv.grpregOverlap
> ### Title: Cross-validation for choosing regularization parameter lambda
> ### Aliases: cv.grpregOverlap
>
> ### ** Examples
>
> ## linear regression, a simulation demo.
> set.seed(123)
> group <- list(gr1 = c(1, 2, 3),
+ gr2 = c(1, 4),
+ gr3 = c(2, 4, 5),
+ gr4 = c(3, 5),
+ gr5 = c(6))
> beta.latent.T <- c(5, 5, 5, 0, 0, 0, 0, 0, 5, 5, 0) # true latent coefficients.
> # beta.T <- c(5, 5, 10, 0, 5, 0), true variables: 1, 2, 3, 5; true groups: 1, 4.
> X <- matrix(rnorm(n = 6*100), ncol = 6)
> X.latent <- expandX(X, group)
> y <- X.latent %*% beta.latent.T + rnorm(100)
>
> cvfit <- cv.grpregOverlap(X, y, group, penalty = 'grMCP')
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
grpregOverlap
--- call from context ---
grpregOverlap(X = X, y = y, group = group, returnX = TRUE, ...)
--- call from argument ---
if (class(X) != "matrix") {
tmp <- try(X <- as.matrix(X), silent = TRUE)
if (class(tmp)[1] == "try-error") {
stop("X must be a matrix or able to be coerced to a matrix")
}
}
--- R stacktrace ---
where 1: grpregOverlap(X = X, y = y, group = group, returnX = TRUE, ...)
where 2: cv.grpregOverlap(X, y, group, penalty = "grMCP")
--- value of length: 2 type: logical ---
[1] FALSE TRUE
--- function from context ---
function (X, y, group, penalty = c("grLasso", "grMCP", "grSCAD",
"gel", "cMCP", "gLasso", "gMCP"), family = c("gaussian",
"binomial", "poisson", "cox"), nlambda = 100, lambda, lambda.min = {
if (nrow(X) > ncol(X))
1e-04
else 0.05
}, alpha = 1, eps = 0.001, max.iter = 1000, dfmax = ncol(X),
gmax = length(group), gamma = ifelse(penalty == "grSCAD",
4, 3), tau = 1/3, group.multiplier, returnX = FALSE,
returnOverlap = FALSE, warn = TRUE, ...)
{
if (class(X) != "matrix") {
tmp <- try(X <- as.matrix(X), silent = TRUE)
if (class(tmp)[1] == "try-error") {
stop("X must be a matrix or able to be coerced to a matrix")
}
}
if (storage.mode(X) == "integer")
X <- 1 * X
incid.mat <- incidenceMatrix(X, group)
over.mat <- over.temp <- Matrix(incid.mat %*% t(incid.mat))
grp.vec <- rep(1:nrow(over.mat), times = diag(over.mat))
X.latent <- expandX(X, group)
diag(over.temp) <- 0
if (all(over.temp == 0)) {
cat("Note: There are NO overlaps between groups at all!",
"\n")
cat(" Now conducting non-overlapping group selection ...")
}
gs <- diag(over.mat)
gs <- gs[gs != 0]
penalty <- match.arg(penalty)
if (missing(group.multiplier)) {
if (strtrim(penalty, 2) == "gr") {
group.multiplier <- sqrt(gs)
}
else {
group.multiplier <- rep(1, length(group))
}
}
family <- match.arg(family)
if (family != "cox") {
fit <- grpreg(X = X.latent, y = y, group = grp.vec, penalty = penalty,
family = family, nlambda = nlambda, lambda = lambda,
lambda.min = lambda.min, alpha = alpha, eps = eps,
max.iter = max.iter, dfmax = dfmax, gmax = gmax,
gamma = gamma, tau = tau, group.multiplier = group.multiplier,
warn = warn, ...)
}
else {
fit <- grpsurv(X = X.latent, y = y, group = grp.vec,
penalty = penalty, gamma = gamma, alpha = alpha,
nlambda = nlambda, lambda = lambda, lambda.min = lambda.min,
eps = eps, max.iter = max.iter, dfmax = dfmax, gmax = gmax,
tau = tau, group.multiplier = group.multiplier, warn = warn,
...)
}
fit$beta.latent <- fit$beta
fit$beta <- gamma2beta(gamma = fit$beta, incid.mat, grp.vec,
family = family)
fit$incidence.mat <- incid.mat
fit$group <- group
fit$grp.vec <- grp.vec
fit$family <- family
if (returnX) {
fit$X.latent <- X.latent
}
if (returnOverlap) {
fit$overlap.mat <- over.mat
}
if (family != "cox") {
val <- structure(fit, class = c("grpregOverlap", "grpreg"))
}
else {
val <- structure(fit, class = c("grpsurvOverlap", "grpregOverlap"))
}
val
}
<bytecode: 0xc49d150>
<environment: namespace:grpregOverlap>
--- function search by body ---
Function grpregOverlap in namespace grpregOverlap has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(X) != "matrix") { : the condition has length > 1
Calls: cv.grpregOverlap -> grpregOverlap
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 2.2-0
Check: examples
Result: ERROR
Running examples in ‘grpregOverlap-Ex.R’ failed
The error most likely occurred in:
> ### Name: cv.grpregOverlap
> ### Title: Cross-validation for choosing regularization parameter lambda
> ### Aliases: cv.grpregOverlap
>
> ### ** Examples
>
> ## linear regression, a simulation demo.
> set.seed(123)
> group <- list(gr1 = c(1, 2, 3),
+ gr2 = c(1, 4),
+ gr3 = c(2, 4, 5),
+ gr4 = c(3, 5),
+ gr5 = c(6))
> beta.latent.T <- c(5, 5, 5, 0, 0, 0, 0, 0, 5, 5, 0) # true latent coefficients.
> # beta.T <- c(5, 5, 10, 0, 5, 0), true variables: 1, 2, 3, 5; true groups: 1, 4.
> X <- matrix(rnorm(n = 6*100), ncol = 6)
> X.latent <- expandX(X, group)
> y <- X.latent %*% beta.latent.T + rnorm(100)
>
> cvfit <- cv.grpregOverlap(X, y, group, penalty = 'grMCP')
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
grpregOverlap
--- call from context ---
grpregOverlap(X = X, y = y, group = group, returnX = TRUE, ...)
--- call from argument ---
if (class(X) != "matrix") {
tmp <- try(X <- as.matrix(X), silent = TRUE)
if (class(tmp)[1] == "try-error") {
stop("X must be a matrix or able to be coerced to a matrix")
}
}
--- R stacktrace ---
where 1: grpregOverlap(X = X, y = y, group = group, returnX = TRUE, ...)
where 2: cv.grpregOverlap(X, y, group, penalty = "grMCP")
--- value of length: 2 type: logical ---
[1] FALSE TRUE
--- function from context ---
function (X, y, group, penalty = c("grLasso", "grMCP", "grSCAD",
"gel", "cMCP", "gLasso", "gMCP"), family = c("gaussian",
"binomial", "poisson", "cox"), nlambda = 100, lambda, lambda.min = {
if (nrow(X) > ncol(X))
1e-04
else 0.05
}, alpha = 1, eps = 0.001, max.iter = 1000, dfmax = ncol(X),
gmax = length(group), gamma = ifelse(penalty == "grSCAD",
4, 3), tau = 1/3, group.multiplier, returnX = FALSE,
returnOverlap = FALSE, warn = TRUE, ...)
{
if (class(X) != "matrix") {
tmp <- try(X <- as.matrix(X), silent = TRUE)
if (class(tmp)[1] == "try-error") {
stop("X must be a matrix or able to be coerced to a matrix")
}
}
if (storage.mode(X) == "integer")
X <- 1 * X
incid.mat <- incidenceMatrix(X, group)
over.mat <- over.temp <- Matrix(incid.mat %*% t(incid.mat))
grp.vec <- rep(1:nrow(over.mat), times = diag(over.mat))
X.latent <- expandX(X, group)
diag(over.temp) <- 0
if (all(over.temp == 0)) {
cat("Note: There are NO overlaps between groups at all!",
"\n")
cat(" Now conducting non-overlapping group selection ...")
}
gs <- diag(over.mat)
gs <- gs[gs != 0]
penalty <- match.arg(penalty)
if (missing(group.multiplier)) {
if (strtrim(penalty, 2) == "gr") {
group.multiplier <- sqrt(gs)
}
else {
group.multiplier <- rep(1, length(group))
}
}
family <- match.arg(family)
if (family != "cox") {
fit <- grpreg(X = X.latent, y = y, group = grp.vec, penalty = penalty,
family = family, nlambda = nlambda, lambda = lambda,
lambda.min = lambda.min, alpha = alpha, eps = eps,
max.iter = max.iter, dfmax = dfmax, gmax = gmax,
gamma = gamma, tau = tau, group.multiplier = group.multiplier,
warn = warn, ...)
}
else {
fit <- grpsurv(X = X.latent, y = y, group = grp.vec,
penalty = penalty, gamma = gamma, alpha = alpha,
nlambda = nlambda, lambda = lambda, lambda.min = lambda.min,
eps = eps, max.iter = max.iter, dfmax = dfmax, gmax = gmax,
tau = tau, group.multiplier = group.multiplier, warn = warn,
...)
}
fit$beta.latent <- fit$beta
fit$beta <- gamma2beta(gamma = fit$beta, incid.mat, grp.vec,
family = family)
fit$incidence.mat <- incid.mat
fit$group <- group
fit$grp.vec <- grp.vec
fit$family <- family
if (returnX) {
fit$X.latent <- X.latent
}
if (returnOverlap) {
fit$overlap.mat <- over.mat
}
if (family != "cox") {
val <- structure(fit, class = c("grpregOverlap", "grpreg"))
}
else {
val <- structure(fit, class = c("grpsurvOverlap", "grpregOverlap"))
}
val
}
<bytecode: 0xbbc0918>
<environment: namespace:grpregOverlap>
--- function search by body ---
Function grpregOverlap in namespace grpregOverlap has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(X) != "matrix") { : the condition has length > 1
Calls: cv.grpregOverlap -> grpregOverlap
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc