CRAN Package Check Results for Package spsur

Last updated on 2019-11-26 00:52:13 CET.

Check Details

Version: 1.0.0.3
Check: examples
Result: ERROR
    Running examples in 'spsur-Ex.R' failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: dgp_spsur
    > ### Title: Generation of a random dataset with a spatial SUR structure.
    > ### Aliases: dgp_spsur
    >
    > ### ** Examples
    >
    > ####################################
    > ######## CROSS SECTION DATA ########
    > ####################################
    >
    > ####################################
    > #### Example 1: DGP SLM model
    > ####################################
    > rm(list = ls()) # Clean memory
    > Tm <- 1 # Number of time periods
    > G <- 3 # Number of equations
    > N <- 50 # Number of spatial elements
    > p <- 3 # Number of independent variables
    > Sigma <- matrix(0.3, ncol = G, nrow = G)
    > diag(Sigma) <- 1
    > Betas <- c(1,2,3,1,-1,0.5,1,-0.5,2)
    > lambda <- 0.5 # level of spatial dependence
    > rho <- 0.0 # spatial autocorrelation error term = 0
    > # random coordinates
    > co <- cbind(runif(N,0,1),runif(N,0,1))
    > W <- spdep::nb2mat(spdep::knn2nb(spdep::knearneigh(co, k = 5,
    + longlat = FALSE)))
    > DGP <- dgp_spsur(Sigma = Sigma, Betas = Betas,
    + rho = rho, lambda = lambda, Tm = Tm,
    + G = G, N = N, p = p, W = W)
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    spsur
     --- call from context ---
    dgp_spsur(Sigma = Sigma, Betas = Betas, rho = rho, lambda = lambda,
     Tm = Tm, G = G, N = N, p = p, W = W)
     --- call from argument ---
    if (class(W) != "matrix") W <- as.matrix(W)
     --- R stacktrace ---
    where 1: dgp_spsur(Sigma = Sigma, Betas = Betas, rho = rho, lambda = lambda,
     Tm = Tm, G = G, N = N, p = p, W = W)
    
     --- value of length: 2 type: logical ---
    [1] FALSE TRUE
     --- function from context ---
    function (Sigma, Tm = 1, G, N, Betas, Thetas = NULL, rho = NULL,
     lambda = NULL, p = NULL, W = NULL, X = NULL, pdfU = "nvrnorm",
     pdfX = "nvrnorm")
    {
     if (!is.null(W)) {
     if (class(W) != "matrix")
     W <- as.matrix(W)
     rsumW <- rowSums(W)
     rsumW[rsumW == 0] <- 1
     nW <- dim(W)[1]
     W <- W/matrix(rep(rsumW, each = nW), nrow = nW, ncol = nW,
     byrow = TRUE)
     W <- Matrix::Matrix(W)
     }
     else W <- Matrix::Diagonal(N)
     if (Tm > 1 && G == 1) {
     G <- Tm
     Tm <- 1
     }
     if (!is.null(Thetas))
     durbin <- TRUE
     else durbin <- FALSE
     if (!is.null(p) & length(p) == 1)
     p <- matrix(p, nrow = G, ncol = 1)
     if (is.null(lambda))
     lambda <- rep(0, G)
     if (is.null(rho))
     rho <- rep(0, G)
     if (length(lambda) == 1)
     lambda <- as.numeric(matrix(lambda, nrow = G, ncol = 1))
     if (length(rho) == 1)
     rho <- as.numeric(matrix(rho, nrow = G, ncol = 1))
     if (is.null(X)) {
     if (is.null(p))
     stop("Arguments X and p can not be NULL simultaneously")
     if (pdfX == "nvrunif") {
     X <- cbind(matrix(1, N, 1), matrix(runif(N * (p[1] -
     1)), N, (p[1] - 1)))
     for (i in 1:(G - 1)) {
     X <- Matrix::bdiag(X, cbind(matrix(1, N, 1),
     matrix(runif(N * (p[i + 1] - 1)), N, (p[i +
     1] - 1))))
     }
     if (Tm > 1) {
     for (i in 1:(Tm - 1)) {
     X2 <- cbind(matrix(1, N, 1), matrix(runif(N *
     (p[1] - 1)), N, (p[1] - 1)))
     for (i in 1:(G - 1)) {
     X2 <- Matrix::bdiag(X2, cbind(matrix(1, N,
     1), matrix(runif(N * (p[i + 1] - 1)), N,
     (p[i + 1] - 1))))
     }
     X <- rbind(X, X2)
     }
     }
     }
     else if (pdfX == "nvrnorm") {
     X <- cbind(matrix(1, N, 1), matrix(rnorm(N * (p[1] -
     1), 0, 1), N, (p[1] - 1)))
     for (i in 1:(G - 1)) {
     X <- Matrix::bdiag(X, cbind(matrix(1, N, 1),
     matrix(rnorm(N * (p[i + 1] - 1), 0, 1), N,
     (p[i + 1] - 1))))
     }
     if (Tm > 1) {
     for (i in 1:(Tm - 1)) {
     X2 <- cbind(matrix(1, N, 1), matrix(rnorm(N *
     (p[1] - 1), 0, 1), N, (p[1] - 1)))
     for (i in 1:(G - 1)) {
     X2 <- Matrix::bdiag(X2, cbind(matrix(1, N,
     1), matrix(rnorm(N * (p[i + 1] - 1), 0,
     1), N, (p[i + 1] - 1))))
     }
     X <- rbind(X, X2)
     }
     }
     }
     else stop("pdfX only can be nvrnorm or nvrunif")
     nam <- c(paste0("Intercep_", 1), paste(paste0("X", 1,
     "_"), 1:(p[1] - 1), sep = ""))
     if (length(p > 1)) {
     for (i in 2:(length(p))) {
     nam <- c(nam, c(paste0("Intercep_", i), paste(paste0("X",
     i, "_"), 1:(p[i] - 1), sep = "")))
     }
     }
     dimnames(X)[[2]] <- nam
     }
     if (is.null(p)) {
     if ((ncol(X)%%G) != 0)
     stop("Argument p need to be set")
     p <- rep(ncol(X)/G, G)
     }
     IT <- Matrix::Diagonal(Tm)
     IR <- Matrix::Diagonal(N)
     IG <- Matrix::Diagonal(G)
     IGR <- Matrix::Diagonal(G * N)
     if (durbin) {
     WX <- (IT %x% IG %x% W) %*% X
     dimnames(WX)[[2]] <- paste0("W_", colnames(X))
     Xdurbin <- NULL
     pdurbin <- p - 1
     for (i in 1:length(p)) {
     if (i == 1) {
     Xdurbin <- cbind(X[, 1:p[i]], WX[, 2:p[i]])
     Coeff <- c(Betas[1:p[1]], Thetas[1:pdurbin[1]])
     }
     else {
     Xdurbin <- cbind(Xdurbin, X[, (cumsum(p)[i -
     1] + 1):cumsum(p)[i]], WX[, (cumsum(p)[i -
     1] + 2):cumsum(p)[i]])
     Coeff <- c(Coeff, Betas[(cumsum(p)[i - 1] + 1):cumsum(p)[i]],
     Thetas[(cumsum(pdurbin)[i - 1] + 1):cumsum(pdurbin)[i]])
     }
     }
     }
     S <- Sigma
     OME <- (IT %x% S) %x% IR
     chol_OME <- Matrix::Cholesky(OME)
     M <- Matrix::Matrix(0, ncol = 1, nrow = Tm * G * N)
     U <- matrix(sparseMVN::rmvn.sparse(n = 1, mu = M, CH = chol_OME,
     prec = FALSE), ncol = 1)
     U <- Matrix::Matrix(U)
     if (pdfU == "lognvrnorm")
     U <- exp(U)
     if (pdfU != "lognvrnorm" && pdfU != "nvrnorm")
     print(" Improper pdf. The errors will be drawn from a multivariate Normal ")
     IBU <- Matrix::solve(IT %x% (IGR - diag(rho) %x% W), U)
     if (durbin) {
     Y <- Matrix::solve(IT %x% (IGR - diag(lambda) %x% W),
     (Xdurbin %*% Coeff + IBU))
     }
     else {
     Y <- Matrix::solve(IT %x% (IGR - diag(lambda) %x% W),
     (X %*% Betas + IBU))
     }
     results <- list(X = as.matrix(X), Y = as.matrix(Y))
    }
    <bytecode: 0x4d4d340>
    <environment: namespace:spsur>
     --- function search by body ---
    Function dgp_spsur in namespace spsur has this body.
     ----------- END OF FAILURE REPORT --------------
    Fatal error: the condition has length > 1
Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.0.0.3
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building 'spsur-vignette.Rmd' using rmarkdown
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    spsur
     --- call from context ---
    lmtestspsur(Form = spcformula, data = spc, W = Wspc)
     --- call from argument ---
    if (class(W) != "matrix") W <- as.matrix(W)
     --- R stacktrace ---
    where 1: lmtestspsur(Form = spcformula, data = spc, W = Wspc)
    where 2: eval(expr, envir, enclos)
    where 3: eval(expr, envir, enclos)
    where 4: withVisible(eval(expr, envir, enclos))
    where 5: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler,
     error = eHandler, message = mHandler)
    where 6: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir,
     enclos)), warning = wHandler, error = eHandler, message = mHandler))
    where 7: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr,
     envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
    where 8: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos,
     debug = debug, last = i == length(out), use_try = stop_on_error !=
     2L, keep_warning = keep_warning, keep_message = keep_message,
     output_handler = output_handler, include_timing = include_timing)
    where 9: evaluate::evaluate(...)
    where 10: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning),
     keep_message = !isFALSE(options$message), stop_on_error = if (options$error &&
     options$include) 0L else 2L, output_handler = knit_handlers(options$render,
     options))
    where 11: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE,
     keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message),
     stop_on_error = if (options$error && options$include) 0L else 2L,
     output_handler = knit_handlers(options$render, options)))
    where 12: block_exec(params)
    where 13: call_block(x)
    where 14: process_group.block(group)
    where 15: process_group(group)
    where 16: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
     error = function(e) {
     setwd(wd)
     cat(res, sep = "\n", file = output %n% "")
     message("Quitting from lines ", paste(current_lines(i),
     collapse = "-"), " (", knit_concord$get("infile"),
     ") ")
     })
    where 17: process_file(text, output)
    where 18: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet,
     encoding = encoding)
    where 19: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
     ...)
    where 20: vweave_rmarkdown(...)
    where 21: engine$weave(file, quiet = quiet, encoding = enc)
    where 22: doTryCatch(return(expr), name, parentenv, handler)
    where 23: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    where 24: tryCatchList(expr, classes, parentenv, handlers)
    where 25: tryCatch({
     engine$weave(file, quiet = quiet, encoding = enc)
     setwd(startdir)
     output <- find_vignette_product(name, by = "weave", engine = engine)
     if (!have.makefile && vignette_is_tex(output)) {
     texi2pdf(file = output, clean = FALSE, quiet = quiet)
     output <- find_vignette_product(name, by = "texi2pdf",
     engine = engine)
     }
     outputs <- c(outputs, output)
    }, error = function(e) {
     thisOK <<- FALSE
     fails <<- c(fails, file)
     message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",
     file, conditionMessage(e)))
    })
    where 26: tools:::buildVignettes(dir = "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/spsur.Rcheck/vign_test/spsur",
     ser_elibs = "/tmp/RtmpZ5zyTk/file7e235b30fb4b.rds")
    
     --- value of length: 2 type: logical ---
    [1] FALSE TRUE
     --- function from context ---
    function (Form = NULL, data = NULL, W = NULL, X = NULL, Y = NULL,
     time = NULL, G = NULL, N = NULL, Tm = NULL, print_table = TRUE)
    {
     if (is.null(W))
     stop("W matrix is needed")
     if (!is.null(W)) {
     if (class(W) != "matrix")
     W <- as.matrix(W)
     rsumW <- rowSums(W)
     rsumW[rsumW == 0] <- 1
     nW <- dim(W)[1]
     W <- W/matrix(rep(rsumW, each = nW), nrow = nW, ncol = nW,
     byrow = TRUE)
     W <- Matrix::Matrix(W)
     }
     if (is.null(time)) {
     if (!is.null(Form) && !is.null(data)) {
     if (!any(class(Form) == "Formula"))
     Form <- Formula::Formula(Form)
     get_XY <- get_data_spsur(formula = Form, data = data,
     W = W)
     Y <- get_XY$Y
     X <- get_XY$X
     G <- get_XY$G
     N <- get_XY$N
     Tm <- get_XY$Tm
     p <- get_XY$p
     rm(get_XY)
     }
     else {
     if (G == 1 && Tm > 1) {
     G <- Tm
     Tm <- 1
     }
     }
     }
     else {
     if (class(time) != "factor")
     time <- as.factor(time)
     time <- droplevels(time)
     if (length(time) != nrow(data))
     stop("time must have same length than the\n number of rows in data")
     mt <- terms(Form)
     G <- length(levels(time))
     Ylist <- vector("list", G)
     Xlist <- vector("list", G)
     p <- NULL
     namesX <- NULL
     levels_time <- levels(time)
     for (i in 1:G) {
     data_i <- model.frame(mt, data = data[time == levels_time[i],
     ])
     Ylist[[i]] <- data_i[, 1]
     Xlist[[i]] <- model.matrix(mt, data = data[time ==
     levels_time[i], ])
     p <- c(p, ncol(Xlist[[i]]))
     namesX <- c(namesX, paste(colnames(Xlist[[i]]), i,
     sep = "_"))
     }
     Y <- matrix(unlist(Ylist), ncol = 1)
     X <- as.matrix(Matrix::bdiag(Xlist))
     colnames(X) <- namesX
     N <- length(Ylist[[1]])
     Tm <- 1
     }
     res <- sur3_spdiag(Tm = Tm, G = G, N = N, Y = Y, X = X, W = W)
     table_results <- cbind(res$stat, res$df, pchisq(res$stat,
     res$df, lower.tail = FALSE))
     rownames(table_results) <- res$stat_names
     colnames(table_results) <- c("LM-Stat.", "DF", "p-value")
     if (print_table)
     printCoefmat(table_results, P.values = TRUE, has.Pvalue = TRUE,
     digits = 4)
     return(res)
    }
    <bytecode: 0x71b2f50>
    <environment: namespace:spsur>
     --- function search by body ---
    Function lmtestspsur in namespace spsur has this body.
     ----------- END OF FAILURE REPORT --------------
    Fatal error: the condition has length > 1
Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.0.0.3
Check: examples
Result: ERROR
    Running examples in ‘spsur-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: dgp_spsur
    > ### Title: Generation of a random dataset with a spatial SUR structure.
    > ### Aliases: dgp_spsur
    >
    > ### ** Examples
    >
    > ####################################
    > ######## CROSS SECTION DATA ########
    > ####################################
    >
    > ####################################
    > #### Example 1: DGP SLM model
    > ####################################
    > rm(list = ls()) # Clean memory
    > Tm <- 1 # Number of time periods
    > G <- 3 # Number of equations
    > N <- 50 # Number of spatial elements
    > p <- 3 # Number of independent variables
    > Sigma <- matrix(0.3, ncol = G, nrow = G)
    > diag(Sigma) <- 1
    > Betas <- c(1,2,3,1,-1,0.5,1,-0.5,2)
    > lambda <- 0.5 # level of spatial dependence
    > rho <- 0.0 # spatial autocorrelation error term = 0
    > # random coordinates
    > co <- cbind(runif(N,0,1),runif(N,0,1))
    > W <- spdep::nb2mat(spdep::knn2nb(spdep::knearneigh(co, k = 5,
    + longlat = FALSE)))
    > DGP <- dgp_spsur(Sigma = Sigma, Betas = Betas,
    + rho = rho, lambda = lambda, Tm = Tm,
    + G = G, N = N, p = p, W = W)
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    spsur
     --- call from context ---
    dgp_spsur(Sigma = Sigma, Betas = Betas, rho = rho, lambda = lambda,
     Tm = Tm, G = G, N = N, p = p, W = W)
     --- call from argument ---
    if (class(W) != "matrix") W <- as.matrix(W)
     --- R stacktrace ---
    where 1: dgp_spsur(Sigma = Sigma, Betas = Betas, rho = rho, lambda = lambda,
     Tm = Tm, G = G, N = N, p = p, W = W)
    
     --- value of length: 2 type: logical ---
    [1] FALSE TRUE
     --- function from context ---
    function (Sigma, Tm = 1, G, N, Betas, Thetas = NULL, rho = NULL,
     lambda = NULL, p = NULL, W = NULL, X = NULL, pdfU = "nvrnorm",
     pdfX = "nvrnorm")
    {
     if (!is.null(W)) {
     if (class(W) != "matrix")
     W <- as.matrix(W)
     rsumW <- rowSums(W)
     rsumW[rsumW == 0] <- 1
     nW <- dim(W)[1]
     W <- W/matrix(rep(rsumW, each = nW), nrow = nW, ncol = nW,
     byrow = TRUE)
     W <- Matrix::Matrix(W)
     }
     else W <- Matrix::Diagonal(N)
     if (Tm > 1 && G == 1) {
     G <- Tm
     Tm <- 1
     }
     if (!is.null(Thetas))
     durbin <- TRUE
     else durbin <- FALSE
     if (!is.null(p) & length(p) == 1)
     p <- matrix(p, nrow = G, ncol = 1)
     if (is.null(lambda))
     lambda <- rep(0, G)
     if (is.null(rho))
     rho <- rep(0, G)
     if (length(lambda) == 1)
     lambda <- as.numeric(matrix(lambda, nrow = G, ncol = 1))
     if (length(rho) == 1)
     rho <- as.numeric(matrix(rho, nrow = G, ncol = 1))
     if (is.null(X)) {
     if (is.null(p))
     stop("Arguments X and p can not be NULL simultaneously")
     if (pdfX == "nvrunif") {
     X <- cbind(matrix(1, N, 1), matrix(runif(N * (p[1] -
     1)), N, (p[1] - 1)))
     for (i in 1:(G - 1)) {
     X <- Matrix::bdiag(X, cbind(matrix(1, N, 1),
     matrix(runif(N * (p[i + 1] - 1)), N, (p[i +
     1] - 1))))
     }
     if (Tm > 1) {
     for (i in 1:(Tm - 1)) {
     X2 <- cbind(matrix(1, N, 1), matrix(runif(N *
     (p[1] - 1)), N, (p[1] - 1)))
     for (i in 1:(G - 1)) {
     X2 <- Matrix::bdiag(X2, cbind(matrix(1, N,
     1), matrix(runif(N * (p[i + 1] - 1)), N,
     (p[i + 1] - 1))))
     }
     X <- rbind(X, X2)
     }
     }
     }
     else if (pdfX == "nvrnorm") {
     X <- cbind(matrix(1, N, 1), matrix(rnorm(N * (p[1] -
     1), 0, 1), N, (p[1] - 1)))
     for (i in 1:(G - 1)) {
     X <- Matrix::bdiag(X, cbind(matrix(1, N, 1),
     matrix(rnorm(N * (p[i + 1] - 1), 0, 1), N,
     (p[i + 1] - 1))))
     }
     if (Tm > 1) {
     for (i in 1:(Tm - 1)) {
     X2 <- cbind(matrix(1, N, 1), matrix(rnorm(N *
     (p[1] - 1), 0, 1), N, (p[1] - 1)))
     for (i in 1:(G - 1)) {
     X2 <- Matrix::bdiag(X2, cbind(matrix(1, N,
     1), matrix(rnorm(N * (p[i + 1] - 1), 0,
     1), N, (p[i + 1] - 1))))
     }
     X <- rbind(X, X2)
     }
     }
     }
     else stop("pdfX only can be nvrnorm or nvrunif")
     nam <- c(paste0("Intercep_", 1), paste(paste0("X", 1,
     "_"), 1:(p[1] - 1), sep = ""))
     if (length(p > 1)) {
     for (i in 2:(length(p))) {
     nam <- c(nam, c(paste0("Intercep_", i), paste(paste0("X",
     i, "_"), 1:(p[i] - 1), sep = "")))
     }
     }
     dimnames(X)[[2]] <- nam
     }
     if (is.null(p)) {
     if ((ncol(X)%%G) != 0)
     stop("Argument p need to be set")
     p <- rep(ncol(X)/G, G)
     }
     IT <- Matrix::Diagonal(Tm)
     IR <- Matrix::Diagonal(N)
     IG <- Matrix::Diagonal(G)
     IGR <- Matrix::Diagonal(G * N)
     if (durbin) {
     WX <- (IT %x% IG %x% W) %*% X
     dimnames(WX)[[2]] <- paste0("W_", colnames(X))
     Xdurbin <- NULL
     pdurbin <- p - 1
     for (i in 1:length(p)) {
     if (i == 1) {
     Xdurbin <- cbind(X[, 1:p[i]], WX[, 2:p[i]])
     Coeff <- c(Betas[1:p[1]], Thetas[1:pdurbin[1]])
     }
     else {
     Xdurbin <- cbind(Xdurbin, X[, (cumsum(p)[i -
     1] + 1):cumsum(p)[i]], WX[, (cumsum(p)[i -
     1] + 2):cumsum(p)[i]])
     Coeff <- c(Coeff, Betas[(cumsum(p)[i - 1] + 1):cumsum(p)[i]],
     Thetas[(cumsum(pdurbin)[i - 1] + 1):cumsum(pdurbin)[i]])
     }
     }
     }
     S <- Sigma
     OME <- (IT %x% S) %x% IR
     chol_OME <- Matrix::Cholesky(OME)
     M <- Matrix::Matrix(0, ncol = 1, nrow = Tm * G * N)
     U <- matrix(sparseMVN::rmvn.sparse(n = 1, mu = M, CH = chol_OME,
     prec = FALSE), ncol = 1)
     U <- Matrix::Matrix(U)
     if (pdfU == "lognvrnorm")
     U <- exp(U)
     if (pdfU != "lognvrnorm" && pdfU != "nvrnorm")
     print(" Improper pdf. The errors will be drawn from a multivariate Normal ")
     IBU <- Matrix::solve(IT %x% (IGR - diag(rho) %x% W), U)
     if (durbin) {
     Y <- Matrix::solve(IT %x% (IGR - diag(lambda) %x% W),
     (Xdurbin %*% Coeff + IBU))
     }
     else {
     Y <- Matrix::solve(IT %x% (IGR - diag(lambda) %x% W),
     (X %*% Betas + IBU))
     }
     results <- list(X = as.matrix(X), Y = as.matrix(Y))
    }
    <bytecode: 0x55f2495c7f20>
    <environment: namespace:spsur>
     --- function search by body ---
    Function dgp_spsur in namespace spsur has this body.
     ----------- END OF FAILURE REPORT --------------
    Fatal error: the condition has length > 1
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.0.0.3
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘spsur-vignette.Rmd’ using rmarkdown
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    spsur
     --- call from context ---
    lmtestspsur(Form = spcformula, data = spc, W = Wspc)
     --- call from argument ---
    if (class(W) != "matrix") W <- as.matrix(W)
     --- R stacktrace ---
    where 1: lmtestspsur(Form = spcformula, data = spc, W = Wspc)
    where 2: eval(expr, envir, enclos)
    where 3: eval(expr, envir, enclos)
    where 4: withVisible(eval(expr, envir, enclos))
    where 5: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler,
     error = eHandler, message = mHandler)
    where 6: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir,
     enclos)), warning = wHandler, error = eHandler, message = mHandler))
    where 7: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr,
     envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
    where 8: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos,
     debug = debug, last = i == length(out), use_try = stop_on_error !=
     2L, keep_warning = keep_warning, keep_message = keep_message,
     output_handler = output_handler, include_timing = include_timing)
    where 9: evaluate::evaluate(...)
    where 10: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning),
     keep_message = !isFALSE(options$message), stop_on_error = if (options$error &&
     options$include) 0L else 2L, output_handler = knit_handlers(options$render,
     options))
    where 11: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE,
     keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message),
     stop_on_error = if (options$error && options$include) 0L else 2L,
     output_handler = knit_handlers(options$render, options)))
    where 12: block_exec(params)
    where 13: call_block(x)
    where 14: process_group.block(group)
    where 15: process_group(group)
    where 16: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
     error = function(e) {
     setwd(wd)
     cat(res, sep = "\n", file = output %n% "")
     message("Quitting from lines ", paste(current_lines(i),
     collapse = "-"), " (", knit_concord$get("infile"),
     ") ")
     })
    where 17: process_file(text, output)
    where 18: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet,
     encoding = encoding)
    where 19: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
     ...)
    where 20: vweave_rmarkdown(...)
    where 21: engine$weave(file, quiet = quiet, encoding = enc)
    where 22: doTryCatch(return(expr), name, parentenv, handler)
    where 23: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    where 24: tryCatchList(expr, classes, parentenv, handlers)
    where 25: tryCatch({
     engine$weave(file, quiet = quiet, encoding = enc)
     setwd(startdir)
     output <- find_vignette_product(name, by = "weave", engine = engine)
     if (!have.makefile && vignette_is_tex(output)) {
     texi2pdf(file = output, clean = FALSE, quiet = quiet)
     output <- find_vignette_product(name, by = "texi2pdf",
     engine = engine)
     }
     outputs <- c(outputs, output)
    }, error = function(e) {
     thisOK <<- FALSE
     fails <<- c(fails, file)
     message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",
     file, conditionMessage(e)))
    })
    where 26: tools:::buildVignettes(dir = "/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/spsur.Rcheck/vign_test/spsur",
     ser_elibs = "/home/hornik/tmp/scratch/Rtmpf7WdWV/file20f21c48c405.rds")
    
     --- value of length: 2 type: logical ---
    [1] FALSE TRUE
     --- function from context ---
    function (Form = NULL, data = NULL, W = NULL, X = NULL, Y = NULL,
     time = NULL, G = NULL, N = NULL, Tm = NULL, print_table = TRUE)
    {
     if (is.null(W))
     stop("W matrix is needed")
     if (!is.null(W)) {
     if (class(W) != "matrix")
     W <- as.matrix(W)
     rsumW <- rowSums(W)
     rsumW[rsumW == 0] <- 1
     nW <- dim(W)[1]
     W <- W/matrix(rep(rsumW, each = nW), nrow = nW, ncol = nW,
     byrow = TRUE)
     W <- Matrix::Matrix(W)
     }
     if (is.null(time)) {
     if (!is.null(Form) && !is.null(data)) {
     if (!any(class(Form) == "Formula"))
     Form <- Formula::Formula(Form)
     get_XY <- get_data_spsur(formula = Form, data = data,
     W = W)
     Y <- get_XY$Y
     X <- get_XY$X
     G <- get_XY$G
     N <- get_XY$N
     Tm <- get_XY$Tm
     p <- get_XY$p
     rm(get_XY)
     }
     else {
     if (G == 1 && Tm > 1) {
     G <- Tm
     Tm <- 1
     }
     }
     }
     else {
     if (class(time) != "factor")
     time <- as.factor(time)
     time <- droplevels(time)
     if (length(time) != nrow(data))
     stop("time must have same length than the\n number of rows in data")
     mt <- terms(Form)
     G <- length(levels(time))
     Ylist <- vector("list", G)
     Xlist <- vector("list", G)
     p <- NULL
     namesX <- NULL
     levels_time <- levels(time)
     for (i in 1:G) {
     data_i <- model.frame(mt, data = data[time == levels_time[i],
     ])
     Ylist[[i]] <- data_i[, 1]
     Xlist[[i]] <- model.matrix(mt, data = data[time ==
     levels_time[i], ])
     p <- c(p, ncol(Xlist[[i]]))
     namesX <- c(namesX, paste(colnames(Xlist[[i]]), i,
     sep = "_"))
     }
     Y <- matrix(unlist(Ylist), ncol = 1)
     X <- as.matrix(Matrix::bdiag(Xlist))
     colnames(X) <- namesX
     N <- length(Ylist[[1]])
     Tm <- 1
     }
     res <- sur3_spdiag(Tm = Tm, G = G, N = N, Y = Y, X = X, W = W)
     table_results <- cbind(res$stat, res$df, pchisq(res$stat,
     res$df, lower.tail = FALSE))
     rownames(table_results) <- res$stat_names
     colnames(table_results) <- c("LM-Stat.", "DF", "p-value")
     if (print_table)
     printCoefmat(table_results, P.values = TRUE, has.Pvalue = TRUE,
     digits = 4)
     return(res)
    }
    <bytecode: 0x5618e0825c88>
    <environment: namespace:spsur>
     --- function search by body ---
    Function lmtestspsur in namespace spsur has this body.
     ----------- END OF FAILURE REPORT --------------
    Fatal error: the condition has length > 1
Flavor: r-devel-linux-x86_64-debian-gcc