CRAN Package Check Results for Package rbridge

Last updated on 2020-01-27 00:48:17 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0 43.38 65.07 108.45 ERROR
r-devel-linux-x86_64-debian-gcc 1.0 28.98 50.50 79.48 OK
r-devel-linux-x86_64-fedora-clang 1.0 133.69 NOTE
r-devel-linux-x86_64-fedora-gcc 1.0 132.06 NOTE
r-devel-windows-ix86+x86_64 1.0 81.00 154.00 235.00 OK
r-devel-windows-ix86+x86_64-gcc8 1.0 120.00 126.00 246.00 OK
r-patched-linux-x86_64 1.0 34.92 58.35 93.27 OK
r-patched-solaris-x86 1.0 151.40 NOTE
r-release-linux-x86_64 1.0 36.45 57.66 94.11 OK
r-release-windows-ix86+x86_64 1.0 77.00 105.00 182.00 OK
r-release-osx-x86_64 1.0 NOTE
r-oldrel-windows-ix86+x86_64 1.0 74.00 125.00 199.00 OK
r-oldrel-osx-x86_64 1.0 NOTE

Check Details

Version: 1.0
Check: examples
Result: ERROR
    Running examples in 'rbridge-Ex.R' failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: bridge
    > ### Title: Fit a Bridge Estimation
    > ### Aliases: bridge
    >
    > ### ** Examples
    >
    > set.seed(2019)
    > beta <- c(3, 1.5, 0, 0, 2, 0, 0, 0)
    > p <- length(beta)
    > beta <- matrix(beta, nrow = p, ncol = 1)
    >
    > n = 100
    > X = matrix(rnorm(n*p),n,p)
    > y = X%*%beta + rnorm(n)
    >
    > model1 <- bridge(X, y, q = 1)
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    rbridge
     --- call from context ---
    bridge(X, y, q = 1)
     --- call from argument ---
    if (class(X) != "matrix") {
     tmp <- try(X <- model.matrix(~0 + ., data = 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: bridge(X, y, q = 1)
    
     --- value of length: 2 type: logical ---
    [1] FALSE TRUE
     --- function from context ---
    function (X, y, q = 1, lambda.min = ifelse(n > p, 0.001, 0.05),
     nlambda = 100, lambda, eta = 1e-07, converge = 10^10)
    {
     if (class(X) != "matrix") {
     tmp <- try(X <- model.matrix(~0 + ., data = 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")
     storage.mode(X) <- "double"
     if (class(y) != "numeric") {
     tmp <- try(y <- as.numeric(y), silent = TRUE)
     if (class(tmp)[1] == "try-error")
     stop("y must numeric or able to be coerced to numeric")
     }
     if (nlambda < 2)
     stop("nlambda must be at least 2")
     if (q > 2)
     stop("a must be less than 2; choose a small positive number instead")
     if (any(is.na(y)) | any(is.na(X)))
     stop("Missing data (NA's) detected. Take actions (e.g., removing cases, removing features, imputation) to eliminate missing data before passing X and y to ncvreg")
     if (length(y) != nrow(X))
     stop("X and y do not have the same number of observations")
     stdX <- standard(X)
     XX <- stdX$xx
     p <- ncol(XX)
     ns <- c(1:p)
     yy <- y - mean(y)
     n <- length(yy)
     if (missing(lambda)) {
     lambda <- Lambdas_Grid(XX, yy, q, lambda.min, nlambda)
     user.lambda <- FALSE
     }
     else {
     nlambda <- length(lambda)
     user.lambda <- TRUE
     }
     fit <- Bridge(XX, yy, q, lambda, converge, eta)
     constant <- rep(mean(y), nlambda)
     betas <- matrix(fit, p, nlambda)
     unbetas <- matrix(0, nrow = (ncol(X) + 1), ncol = length(lambda))
     bbetas <- betas/as.vector(stdX$s)
     unbetas[ns + 1, ] <- bbetas
     unbetas[1, ] <- constant - crossprod(as.vector(stdX$c), bbetas)
     varnames <- if (is.null(colnames(X)))
     paste("V", 1:ncol(X), sep = "")
     else colnames(X)
     varnames <- c("(Intercept)", varnames)
     dimnames(unbetas) <- list(varnames, lambda)
     output <- structure(list(betas = unbetas, lambda = lambda),
     class = "bridge")
     output
    }
    <bytecode: 0xa133230>
    <environment: namespace:rbridge>
     --- function search by body ---
    Function bridge in namespace rbridge has this body.
     ----------- END OF FAILURE REPORT --------------
    Error in if (class(X) != "matrix") { : the condition has length > 1
    Calls: bridge
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.0
Check: tests
Result: ERROR
     Running 'testthat.R' [5s/5s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > library(testthat)
     > library(rbridge)
     >
     > test_check("rbridge")
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
     :
     --- package (from environment) ---
     rbridge
     --- call from context ---
     rbridge(X, y, q = 1, R1.mat, r1.vec)
     --- call from argument ---
     if (class(X) != "matrix") {
     tmp <- try(X <- model.matrix(~0 + ., data = 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 at testthat/test.R#24: rbridge(X, y, q = 1, R1.mat, r1.vec)
     where 2: eval(code, test_env)
     where 3: eval(code, test_env)
     where 4: withCallingHandlers({
     eval(code, test_env)
     if (!handled && !is.null(test)) {
     skip_empty()
     }
     }, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
     message = handle_message, error = handle_error)
     where 5: doTryCatch(return(expr), name, parentenv, handler)
     where 6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     where 7: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
     where 8: doTryCatch(return(expr), name, parentenv, handler)
     where 9: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
     names[nh], parentenv, handlers[[nh]])
     where 10: tryCatchList(expr, classes, parentenv, handlers)
     where 11: tryCatch(withCallingHandlers({
     eval(code, test_env)
     if (!handled && !is.null(test)) {
     skip_empty()
     }
     }, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
     message = handle_message, error = handle_error), error = handle_fatal,
     skip = function(e) {
     })
     where 12: test_code(NULL, exprs, env)
     where 13: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
     where 14: force(code)
     where 15: doWithOneRestart(return(expr), restart)
     where 16: withOneRestart(expr, restarts[[1L]])
     where 17: withRestarts(testthat_abort_reporter = function() NULL, force(code))
     where 18: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
     {
     reporter$start_file(basename(path))
     lister$start_file(basename(path))
     source_file(path, new.env(parent = env), chdir = TRUE,
     wrap = wrap)
     reporter$.end_context()
     reporter$end_file()
     })
     where 19: FUN(X[[i]], ...)
     where 20: lapply(paths, test_file, env = env, reporter = current_reporter,
     start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
     where 21: force(code)
     where 22: doWithOneRestart(return(expr), restart)
     where 23: withOneRestart(expr, restarts[[1L]])
     where 24: withRestarts(testthat_abort_reporter = function() NULL, force(code))
     where 25: with_reporter(reporter = current_reporter, results <- lapply(paths,
     test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,
     load_helpers = FALSE, wrap = wrap))
     where 26: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
     stop_on_warning = stop_on_warning, wrap = wrap)
     where 27: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,
     ..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
     wrap = wrap)
     where 28: test_package_dir(package = package, test_path = test_path, filter = filter,
     reporter = reporter, ..., stop_on_failure = stop_on_failure,
     stop_on_warning = stop_on_warning, wrap = wrap)
     where 29: test_check("rbridge")
    
     --- value of length: 2 type: logical ---
     [1] FALSE TRUE
     --- function from context ---
     function (X, y, q = 1, R, r, lambda.min = ifelse(n > p, 0.001,
     0.05), nlambda = 100, lambda, eta = 1e-07, converge = 10^10)
     {
     if (class(X) != "matrix") {
     tmp <- try(X <- model.matrix(~0 + ., data = 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")
     storage.mode(X) <- "double"
     if (class(y) != "numeric") {
     tmp <- try(y <- as.numeric(y), silent = TRUE)
     if (class(tmp)[1] == "try-error")
     stop("y must numeric or able to be coerced to numeric")
     }
     if (nlambda < 2)
     stop("nlambda must be at least 2")
     if (q > 2)
     stop("a must be less than 2; choose a small positive number instead")
     if (any(is.na(y)) | any(is.na(X)))
     stop("Missing data (NA's) detected. Take actions (e.g., removing cases, removing features, imputation) to eliminate missing data before passing X and y to ncvreg")
     if (length(y) != nrow(X))
     stop("X and y do not have the same number of observations")
     stdX <- standard(X)
     XX <- stdX$xx
     p <- ncol(XX)
     ns <- c(1:p)
     yy <- y - mean(y)
     n <- length(yy)
     if (missing(lambda)) {
     lambda <- Lambdas_Grid(XX, yy, q, lambda.min, nlambda)
     user.lambda <- FALSE
     }
     else {
     nlambda <- length(lambda)
     user.lambda <- TRUE
     }
     fit <- RBridge(XX, yy, q, lambda, R, r, converge, eta)
     constant <- rep(mean(y), nlambda)
     betas <- matrix(fit, p, nlambda)
     unbetas <- matrix(0, nrow = (ncol(X) + 1), ncol = length(lambda))
     bbetas <- betas/as.vector(stdX$s)
     unbetas[ns + 1, ] <- bbetas
     unbetas[1, ] <- constant - crossprod(as.vector(stdX$c), bbetas)
     varnames <- if (is.null(colnames(X)))
     paste("V", 1:ncol(X), sep = "")
     else colnames(X)
     varnames <- c("(Intercept)", varnames)
     dimnames(unbetas) <- list(varnames, lambda)
     output <- structure(list(betas = unbetas, lambda = lambda),
     class = "rbridge")
     output
     }
     <bytecode: 0x984d450>
     <environment: namespace:rbridge>
     --- function search by body ---
     Function rbridge in namespace rbridge has this body.
     ----------- END OF FAILURE REPORT --------------
     -- 1. Error: (unknown) (@test.R#24) -------------------------------------------
     the condition has length > 1
     Backtrace:
     1. rbridge::rbridge(X, y, q = 1, R1.mat, r1.vec)
    
     == testthat results ===========================================================
     [ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
     1. Error: (unknown) (@test.R#24)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.0
Check: dependencies in R code
Result: NOTE
    Namespace in Imports field not imported from: ‘dplyr’
     All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-solaris-x86, r-release-osx-x86_64, r-oldrel-osx-x86_64