CRAN Package Check Results for Package spANOVA

Last updated on 2020-01-27 00:48:23 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.99.1 20.41 147.81 168.22 ERROR
r-devel-linux-x86_64-debian-gcc 0.99.1 16.85 121.99 138.84 OK
r-devel-linux-x86_64-fedora-clang 0.99.1 217.96 WARN
r-devel-linux-x86_64-fedora-gcc 0.99.1 210.02 OK
r-devel-windows-ix86+x86_64 0.99.1 1.00 7.00 8.00 ERROR
r-devel-windows-ix86+x86_64-gcc8 0.99.1 59.00 151.00 210.00 OK
r-patched-linux-x86_64 0.99.1 17.71 145.46 163.17 OK
r-patched-solaris-x86 0.99.1 334.50 OK
r-release-linux-x86_64 0.99.1 16.78 143.33 160.11 OK
r-release-windows-ix86+x86_64 0.99.1 26.00 141.00 167.00 OK
r-release-osx-x86_64 0.99.1 WARN
r-oldrel-windows-ix86+x86_64 0.99.1 21.00 130.00 151.00 OK
r-oldrel-osx-x86_64 0.99.1 WARN

Check Details

Version: 0.99.1
Check: examples
Result: ERROR
    Running examples in 'spANOVA-Ex.R' failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: aovSar.crd
    > ### Title: Using a SAR model to handle spatial dependence in a Completely
    > ### Randomized Design
    > ### Aliases: aovSar.crd
    >
    > ### ** Examples
    >
    > data("crd_simulated")
    > resp <- crd_simulated$y
    > treat <- crd_simulated$trat
    > coord <- cbind(crd_simulated$coordX, crd_simulated$coordY)
    > cv <- aovSar.crd(resp, treat, coord)
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    spANOVA
     --- call from context ---
    aovSar.crd(resp, treat, coord)
     --- call from argument ---
    if (!(is.matrix(coord) | class(coord) == "SpatialPoints")) {
     stop("'coord' must be a matrix or SpatialPoints object")
    }
     --- R stacktrace ---
    where 1: aovSar.crd(resp, treat, coord)
    
     --- value of length: 2 type: logical ---
    [1] FALSE FALSE
     --- function from context ---
    function (resp, treat, coord, seq.radius)
    {
     if (!(is.vector(resp) | is.numeric(resp))) {
     stop("'resp' must be a vector or numeric")
     }
     if (!(is.vector(treat) | is.numeric(treat))) {
     stop("'treat' must be a vector or numeric")
     }
     if (!(is.matrix(coord) | class(coord) == "SpatialPoints")) {
     stop("'coord' must be a matrix or SpatialPoints object")
     }
     if (ncol(coord) < 2) {
     stop("'coord' must have at least two columns")
     }
     if (missing(seq.radius)) {
     max.dist <- max(dist(coord))
     seq.radius <- seq(0, 0.5 * max.dist, l = 11)[-1]
     }
     params <- data.frame(radius = 0, rho = 0, AIC = 0)
     anova.list <- list()
     n <- length(resp)
     p.radius <- length(seq.radius)
     Y_ajus <- NULL
     treat <- factor(treat)
     for (i in 1:p.radius) {
     nb <- dnearneigh(coord, 0, seq.radius[i])
     w <- try(nb2mat(nb, style = "W"), silent = TRUE)
     test <- grepl("Error", w)
     k <- 0.1
     while (test[1] == TRUE) {
     seq.radius <- seq(0, (0.5 + k) * max.dist, l = 11)[-1]
     nb <- dnearneigh(coord, 0, seq.radius[i])
     w <- try(nb2mat(nb, style = "W"), silent = TRUE)
     test <- grepl("Error", w)
     k <- k + 0.1
     }
     listw <- nb2listw(nb, glist = NULL, style = "W")
     SAR <- lagsarlm(resp ~ treat, listw = listw, method = "eigen",
     tol.solve = 1e-15)
     ajuste <- summary(SAR)
     rho <- as.numeric(ajuste["rho"]$rho)
     params[i, ] <- c(raio = seq.radius[i], rho = rho, AIC = AIC(SAR))
     }
     best.par <- which.min(params$AIC)
     beta <- mean(resp)
     nb <- dnearneigh(coord, 0, seq.radius[best.par])
     w <- nb2mat(nb, style = "W")
     Y_ajus <- resp - (params[best.par, "rho"] * w %*% resp -
     params[best.par, "rho"] * beta)
     aov.cl <- anova(aov(resp ~ treat))
     model.adj <- aov(Y_ajus ~ treat)
     aov.adj <- anova(model.adj)
     Sqt.nadj <- sum(aov.cl[, 2])
     gltrat <- aov.adj[1][[1]][1]
     glerror <- aov.adj[1][[1]][2]
     gltot <- sum(gltrat, glerror)
     sqtrat <- aov.adj[2][[1]][1]
     sqerror <- aov.adj[2][[1]][2]
     sqtot <- sum(sqtrat, sqerror)
     sqtotcor <- Sqt.nadj - sqtot
     mstrat <- sqtrat/gltrat
     mserror <- sqerror/glerror
     ftrat <- mstrat/mserror
     pvalue <- pf(ftrat, gltrat, glerror, lower.tail = FALSE)
     name.y <- paste(deparse(substitute(resp)))
     name.x <- paste(deparse(substitute(treat)))
     outpt <- list(DF = round(c(gltrat, glerror, gltot), 0), SS = c(sqtrat,
     sqerror, sqtotcor), MS = c(mstrat, mserror), Fc = c(ftrat),
     residuals = resid(model.adj), p.value = c(pvalue), rho = params[best.par,
     "rho"], Par = params, y_orig = resp, y_ajus = Y_ajus,
     treat = treat, modelAdj = model.adj, modelstd = aov.cl,
     namey = name.y, namex = name.x)
     class(outpt) <- c("SARanova", "SARcrd", class(aov.adj))
     return(outpt)
    }
    <bytecode: 0xc037d28>
    <environment: namespace:spANOVA>
     --- function search by body ---
    Function aovSar.crd in namespace spANOVA has this body.
     ----------- END OF FAILURE REPORT --------------
    Error in if (!(is.matrix(coord) | class(coord) == "SpatialPoints")) { :
     the condition has length > 1
    Calls: aovSar.crd
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.99.1
Check: package dependencies
Result: WARN
    Requires orphaned package: ‘geoR’
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 0.99.1
Check: whether package can be installed
Result: ERROR
    Installation failed.
Flavor: r-devel-windows-ix86+x86_64

Version: 0.99.1
Check: dependencies in R code
Result: NOTE
    No protocol specified
    No protocol specified
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 0.99.1
Check: S3 generic/method consistency
Result: WARN
    No protocol specified
    No protocol specified
    See section ‘Generic functions and methods’ in the ‘Writing R
    Extensions’ manual.
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 0.99.1
Check: replacement functions
Result: WARN
    No protocol specified
    No protocol specified
    The argument of a replacement function which corresponds to the right
    hand side must be named ‘value’.
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 0.99.1
Check: foreign function calls
Result: NOTE
    No protocol specified
    No protocol specified
    See chapter ‘System and foreign language interfaces’ in the ‘Writing R
    Extensions’ manual.
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 0.99.1
Check: R code for possible problems
Result: NOTE
    No protocol specified
    No protocol specified
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 0.99.1
Check: for missing documentation entries
Result: WARN
    No protocol specified
    No protocol specified
    All user-level objects in a package should have documentation entries.
    See chapter ‘Writing R documentation files’ in the ‘Writing R
    Extensions’ manual.
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 0.99.1
Check: for code/documentation mismatches
Result: WARN
    No protocol specified
    No protocol specified
    No protocol specified
    No protocol specified
    No protocol specified
    No protocol specified
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 0.99.1
Check: Rd \usage sections
Result: NOTE
    No protocol specified
    No protocol specified
    The \usage entries for S3 methods should use the \method markup and not
    their full name.
    See chapter ‘Writing R documentation files’ in the ‘Writing R
    Extensions’ manual.
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64