CRAN Package Check Results for Maintainer ‘Aleksandra Grudziaz <aleksandra.grudziaz at gmail.com>’

Last updated on 2018-09-26 01:46:57 CEST.

Package ERROR OK
survxai 1 11

Package survxai

Current CRAN status: ERROR: 1, OK: 11

Version: 0.2.0
Check: tests
Result: ERROR
     Running ‘testthat.R’ [98s/102s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(survxai)
     Loading required package: prodlim
     Welcome to survxai (version: 0.2.0).
     Information about the package can be found in the GitHub repository: https://github.com/MI2DataLab/survxai
     >
     > test_check("survxai")
     ── 1. Error: (unknown) (@test_plot_ceteris_paribus.R#3) ───────────────────────
     arguments imply differing number of rows: 0, 138
     1: source("objects_for_tests.R") at testthat/test_plot_ceteris_paribus.R:3
     2: withVisible(eval(ei, envir))
     3: eval(ei, envir)
     4: eval(ei, envir)
     5: model_performance(surve_rf)
     6: tryCatch({
     p <- pec(explainer$model, data = data, splitMethod = "none", formula = reference_formula)
     }, error = function(e) {
     p <- pec(explainer, data = data, splitMethod = "none", formula = reference_formula,
     reference = TRUE)
     return(p)
     })
     7: tryCatchList(expr, classes, parentenv, handlers)
     8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     9: value[[3L]](cond)
     10: pec(explainer, data = data, splitMethod = "none", formula = reference_formula, reference = TRUE)
     ...
     17: predict(object, newdata = newdata, importance = "none")
     18: predict.rfsrc(object, newdata = newdata, importance = "none")
     19: generic.predict.rfsrc(object, newdata, ensemble = ensemble, m.target = m.target,
     importance = importance, block.size = block.size, na.action = na.action, outcome = outcome,
     proximity = proximity, forest.wt = forest.wt, ptn.count = ptn.count, distance = distance,
     var.used = var.used, split.depth = split.depth, seed = seed, do.trace = do.trace,
     membership = membership, statistics = statistics, ...)
     20: map.factor(xvar.newdata, xfactor)
     21: data.frame(mclapply(1:length(gfactor$factor), function(k) {
     ptk <- (colnames(gvar) == gfactor$factor[k])
     factor.k <- gfactor$levels[[k]][gvar[, ptk]]
     labels.k <- gfactor$levels[[k]][sort(unique(gvar[, ptk]))]
     gk <- factor(factor.k, labels = labels.k, levels = labels.k, exclude = NULL)
     if (length(setdiff(gfactor$levels[[k]], labels.k)) > 0) {
     gk <- factor(as.character(gk), levels = gfactor$levels[[k]])
     }
     gk
     }))
     22: as.data.frame(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors)
     23: as.data.frame.list(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors)
     24: do.call(data.frame, c(x, alis))
     25: (function (..., row.names = NULL, check.rows = FALSE, check.names = TRUE, fix.empty.names = TRUE,
     stringsAsFactors = default.stringsAsFactors())
     {
     data.row.names <- if (check.rows && is.null(row.names))
     function(current, new, i) {
     if (is.character(current))
     new <- as.character(new)
     if (is.character(new))
     current <- as.character(current)
     if (anyDuplicated(new))
     return(current)
     if (is.null(current))
     return(new)
     if (all(current == new) || all(current == ""))
     return(new)
     stop(gettextf("mismatch of row names in arguments of 'data.frame', item %d",
     i), domain = NA)
     }
     else function(current, new, i) {
     if (is.null(current)) {
     if (anyDuplicated(new)) {
     warning(gettextf("some row.names duplicated: %s --> row.names NOT used",
     paste(which(duplicated(new)), collapse = ",")), domain = NA)
     current
     }
     else new
     }
     else current
     }
     object <- as.list(substitute(list(...)))[-1L]
     mirn <- missing(row.names)
     mrn <- is.null(row.names)
     x <- list(...)
     n <- length(x)
     if (n < 1L) {
     if (!mrn) {
     if (is.object(row.names) || !is.integer(row.names))
     row.names <- as.character(row.names)
     if (anyNA(row.names))
     stop("row names contain missing values")
     if (anyDuplicated(row.names))
     stop(gettextf("duplicate row.names: %s", paste(unique(row.names[duplicated(row.names)]),
     collapse = ", ")), domain = NA)
     }
     else row.names <- integer()
     return(structure(list(), names = character(), row.names = row.names, class = "data.frame"))
     }
     vnames <- names(x)
     if (length(vnames) != n)
     vnames <- character(n)
     no.vn <- !nzchar(vnames)
     vlist <- vnames <- as.list(vnames)
     nrows <- ncols <- integer(n)
     for (i in seq_len(n)) {
     xi <- if (is.character(x[[i]]) || is.list(x[[i]]))
     as.data.frame(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors)
     else as.data.frame(x[[i]], optional = TRUE)
     nrows[i] <- .row_names_info(xi)
     ncols[i] <- length(xi)
     namesi <- names(xi)
     if (ncols[i] > 1L) {
     if (length(namesi) == 0L)
     namesi <- seq_len(ncols[i])
     vnames[[i]] <- if (no.vn[i])
     namesi
     else paste(vnames[[i]], namesi, sep = ".")
     }
     else if (length(namesi)) {
     vnames[[i]] <- namesi
     }
     else if (fix.empty.names && no.vn[[i]]) {
     tmpname <- deparse(object[[i]], nlines = 1L)[1L]
     if (substr(tmpname, 1L, 2L) == "I(") {
     ntmpn <- nchar(tmpname, "c")
     if (substr(tmpname, ntmpn, ntmpn) == ")")
     tmpname <- substr(tmpname, 3L, ntmpn - 1L)
     }
     vnames[[i]] <- tmpname
     }
     if (mirn && nrows[i] > 0L) {
     rowsi <- attr(xi, "row.names")
     if (any(nzchar(rowsi)))
     row.names <- data.row.names(row.names, rowsi, i)
     }
     nrows[i] <- abs(nrows[i])
     vlist[[i]] <- xi
     }
     nr <- max(nrows)
     for (i in seq_len(n)[nrows < nr]) {
     xi <- vlist[[i]]
     if (nrows[i] > 0L && (nr%%nrows[i] == 0L)) {
     xi <- unclass(xi)
     fixed <- TRUE
     for (j in seq_along(xi)) {
     xi1 <- xi[[j]]
     if (is.vector(xi1) || is.factor(xi1))
     xi[[j]] <- rep(xi1, length.out = nr)
     else if (is.character(xi1) && inherits(xi1, "AsIs"))
     xi[[j]] <- structure(rep(xi1, length.out = nr), class = class(xi1))
     else if (inherits(xi1, "Date") || inherits(xi1, "POSIXct"))
     xi[[j]] <- rep(xi1, length.out = nr)
     else {
     fixed <- FALSE
     break
     }
     }
     if (fixed) {
     vlist[[i]] <- xi
     next
     }
     }
     stop(gettextf("arguments imply differing number of rows: %s", paste(unique(nrows),
     collapse = ", ")), domain = NA)
     }
     value <- unlist(vlist, recursive = FALSE, use.names = FALSE)
     vnames <- unlist(vnames[ncols > 0L])
     if (fix.empty.names && any(noname <- !nzchar(vnames)))
     vnames[noname] <- paste0("Var.", seq_along(vnames))[noname]
     if (check.names) {
     if (fix.empty.names)
     vnames <- make.names(vnames, unique = TRUE)
     else {
     nz <- nzchar(vnames)
     vnames[nz] <- make.names(vnames[nz], unique = TRUE)
     }
     }
     names(value) <- vnames
     if (!mrn) {
     if (length(row.names) == 1L && nr != 1L) {
     if (is.character(row.names))
     row.names <- match(row.names, vnames, 0L)
     if (length(row.names) != 1L || row.names < 1L || row.names > length(vnames))
     stop("'row.names' should specify one of the variables")
     i <- row.names
     row.names <- value[[i]]
     value <- value[-i]
     }
     else if (!is.null(row.names) && length(row.names) != nr)
     stop("row names supplied are of the wrong length")
     }
     else if (!is.null(row.names) && length(row.names) != nr) {
     warning("row names were found from a short variable and have been discarded")
     row.names <- NULL
     }
     class(value) <- "data.frame"
     if (is.null(row.names))
     attr(value, "row.names") <- .set_row_names(nr)
     else {
     if (is.object(row.names) || !is.integer(row.names))
     row.names <- as.character(row.names)
     if (anyNA(row.names))
     stop("row names contain missing values")
     if (anyDuplicated(row.names))
     stop(gettextf("duplicate row.names: %s", paste(unique(row.names[duplicated(row.names)]),
     collapse = ", ")), domain = NA)
     row.names(value) <- row.names
     }
     value
     })(NULL, structure(c(4L, 4L, 4L, 3L, 4L, 3L, 4L, 4L, 3L, 4L, 4L, 4L, 3L, 3L, 3L,
     3L, 4L, 4L, 2L, 2L, 4L, 4L, 2L, 3L, 3L, 2L, 4L, 4L, 4L, 2L, 3L, 2L, 4L, 3L, 4L, 2L,
     3L, 4L, 4L, 4L, 3L, 4L, 4L, 3L, 1L, 3L, 3L, 4L, 4L, 3L, 3L, 3L, 3L, 3L, 3L, 2L, 3L,
     3L, 4L, 4L, 4L, 3L, 3L, 1L, 2L, 4L, 4L, 3L, 3L, 3L, 3L, 3L, 4L, 4L, 3L, 3L, 4L, 4L,
     3L, 2L, 2L, 3L, 2L, 3L, 4L, 3L, 4L, 4L, 2L, 3L, 3L, 4L, 2L, 3L, 3L, 4L, 4L, 3L, 4L,
     4L, 2L, 3L, 2L, 2L, 1L, 2L, 3L, 3L, 2L, 2L, 3L, 4L, 2L, 1L, 2L, 3L, 2L, 3L, 3L, 3L,
     3L, 4L, 4L, 3L, 3L, 2L, 2L, 2L, 1L, 3L, 4L, 3L, 1L, 3L, 3L, 3L, 4L, 2L), .Label = c("1",
     "2", "3", "4"), class = "factor"), check.names = FALSE, fix.empty.names = TRUE, stringsAsFactors = TRUE)
     26: stop(gettextf("arguments imply differing number of rows: %s", paste(unique(nrows),
     collapse = ", ")), domain = NA)
    
     Model label: coxph
     Model class: cph,rms,coxph
     Data head :
     sex bili stage
     2 1 1.1 3
     3 0 1.4 4
     contribution
     bili 10.103%
     stage 7.714%
     sex 1.069%
     Model performance for Brier Score method.
     time prediction error
     1 0.1397260 ~ 0.75%
     2 0.1945205 ~ 1.43%
     3 0.3589041 ~ 2.28%
     4 0.3835616 ~ 2.99%
     5 0.5232877 ~ 3.96%
     6 0.5424658 ~ 4.67%
     7 0.5917808 ~ 4.24%
     8 0.6109589 ~ 4.86%
     9 0.8931507 ~ 5.69%
     10 1.2602740 ~ 6.6%
     x y value type label var
     1 0.1397260 0.9922858 1 pdp coxph sex
     2 0.1945205 0.9922858 1 pdp coxph sex
     3 0.3589041 0.9762765 1 pdp coxph sex
     4 0.3835616 0.9762765 1 pdp coxph sex
     5 0.5232877 0.9613915 1 pdp coxph sex
     6 0.5424658 0.9613915 1 pdp coxph sex
     y_hat new_x vname x_quant quant relative_quant label time class
     1 0.9978522 0 sex 0 0 0 coxph 0.1397260 factor
     2 0.9978522 0 sex 0 0 0 coxph 0.1945205 factor
     3 0.9927118 0 sex 0 0 0 coxph 0.3589041 factor
     4 0.9927118 0 sex 0 0 0 coxph 0.3835616 factor
     5 0.9870411 0 sex 0 0 0 coxph 0.5232877 factor
     6 0.9870411 0 sex 0 0 0 coxph 0.5424658 factor
     ══ testthat results ═══════════════════════════════════════════════════════════
     OK: 39 SKIPPED: 0 FAILED: 1
     1. Error: (unknown) (@test_plot_ceteris_paribus.R#3)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-patched-linux-x86_64