* using log directory ‘/data/gannet/ripley/R/packages/tests-Suggests/hrIPW.Rcheck’
* using R Under development (unstable) (2022-05-18 r82372)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘hrIPW/DESCRIPTION’ ... OK
* this is package ‘hrIPW’ version ‘0.1.3’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package suggested but not available for checking: ‘RISCA’
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘hrIPW’ can be installed ... [11s/12s] OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [14s/15s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... [16s/16s] ERROR
Running examples in ‘hrIPW-Ex.R’ failed
The error most likely occurred in:

> ### Name: hrIPW
> ### Title: Hazard ratio estimation using Cox model weighted by the
> ###   propensity score
> ### Aliases: hrIPW
> 
> ### ** Examples
> 
> ## Using a simulated cohort
> data(hrData, package = "hrIPW")
> hrIPW(hrData, time = "time", status = "status", exposure = "Trt",
+       variables = paste("X", 1:9, sep = ""), wtype = "ATE-stab")
$coefficient
[1] -0.01717167

$std
[1] 0.03282054

$ciinf
[1] -0.08149875

$cisup
[1] 0.04715541

$p.value
[1] 0.6008359

> 
> # Standard error could be compared with the (robust) Lin's standard error
> # which does not take into account the propensity score estimation step:
> modT <- glm(Trt ~ X1 + X2 + X3 + X4 + X5 + X6 + X7 + X8 + X9, data = hrData, family = "binomial")
> probT <- predict(modT, type = "response")
> hrData$w <- 1/ifelse(hrData$Trt == 1, probT, 1 - probT)
> library(survival)
> coxph(Surv(time, status) ~ Trt + cluster(id), data = hrData, method = "breslow", weights = w)
Call:
coxph(formula = Surv(time, status) ~ Trt, data = hrData, weights = w, 
    method = "breslow", cluster = id)

        coef exp(coef) se(coef) robust se      z     p
Trt -0.01743   0.98272  0.01415   0.03543 -0.492 0.623

Likelihood ratio test=1.52  on 1 df, p=0.2182
n= 10000, number of events= 10000 
> 
> # or with the bootstrap-based standard-error (see Austin 2016):
> ## Not run: 
> ##D f.boot <- function(data, i, wtype) {
> ##D     df <- data[i, ]
> ##D     modT <- glm(Trt ~ X1 + X2 + X3 + X4 + X5 + X6 + X7 + X8 + X9, data = df, family = "binomial")
> ##D     probT <- predict(modT, type = "response")
> ##D     df$w <- 1/ifelse(df$Trt == 1, probT, 1 - probT)
> ##D 
> ##D     return(coxph(Surv(time, status) ~ Trt, data = df, weights = w)$coef)
> ##D }
> ##D 
> ##D library(boot); set.seed(1234)
> ##D rcoefs <- boot(data = hrData, statistic = f.boot, R = 500)$t
> ##D sd(rcoefs)
> ## End(Not run)
> 
> ## Using the DIVAT data base (package IPWsurvival, to be installed)
> data(dataDIVAT2, package = "RISCA")
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called ‘RISCA’
Calls: data -> find.package
Execution halted
* checking PDF version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/data/gannet/ripley/R/packages/tests-Suggests/hrIPW.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 1:48.96, 96.31 + 9.78