CRAN Package Check Results for Package boot

Last updated on 2018-04-29 01:46:35 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.3-20 6.99 77.25 84.24 OK
r-devel-linux-x86_64-debian-gcc 1.3-20 4.92 47.11 52.03 ERROR
r-devel-linux-x86_64-fedora-clang 1.3-20 101.19 OK
r-devel-linux-x86_64-fedora-gcc 1.3-20 99.05 OK
r-devel-windows-ix86+x86_64 1.3-20 17.00 91.00 108.00 OK
r-patched-linux-x86_64 1.3-20 6.15 78.81 84.96 OK
r-patched-solaris-x86 1.3-20 OK
r-release-linux-x86_64 1.3-20 5.12 82.01 87.13 OK
r-release-windows-ix86+x86_64 1.3-20 17.00 91.00 108.00 OK
r-release-osx-x86_64 1.3-20 OK
r-oldrel-windows-ix86+x86_64 1.3-20 12.00 109.00 121.00 OK
r-oldrel-osx-x86_64 1.3-20 OK

Check Details

Version: 1.3-20
Check: examples
Result: ERROR
    Running examples in ‘boot-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: censboot
    > ### Title: Bootstrap for Censored Data
    > ### Aliases: censboot cens.return
    > ### Keywords: survival
    >
    > ### ** Examples
    >
    > library(survival)
    
    Attaching package: ‘survival’
    
    The following object is masked from ‘package:boot’:
    
     aml
    
    > # Example 3.9 of Davison and Hinkley (1997) does a bootstrap on some
    > # remission times for patients with a type of leukaemia. The patients
    > # were divided into those who received maintenance chemotherapy and
    > # those who did not. Here we are interested in the median remission
    > # time for the two groups.
    > data(aml, package = "boot") # not the version in survival.
    > aml.fun <- function(data) {
    + surv <- survfit(Surv(time, cens) ~ group, data = data)
    + out <- NULL
    + st <- 1
    + for (s in 1:length(surv$strata)) {
    + inds <- st:(st + surv$strata[s]-1)
    + md <- min(surv$time[inds[1-surv$surv[inds] >= 0.5]])
    + st <- st + surv$strata[s]
    + out <- c(out, md)
    + }
    + out
    + }
    > aml.case <- censboot(aml, aml.fun, R = 499, strata = aml$group)
    Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
     no non-missing arguments to min; returning Inf
    Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
     no non-missing arguments to min; returning Inf
    Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
     no non-missing arguments to min; returning Inf
    Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
     no non-missing arguments to min; returning Inf
    Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
     no non-missing arguments to min; returning Inf
    Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
     no non-missing arguments to min; returning Inf
    Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
     no non-missing arguments to min; returning Inf
    Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
     no non-missing arguments to min; returning Inf
    Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
     no non-missing arguments to min; returning Inf
    Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
     no non-missing arguments to min; returning Inf
    Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
     no non-missing arguments to min; returning Inf
    Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
     no non-missing arguments to min; returning Inf
    Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
     no non-missing arguments to min; returning Inf
    Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
     no non-missing arguments to min; returning Inf
    Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
     no non-missing arguments to min; returning Inf
    Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
     no non-missing arguments to min; returning Inf
    Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
     no non-missing arguments to min; returning Inf
    Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
     no non-missing arguments to min; returning Inf
    Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
     no non-missing arguments to min; returning Inf
    Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
     no non-missing arguments to min; returning Inf
    Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
     no non-missing arguments to min; returning Inf
    Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
     no non-missing arguments to min; returning Inf
    Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
     no non-missing arguments to min; returning Inf
    Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
     no non-missing arguments to min; returning Inf
    Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
     no non-missing arguments to min; returning Inf
    Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
     no non-missing arguments to min; returning Inf
    >
    > # Now we will look at the same statistic using the conditional
    > # bootstrap and the weird bootstrap. For the conditional bootstrap
    > # the survival distribution is stratified but the censoring
    > # distribution is not.
    >
    > aml.s1 <- survfit(Surv(time, cens) ~ group, data = aml)
    > aml.s2 <- survfit(Surv(time-0.001*cens, 1-cens) ~ 1, data = aml)
    > aml.cond <- censboot(aml, aml.fun, R = 499, strata = aml$group,
    + F.surv = aml.s1, G.surv = aml.s2, sim = "cond")
    Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
     no non-missing arguments to min; returning Inf
    Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
     no non-missing arguments to min; returning Inf
    Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
     no non-missing arguments to min; returning Inf
    Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
     no non-missing arguments to min; returning Inf
    Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
     no non-missing arguments to min; returning Inf
    Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
     no non-missing arguments to min; returning Inf
    Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
     no non-missing arguments to min; returning Inf
    Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
     no non-missing arguments to min; returning Inf
    Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
     no non-missing arguments to min; returning Inf
    Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
     no non-missing arguments to min; returning Inf
    Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
     no non-missing arguments to min; returning Inf
    Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
     no non-missing arguments to min; returning Inf
    Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
     no non-missing arguments to min; returning Inf
    Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
     no non-missing arguments to min; returning Inf
    Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
     no non-missing arguments to min; returning Inf
    Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
     no non-missing arguments to min; returning Inf
    Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
     no non-missing arguments to min; returning Inf
    Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
     no non-missing arguments to min; returning Inf
    Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
     no non-missing arguments to min; returning Inf
    Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
     no non-missing arguments to min; returning Inf
    Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
     no non-missing arguments to min; returning Inf
    Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
     no non-missing arguments to min; returning Inf
    Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
     no non-missing arguments to min; returning Inf
    Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
     no non-missing arguments to min; returning Inf
    Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
     no non-missing arguments to min; returning Inf
    Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
     no non-missing arguments to min; returning Inf
    Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
     no non-missing arguments to min; returning Inf
    Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
     no non-missing arguments to min; returning Inf
    >
    >
    > # For the weird bootstrap we must redefine our function slightly since
    > # the data will not contain the group number.
    > aml.fun1 <- function(data, str) {
    + surv <- survfit(Surv(data[, 1], data[, 2]) ~ str)
    + out <- NULL
    + st <- 1
    + for (s in 1:length(surv$strata)) {
    + inds <- st:(st + surv$strata[s] - 1)
    + md <- min(surv$time[inds[1-surv$surv[inds] >= 0.5]])
    + st <- st + surv$strata[s]
    + out <- c(out, md)
    + }
    + out
    + }
    > aml.wei <- censboot(cbind(aml$time, aml$cens), aml.fun1, R = 499,
    + strata = aml$group, F.surv = aml.s1, sim = "weird")
    Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
     no non-missing arguments to min; returning Inf
    Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
     no non-missing arguments to min; returning Inf
    Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
     no non-missing arguments to min; returning Inf
    Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
     no non-missing arguments to min; returning Inf
    Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
     no non-missing arguments to min; returning Inf
    Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
     no non-missing arguments to min; returning Inf
    Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
     no non-missing arguments to min; returning Inf
    Warning in min(surv$time[inds[1 - surv$surv[inds] >= 0.5]]) :
     no non-missing arguments to min; returning Inf
    >
    > # Now for an example where a cox regression model has been fitted
    > # the data we will look at the melanoma data of Example 7.6 from
    > # Davison and Hinkley (1997). The fitted model assumes that there
    > # is a different survival distribution for the ulcerated and
    > # non-ulcerated groups but that the thickness of the tumour has a
    > # common effect. We will also assume that the censoring distribution
    > # is different in different age groups. The statistic of interest
    > # is the linear predictor. This is returned as the values at a
    > # number of equally spaced points in the range of interest.
    > data(melanoma, package = "boot")
    > library(splines)# for ns
    > mel.cox <- coxph(Surv(time, status == 1) ~ ns(thickness, df=4) + strata(ulcer),
    + data = melanoma)
    > mel.surv <- survfit(mel.cox)
    > agec <- cut(melanoma$age, c(0, 39, 49, 59, 69, 100))
    > mel.cens <- survfit(Surv(time - 0.001*(status == 1), status != 1) ~
    + strata(agec), data = melanoma)
    > mel.fun <- function(d) {
    + t1 <- ns(d$thickness, df=4)
    + cox <- coxph(Surv(d$time, d$status == 1) ~ t1+strata(d$ulcer))
    + ind <- !duplicated(d$thickness)
    + u <- d$thickness[!ind]
    + eta <- cox$linear.predictors[!ind]
    + sp <- smooth.spline(u, eta, df=20)
    + th <- seq(from = 0.25, to = 10, by = 0.25)
    + predict(sp, th)$y
    + }
    > mel.str <- cbind(melanoma$ulcer, agec)
    >
    > # this is slow!
    > mel.mod <- censboot(melanoma, mel.fun, R = 499, F.surv = mel.surv,
    + G.surv = mel.cens, cox = mel.cox, strata = mel.str, sim = "model")
    Error in call[[1L]] : object of type 'symbol' is not subsettable
    Calls: censboot ... model.frame.default -> makepredictcall -> makepredictcall.ns -> eval
    Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc