CRAN Package Check Results for Package sensiPhy

Last updated on 2019-12-09 05:47:28 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.8.3 20.91 150.97 171.88 ERROR
r-devel-linux-x86_64-debian-gcc 0.8.3 14.69 174.65 189.34 OK
r-devel-linux-x86_64-fedora-clang 0.8.3 310.05 OK
r-devel-linux-x86_64-fedora-gcc 0.8.3 306.29 OK
r-devel-windows-ix86+x86_64 0.8.3 30.00 283.00 313.00 OK
r-devel-windows-ix86+x86_64-gcc8 0.8.3 33.00 332.00 365.00 OK
r-patched-linux-x86_64 0.8.3 17.26 206.88 224.14 OK
r-patched-solaris-x86 0.8.3 370.30 OK
r-release-linux-x86_64 0.8.3 16.75 209.14 225.89 OK
r-release-windows-ix86+x86_64 0.8.3 31.00 218.00 249.00 OK
r-release-osx-x86_64 0.8.3 OK
r-oldrel-windows-ix86+x86_64 0.8.3 20.00 189.00 209.00 OK
r-oldrel-osx-x86_64 0.8.3 OK

Check Details

Version: 0.8.3
Check: examples
Result: ERROR
    Running examples in 'sensiPhy-Ex.R' failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: intra_clade_phyglm
    > ### Title: Interaction between intraspecific variability and influential
    > ### clade detection - Phylogenetic Logistic Regression
    > ### Aliases: intra_clade_phyglm
    >
    > ### ** Examples
    >
    > ## Not run:
    > ##D set.seed(6987)
    > ##D phy = rtree(100)
    > ##D x = rTrait(n=1,phy=phy,parameters=list(ancestral.state=2,optimal.value=2,sigma2=1,alpha=1))
    > ##D X = cbind(rep(1,100),x)
    > ##D y = rbinTrait(n=1,phy=phy, beta=c(-1,0.5), alpha=.7 ,X=X)
    > ##D z = rnorm(n = length(x),mean = mean(x),sd = 0.1*mean(x))
    > ##D cla <- rep(c("A","B","C","D"), each = 25)
    > ##D dat = data.frame(y, x, z, cla)
    > ##D intra_clade <- intra_clade_phyglm(formula=y ~ x, data = dat, phy = phy,
    > ##D clade.col = "cla", n.sim = 30, n.intra = 3,
    > ##D x.transf = log, Vx = "z", distrib="normal")
    > ##D sensi_plot(intra_clade)
    > ##D sensi_plot(intra_clade, clade = "B", graphs = 2)
    > ## End(Not run)
    > ## Don't show:
    > set.seed(6987)
    > phy = rtree(100)
    > x = rTrait(n=1,phy=phy,parameters=list(ancestral.state=2,optimal.value=2,sigma2=1,alpha=1))
    > X = cbind(rep(1,100),x)
    > y = rbinTrait(n=1,phy=phy, beta=c(-1,0.5), alpha=.7 ,X=X)
    > z = rnorm(n = length(x),mean = mean(x),sd = 0.1*mean(x))
    > cla <- rep(c("A","B","C","D"), each = 25)
    > dat = data.frame(y, x, z, cla)
    > intra_clade <- intra_clade_phyglm(formula=y ~ x, data = dat, phy = phy,
    + clade.col = "cla", n.sim = 1, n.intra = 1,
    + x.transf = log, Vx = "z", distrib="normal")
    Warning in intra_clade_phyglm(formula = y ~ x, data = dat, phy = phy, clade.col = "cla", :
     distrib=normal: make sure that standard deviation is provided for Vx
    Used dataset has 100 species that match data and phylogeny
    
     |
     | | 0%
     |
     |======================================================================| 100%
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    sensiPhy
     --- call from context ---
    recombine(intra.clade, slot1 = 3, slot2 = 1)
     --- call from argument ---
    if (class(x[[1]]) == "data.frame" | class(x[[1]]) == "matrix" |
     class(x[[1]]) == "numeric") {
     n.rows <- nrow(x[[1]])
     if (is.null(n.rows)) {
     nam <- as.numeric(names(sensi.list))
     n.rows <- length(x[[1]])
     est.name <- names(sensi.list[[1]][[slot1]])[[slot2]]
     N <- rep(nam, each = n.rows)
     res <- data.frame(iteration = N, do.call("rbind", x))
     colnames(res)[2] <- est.name
     return(res)
     }
     else res <- data.frame(iteration = rep(names(x), sapply(x,
     nrow)), do.call(rbind, x))
     res$info <- unlist(lapply(x, rownames))
     return(res)
    } else stop("Check if slot indexing returns a valid data.frame or numeric value withn your list")
     --- R stacktrace ---
    where 1: recombine(intra.clade, slot1 = 3, slot2 = 1)
    where 2: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
    where 3: suppressWarnings(recombine(intra.clade, slot1 = 3, slot2 = 1))
    where 4: intra_clade_phyglm(formula = y ~ x, data = dat, phy = phy, clade.col = "cla",
     n.sim = 1, n.intra = 1, x.transf = log, Vx = "z", distrib = "normal")
    
     --- value of length: 2 type: logical ---
    [1] TRUE FALSE
     --- function from context ---
    function (sensi.list, slot1, slot2 = NULL)
    {
     is <- NULL
     if (is.null(slot2)) {
     x <- lapply(sensi.list, function(x) x[[slot1]])
     if (is(x[[1]], "list"))
     stop("Please also provide a value for slot2")
     if (is.na(match(class(x[[1]]), c("data.frame", "matrix"))))
     stop("Check if slot indexing returns a valid data.frame or numeric value withn your list")
     res <- data.frame(iteration = rep(names(x), sapply(x,
     nrow)), do.call(rbind, x))
     res$info <- unlist(lapply(x, rownames))
     return(res)
     }
     if (is.null(slot2) == FALSE) {
     x <- lapply(sensi.list, function(x) x[[slot1]][[slot2]])
     if (class(x[[1]]) == "data.frame" | class(x[[1]]) ==
     "matrix" | class(x[[1]]) == "numeric") {
     n.rows <- nrow(x[[1]])
     if (is.null(n.rows)) {
     nam <- as.numeric(names(sensi.list))
     n.rows <- length(x[[1]])
     est.name <- names(sensi.list[[1]][[slot1]])[[slot2]]
     N <- rep(nam, each = n.rows)
     res <- data.frame(iteration = N, do.call("rbind",
     x))
     colnames(res)[2] <- est.name
     return(res)
     }
     else res <- data.frame(iteration = rep(names(x),
     sapply(x, nrow)), do.call(rbind, x))
     res$info <- unlist(lapply(x, rownames))
     return(res)
     }
     else stop("Check if slot indexing returns a valid data.frame or numeric value withn your list")
     }
    }
    <bytecode: 0x101891c0>
    <environment: namespace:sensiPhy>
     --- function search by body ---
    Function recombine in namespace sensiPhy has this body.
     ----------- END OF FAILURE REPORT --------------
    Error in if (class(x[[1]]) == "data.frame" | class(x[[1]]) == "matrix" | :
     the condition has length > 1
    Calls: intra_clade_phyglm
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang