Last updated on 2020-02-19 10:48:55 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 3.0.1 | 6.85 | 58.27 | 65.12 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 3.0.1 | 6.40 | 46.66 | 53.06 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 3.0.1 | 82.53 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 3.0.1 | 82.50 | ERROR | |||
| r-devel-windows-ix86+x86_64 | 3.0.1 | 14.00 | 65.00 | 79.00 | OK | |
| r-devel-windows-ix86+x86_64-gcc8 | 3.0.1 | 23.00 | 93.00 | 116.00 | OK | |
| r-patched-linux-x86_64 | 3.0.1 | 6.67 | 52.09 | 58.76 | OK | |
| r-patched-solaris-x86 | 3.0.1 | 110.90 | OK | |||
| r-release-linux-x86_64 | 3.0.1 | 6.97 | 51.71 | 58.68 | OK | |
| r-release-windows-ix86+x86_64 | 3.0.1 | 15.00 | 65.00 | 80.00 | OK | |
| r-release-osx-x86_64 | 3.0.1 | OK | ||||
| r-oldrel-windows-ix86+x86_64 | 3.0.1 | 8.00 | 60.00 | 68.00 | OK | |
| r-oldrel-osx-x86_64 | 3.0.1 | OK |
Version: 3.0.1
Check: examples
Result: ERROR
Running examples in 'grpss-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: grpss
> ### Title: Group screening and selection
> ### Aliases: grpss grpss.default grpss.formula
>
> ### ** Examples
>
> library(MASS)
> set.seed(23)
> n <- 30 # sample size
> p <- 3 # number of predictors in each group
> J <- 50 # group size
> group <- rep(1:J,each = 3) # group indices
> ##autoregressive correlation
> Sigma <- 0.6^abs(matrix(1:(p*J),p*J,p*J) - t(matrix(1:(p*J),p*J,p*J)))
> X <- mvrnorm(n,seq(0,5,length.out = p*J),Sigma)
> betaTrue <- runif(12,-2,5)
> mu <- X%*%matrix(c(betaTrue,rep(0,p*J-12)),ncol = 1)
>
> # normal distribution
> y <- mu + rnorm(n)
>
> # only conduct screening procedure
> (gss01 <- grpss(X,y,group)) # gSIS
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
grpss
--- call from context ---
grpss.default(X, y, group)
--- call from argument ---
if (class(X) != "matrix") {
tempX <- try(X <- as.matrix(X), silent = TRUE)
if (class(tempX)[1] == "try-error")
stop("'X' must be a matrix or can be coerced to a matrix")
}
--- R stacktrace ---
where 1: grpss.default(X, y, group)
where 2: grpss(X, y, group)
--- value of length: 2 type: logical ---
[1] FALSE TRUE
--- function from context ---
function (X, y, group, threshold = NULL, scale = c("standardize",
"normalize", "none"), criterion = c("gSIS", "gHOLP", "gAR2",
"gDC"), family = c("gaussian", "binomial", "poisson"), select = FALSE,
penalty = c("grSCAD", "grLasso", "grMCP", "gel", "cMCP"),
cross.validation = FALSE, norm = c("L1", "L2", "Linf"), q = 1,
perm.seed = 1, nfolds = 10, cv.seed = NULL, parallel = FALSE,
cl = NULL, cores = NULL, ...)
{
if (class(X) != "matrix") {
tempX <- try(X <- as.matrix(X), silent = TRUE)
if (class(tempX)[1] == "try-error")
stop("'X' must be a matrix or can be coerced to a matrix")
}
if (!is.numeric(y))
stop("'y' must be a numeric vector or a matrix")
if (parallel)
registerDoParallel(cl = ifelse(is.null(cl), 3, cl), cores)
type <- match.arg(scale)
criterion <- match.arg(criterion)
family <- match.arg(family)
penalty <- match.arg(penalty)
norm <- match.arg(norm)
ok <- complete.cases(X, y)
if (sum(!ok) > 0)
warning("Missing values exist and have been removed")
X <- X[ok, ]
y <- y[ok]
if (length(group) != ncol(X))
stop("length of group must be equal to ncol(X)")
if (is.null(colnames(X)))
colnames(X) <- paste0("X", group)
X0 <- g0 <- NULL
if (any(group == 0)) {
grp0 <- group == 0
X0 <- X[, grp0]
X <- X[, !grp0]
g0 <- group[grp0]
group <- group[!grp0]
}
X <- XX <- X[, order(group)]
group <- sort(as.numeric(as.factor(group)))
grp.values <- grp.criValues(X, y, group, criterion, family,
type, norm)
grp.index <- grp.values[order(grp.values[, 2], decreasing = TRUE),
]
if (is.null(threshold)) {
set.seed(perm.seed)
grp.values0 <- grp.criValues(X[sample(nrow(X)), ], y,
group, criterion, family, type, norm)[, 2]
set.seed(NULL)
thres <- grp.index[, 2] > as.numeric(quantile(grp.values0,
q))
threshold <- as.integer(sum(thres))
if (threshold == 0 || threshold == max(group))
threshold <- as.integer(length(y)/log(length(y)))
}
grp.select <- sort(grp.index[1:threshold, 1])
X <- cbind(X0, XX[, group %in% grp.select])
if (!select) {
result <- list(call = match.call(), y = y, X = X, group.screen = c(unique(g0),
grp.select), threshold = threshold, criterion = criterion)
class(result) <- "grpss"
}
else {
grp0 <- table(group[group %in% grp.select])
group <- rep(1:length(grp0), times = grp0)
if (cross.validation) {
if (!is.null(cv.seed))
set.seed(cv.seed)
grpfit <- cv.grpreg(X, y, group, family = family,
penalty = penalty, nfolds = nfolds, ...)
}
else {
grpfit <- grpreg(X, y, group, penalty, family, ...)
}
result <- c(list(call = match.call(), group.screen = c(g0,
grp.select), criterion = criterion), grpfit)
class(result) <- if (cross.validation)
"cv.grpreg"
else "grpreg"
}
return(result)
}
<bytecode: 0x66f6498>
<environment: namespace:grpss>
--- function search by body ---
Function grpss.default in namespace grpss has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(X) != "matrix") { : the condition has length > 1
Calls: grpss -> grpss.default
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 3.0.1
Check: examples
Result: ERROR
Running examples in ‘grpss-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: grpss
> ### Title: Group screening and selection
> ### Aliases: grpss grpss.default grpss.formula
>
> ### ** Examples
>
> library(MASS)
> set.seed(23)
> n <- 30 # sample size
> p <- 3 # number of predictors in each group
> J <- 50 # group size
> group <- rep(1:J,each = 3) # group indices
> ##autoregressive correlation
> Sigma <- 0.6^abs(matrix(1:(p*J),p*J,p*J) - t(matrix(1:(p*J),p*J,p*J)))
> X <- mvrnorm(n,seq(0,5,length.out = p*J),Sigma)
> betaTrue <- runif(12,-2,5)
> mu <- X%*%matrix(c(betaTrue,rep(0,p*J-12)),ncol = 1)
>
> # normal distribution
> y <- mu + rnorm(n)
>
> # only conduct screening procedure
> (gss01 <- grpss(X,y,group)) # gSIS
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
grpss
--- call from context ---
grpss.default(X, y, group)
--- call from argument ---
if (class(X) != "matrix") {
tempX <- try(X <- as.matrix(X), silent = TRUE)
if (class(tempX)[1] == "try-error")
stop("'X' must be a matrix or can be coerced to a matrix")
}
--- R stacktrace ---
where 1: grpss.default(X, y, group)
where 2: grpss(X, y, group)
--- value of length: 2 type: logical ---
[1] FALSE TRUE
--- function from context ---
function (X, y, group, threshold = NULL, scale = c("standardize",
"normalize", "none"), criterion = c("gSIS", "gHOLP", "gAR2",
"gDC"), family = c("gaussian", "binomial", "poisson"), select = FALSE,
penalty = c("grSCAD", "grLasso", "grMCP", "gel", "cMCP"),
cross.validation = FALSE, norm = c("L1", "L2", "Linf"), q = 1,
perm.seed = 1, nfolds = 10, cv.seed = NULL, parallel = FALSE,
cl = NULL, cores = NULL, ...)
{
if (class(X) != "matrix") {
tempX <- try(X <- as.matrix(X), silent = TRUE)
if (class(tempX)[1] == "try-error")
stop("'X' must be a matrix or can be coerced to a matrix")
}
if (!is.numeric(y))
stop("'y' must be a numeric vector or a matrix")
if (parallel)
registerDoParallel(cl = ifelse(is.null(cl), 3, cl), cores)
type <- match.arg(scale)
criterion <- match.arg(criterion)
family <- match.arg(family)
penalty <- match.arg(penalty)
norm <- match.arg(norm)
ok <- complete.cases(X, y)
if (sum(!ok) > 0)
warning("Missing values exist and have been removed")
X <- X[ok, ]
y <- y[ok]
if (length(group) != ncol(X))
stop("length of group must be equal to ncol(X)")
if (is.null(colnames(X)))
colnames(X) <- paste0("X", group)
X0 <- g0 <- NULL
if (any(group == 0)) {
grp0 <- group == 0
X0 <- X[, grp0]
X <- X[, !grp0]
g0 <- group[grp0]
group <- group[!grp0]
}
X <- XX <- X[, order(group)]
group <- sort(as.numeric(as.factor(group)))
grp.values <- grp.criValues(X, y, group, criterion, family,
type, norm)
grp.index <- grp.values[order(grp.values[, 2], decreasing = TRUE),
]
if (is.null(threshold)) {
set.seed(perm.seed)
grp.values0 <- grp.criValues(X[sample(nrow(X)), ], y,
group, criterion, family, type, norm)[, 2]
set.seed(NULL)
thres <- grp.index[, 2] > as.numeric(quantile(grp.values0,
q))
threshold <- as.integer(sum(thres))
if (threshold == 0 || threshold == max(group))
threshold <- as.integer(length(y)/log(length(y)))
}
grp.select <- sort(grp.index[1:threshold, 1])
X <- cbind(X0, XX[, group %in% grp.select])
if (!select) {
result <- list(call = match.call(), y = y, X = X, group.screen = c(unique(g0),
grp.select), threshold = threshold, criterion = criterion)
class(result) <- "grpss"
}
else {
grp0 <- table(group[group %in% grp.select])
group <- rep(1:length(grp0), times = grp0)
if (cross.validation) {
if (!is.null(cv.seed))
set.seed(cv.seed)
grpfit <- cv.grpreg(X, y, group, family = family,
penalty = penalty, nfolds = nfolds, ...)
}
else {
grpfit <- grpreg(X, y, group, penalty, family, ...)
}
result <- c(list(call = match.call(), group.screen = c(g0,
grp.select), criterion = criterion), grpfit)
class(result) <- if (cross.validation)
"cv.grpreg"
else "grpreg"
}
return(result)
}
<bytecode: 0x55c086853010>
<environment: namespace:grpss>
--- function search by body ---
Function grpss.default in namespace grpss has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(X) != "matrix") { : the condition has length > 1
Calls: grpss -> grpss.default
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 3.0.1
Check: examples
Result: ERROR
Running examples in ‘grpss-Ex.R’ failed
The error most likely occurred in:
> ### Name: grpss
> ### Title: Group screening and selection
> ### Aliases: grpss grpss.default grpss.formula
>
> ### ** Examples
>
> library(MASS)
> set.seed(23)
> n <- 30 # sample size
> p <- 3 # number of predictors in each group
> J <- 50 # group size
> group <- rep(1:J,each = 3) # group indices
> ##autoregressive correlation
> Sigma <- 0.6^abs(matrix(1:(p*J),p*J,p*J) - t(matrix(1:(p*J),p*J,p*J)))
> X <- mvrnorm(n,seq(0,5,length.out = p*J),Sigma)
> betaTrue <- runif(12,-2,5)
> mu <- X%*%matrix(c(betaTrue,rep(0,p*J-12)),ncol = 1)
>
> # normal distribution
> y <- mu + rnorm(n)
>
> # only conduct screening procedure
> (gss01 <- grpss(X,y,group)) # gSIS
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
grpss
--- call from context ---
grpss.default(X, y, group)
--- call from argument ---
if (class(X) != "matrix") {
tempX <- try(X <- as.matrix(X), silent = TRUE)
if (class(tempX)[1] == "try-error")
stop("'X' must be a matrix or can be coerced to a matrix")
}
--- R stacktrace ---
where 1: grpss.default(X, y, group)
where 2: grpss(X, y, group)
--- value of length: 2 type: logical ---
[1] FALSE TRUE
--- function from context ---
function (X, y, group, threshold = NULL, scale = c("standardize",
"normalize", "none"), criterion = c("gSIS", "gHOLP", "gAR2",
"gDC"), family = c("gaussian", "binomial", "poisson"), select = FALSE,
penalty = c("grSCAD", "grLasso", "grMCP", "gel", "cMCP"),
cross.validation = FALSE, norm = c("L1", "L2", "Linf"), q = 1,
perm.seed = 1, nfolds = 10, cv.seed = NULL, parallel = FALSE,
cl = NULL, cores = NULL, ...)
{
if (class(X) != "matrix") {
tempX <- try(X <- as.matrix(X), silent = TRUE)
if (class(tempX)[1] == "try-error")
stop("'X' must be a matrix or can be coerced to a matrix")
}
if (!is.numeric(y))
stop("'y' must be a numeric vector or a matrix")
if (parallel)
registerDoParallel(cl = ifelse(is.null(cl), 3, cl), cores)
type <- match.arg(scale)
criterion <- match.arg(criterion)
family <- match.arg(family)
penalty <- match.arg(penalty)
norm <- match.arg(norm)
ok <- complete.cases(X, y)
if (sum(!ok) > 0)
warning("Missing values exist and have been removed")
X <- X[ok, ]
y <- y[ok]
if (length(group) != ncol(X))
stop("length of group must be equal to ncol(X)")
if (is.null(colnames(X)))
colnames(X) <- paste0("X", group)
X0 <- g0 <- NULL
if (any(group == 0)) {
grp0 <- group == 0
X0 <- X[, grp0]
X <- X[, !grp0]
g0 <- group[grp0]
group <- group[!grp0]
}
X <- XX <- X[, order(group)]
group <- sort(as.numeric(as.factor(group)))
grp.values <- grp.criValues(X, y, group, criterion, family,
type, norm)
grp.index <- grp.values[order(grp.values[, 2], decreasing = TRUE),
]
if (is.null(threshold)) {
set.seed(perm.seed)
grp.values0 <- grp.criValues(X[sample(nrow(X)), ], y,
group, criterion, family, type, norm)[, 2]
set.seed(NULL)
thres <- grp.index[, 2] > as.numeric(quantile(grp.values0,
q))
threshold <- as.integer(sum(thres))
if (threshold == 0 || threshold == max(group))
threshold <- as.integer(length(y)/log(length(y)))
}
grp.select <- sort(grp.index[1:threshold, 1])
X <- cbind(X0, XX[, group %in% grp.select])
if (!select) {
result <- list(call = match.call(), y = y, X = X, group.screen = c(unique(g0),
grp.select), threshold = threshold, criterion = criterion)
class(result) <- "grpss"
}
else {
grp0 <- table(group[group %in% grp.select])
group <- rep(1:length(grp0), times = grp0)
if (cross.validation) {
if (!is.null(cv.seed))
set.seed(cv.seed)
grpfit <- cv.grpreg(X, y, group, family = family,
penalty = penalty, nfolds = nfolds, ...)
}
else {
grpfit <- grpreg(X, y, group, penalty, family, ...)
}
result <- c(list(call = match.call(), group.screen = c(g0,
grp.select), criterion = criterion), grpfit)
class(result) <- if (cross.validation)
"cv.grpreg"
else "grpreg"
}
return(result)
}
<bytecode: 0x6ce8720>
<environment: namespace:grpss>
--- function search by body ---
Function grpss.default in namespace grpss has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(X) != "matrix") { : the condition has length > 1
Calls: grpss -> grpss.default
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 3.0.1
Check: examples
Result: ERROR
Running examples in ‘grpss-Ex.R’ failed
The error most likely occurred in:
> ### Name: grpss
> ### Title: Group screening and selection
> ### Aliases: grpss grpss.default grpss.formula
>
> ### ** Examples
>
> library(MASS)
> set.seed(23)
> n <- 30 # sample size
> p <- 3 # number of predictors in each group
> J <- 50 # group size
> group <- rep(1:J,each = 3) # group indices
> ##autoregressive correlation
> Sigma <- 0.6^abs(matrix(1:(p*J),p*J,p*J) - t(matrix(1:(p*J),p*J,p*J)))
> X <- mvrnorm(n,seq(0,5,length.out = p*J),Sigma)
> betaTrue <- runif(12,-2,5)
> mu <- X%*%matrix(c(betaTrue,rep(0,p*J-12)),ncol = 1)
>
> # normal distribution
> y <- mu + rnorm(n)
>
> # only conduct screening procedure
> (gss01 <- grpss(X,y,group)) # gSIS
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
grpss
--- call from context ---
grpss.default(X, y, group)
--- call from argument ---
if (class(X) != "matrix") {
tempX <- try(X <- as.matrix(X), silent = TRUE)
if (class(tempX)[1] == "try-error")
stop("'X' must be a matrix or can be coerced to a matrix")
}
--- R stacktrace ---
where 1: grpss.default(X, y, group)
where 2: grpss(X, y, group)
--- value of length: 2 type: logical ---
[1] FALSE TRUE
--- function from context ---
function (X, y, group, threshold = NULL, scale = c("standardize",
"normalize", "none"), criterion = c("gSIS", "gHOLP", "gAR2",
"gDC"), family = c("gaussian", "binomial", "poisson"), select = FALSE,
penalty = c("grSCAD", "grLasso", "grMCP", "gel", "cMCP"),
cross.validation = FALSE, norm = c("L1", "L2", "Linf"), q = 1,
perm.seed = 1, nfolds = 10, cv.seed = NULL, parallel = FALSE,
cl = NULL, cores = NULL, ...)
{
if (class(X) != "matrix") {
tempX <- try(X <- as.matrix(X), silent = TRUE)
if (class(tempX)[1] == "try-error")
stop("'X' must be a matrix or can be coerced to a matrix")
}
if (!is.numeric(y))
stop("'y' must be a numeric vector or a matrix")
if (parallel)
registerDoParallel(cl = ifelse(is.null(cl), 3, cl), cores)
type <- match.arg(scale)
criterion <- match.arg(criterion)
family <- match.arg(family)
penalty <- match.arg(penalty)
norm <- match.arg(norm)
ok <- complete.cases(X, y)
if (sum(!ok) > 0)
warning("Missing values exist and have been removed")
X <- X[ok, ]
y <- y[ok]
if (length(group) != ncol(X))
stop("length of group must be equal to ncol(X)")
if (is.null(colnames(X)))
colnames(X) <- paste0("X", group)
X0 <- g0 <- NULL
if (any(group == 0)) {
grp0 <- group == 0
X0 <- X[, grp0]
X <- X[, !grp0]
g0 <- group[grp0]
group <- group[!grp0]
}
X <- XX <- X[, order(group)]
group <- sort(as.numeric(as.factor(group)))
grp.values <- grp.criValues(X, y, group, criterion, family,
type, norm)
grp.index <- grp.values[order(grp.values[, 2], decreasing = TRUE),
]
if (is.null(threshold)) {
set.seed(perm.seed)
grp.values0 <- grp.criValues(X[sample(nrow(X)), ], y,
group, criterion, family, type, norm)[, 2]
set.seed(NULL)
thres <- grp.index[, 2] > as.numeric(quantile(grp.values0,
q))
threshold <- as.integer(sum(thres))
if (threshold == 0 || threshold == max(group))
threshold <- as.integer(length(y)/log(length(y)))
}
grp.select <- sort(grp.index[1:threshold, 1])
X <- cbind(X0, XX[, group %in% grp.select])
if (!select) {
result <- list(call = match.call(), y = y, X = X, group.screen = c(unique(g0),
grp.select), threshold = threshold, criterion = criterion)
class(result) <- "grpss"
}
else {
grp0 <- table(group[group %in% grp.select])
group <- rep(1:length(grp0), times = grp0)
if (cross.validation) {
if (!is.null(cv.seed))
set.seed(cv.seed)
grpfit <- cv.grpreg(X, y, group, family = family,
penalty = penalty, nfolds = nfolds, ...)
}
else {
grpfit <- grpreg(X, y, group, penalty, family, ...)
}
result <- c(list(call = match.call(), group.screen = c(g0,
grp.select), criterion = criterion), grpfit)
class(result) <- if (cross.validation)
"cv.grpreg"
else "grpreg"
}
return(result)
}
<bytecode: 0x85ec900>
<environment: namespace:grpss>
--- function search by body ---
Function grpss.default in namespace grpss has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(X) != "matrix") { : the condition has length > 1
Calls: grpss -> grpss.default
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc