Last updated on 2026-10-24 01:51:37 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.4.1 | 9.71 | 95.27 | 104.98 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.4.1 | 7.66 | 66.10 | 73.76 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.4.1 | 8.00 | 65.19 | 73.19 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 0.4.1 | 75.36 | OK | |||
| r-devel-windows-x86_64 | 0.4.1 | 11.00 | 107.00 | 118.00 | OK | |
| r-patched-linux-x86_64 | 0.4.1 | 9.88 | 88.50 | 98.38 | OK | |
| r-release-linux-x86_64 | 0.4.1 | 9.66 | 91.02 | 100.68 | OK | |
| r-release-macos-arm64 | 0.4.1 | 3.00 | 27.00 | 30.00 | OK | |
| r-release-macos-x86_64 | 0.4.1 | 7.00 | 99.00 | 106.00 | OK | |
| r-release-windows-x86_64 | 0.4.1 | 13.00 | 101.00 | 114.00 | OK | |
| r-oldrel-macos-arm64 | 0.4.1 | 3.00 | 27.00 | 30.00 | OK | |
| r-oldrel-macos-x86_64 | 0.4.1 | 7.00 | 170.00 | 177.00 | OK | |
| r-oldrel-windows-x86_64 | 0.4.1 | 14.00 | 124.00 | 138.00 | OK |
Version: 0.4.1
Check: examples
Result: ERROR
Running examples in ‘IrregLong-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: iiw
> ### Title: Given a proportional hazards model for visit intensities,
> ### compute inverse-intensity weights.
> ### Aliases: iiw
>
> ### ** Examples
>
> ## Don't show:
> if (requireNamespace("nlme", quietly = TRUE)) (if (getRversion() >= "3.4") withAutoprint else force)({ # examplesIf
+ ## End(Don't show)
+ library(nlme)
+ library(survival)
+ library(geepack)
+ library(data.table)
+ data(Phenobarb)
+ Phenobarb$event <- 1-as.numeric(is.na(Phenobarb$conc))
+ data <- Phenobarb
+ data <- data[data$event==1,]
+ data$id <- as.numeric(data$Subject)
+ data <- data[data$time<16*24,]
+ data <- lagfn(data, lagvars=c("time","conc"), id="Subject", time="time", lagfirst = NA)
+ head(data)
+
+ mph <- coxph(Surv(time.lag,time,event)~I(conc.lag>0 & conc.lag<=20) + I(conc.lag>20 & conc.lag<=30)
+ + I(conc.lag>30)+ cluster(id),,data=data)
+ summary(mph)
+ data$weight <- iiw(mph,data,"id","time",TRUE)
+ head(data)
+ ## Don't show:
+ }) # examplesIf
> library(nlme)
> library(survival)
> library(geepack)
> library(data.table)
Attaching package: ‘data.table’
The following object is masked from ‘package:base’:
%notin%
> data(Phenobarb)
> Phenobarb$event <- 1 - as.numeric(is.na(Phenobarb$conc))
> data <- Phenobarb
> data <- data[data$event == 1, ]
> data$id <- as.numeric(data$Subject)
> data <- data[data$time < 16 * 24, ]
> data <- lagfn(data, lagvars = c("time", "conc"), id = "Subject", time = "time",
+ lagfirst = NA)
> head(data)
Subject Wt Apgar ApgarInd time dose conc event id time.lag conc.lag
1 42 2.8 9 >= 5 14.0 NA 13.3 1 1 NA NA
2 42 2.8 9 >= 5 95.5 NA 13.9 1 1 14.0 13.3
3 28 3.2 9 >= 5 2.0 NA 16.9 1 2 NA NA
4 30 1.8 8 >= 5 6.3 NA 17.9 1 3 NA NA
5 30 1.8 8 >= 5 226.3 NA 16.5 1 3 6.3 17.9
6 56 0.6 4 < 5 20.0 NA 18.8 1 4 NA NA
> mph <- coxph(Surv(time.lag, time, event) ~ I(conc.lag > 0 & conc.lag <=
+ 20) + I(conc.lag > 20 & conc.lag <= 30) + I(conc.lag > 30) + cluster(id), , data = data)
> summary(mph)
Call:
coxph(formula = Surv(time.lag, time, event) ~ I(conc.lag > 0 &
conc.lag <= 20) + I(conc.lag > 20 & conc.lag <= 30) + I(conc.lag >
30), data = data, cluster = id)
n= 95, number of events= 95
(59 observations deleted due to missingness)
coef exp(coef) se(coef) robust se z
I(conc.lag > 0 & conc.lag <= 20)TRUE 0.6546 1.9243 0.3566 0.2914 2.246
I(conc.lag > 20 & conc.lag <= 30)TRUE 0.3741 1.4537 0.3142 0.2621 1.427
I(conc.lag > 30)TRUE NA NA 0.0000 0.0000 NA
Pr(>|z|)
I(conc.lag > 0 & conc.lag <= 20)TRUE 0.0247 *
I(conc.lag > 20 & conc.lag <= 30)TRUE 0.1535
I(conc.lag > 30)TRUE NA
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
exp(coef) exp(-coef) lower .95 upper .95
I(conc.lag > 0 & conc.lag <= 20)TRUE 1.924 0.5197 1.0870 3.406
I(conc.lag > 20 & conc.lag <= 30)TRUE 1.454 0.6879 0.8697 2.430
I(conc.lag > 30)TRUE NA NA NA NA
Concordance= 0.544 (se = 0.023 )
Likelihood ratio test= 3.53 on 2 df, p=0.2
Wald test = 5.19 on 2 df, p=0.07
Score (logrank) test = 3.49 on 2 df, p=0.2, Robust = 6.28 p=0.04
(Note: the likelihood ratio and score tests assume independence of
observations within a cluster, the Wald and robust score tests do not).
> data$weight <- iiw(mph, data, "id", "time", TRUE)
Error in a$specials[[i]] : subscript out of bounds
Calls: <Anonymous> ... iiw -> predict -> predict.coxph -> delete.response -> off
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.4.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘Irreglong-vignette.Rmd’ using rmarkdown
Quitting from Irreglong-vignette.Rmd:104-114 [unnamed-chunk-6]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `a$specials[[i]]`:
! subscript out of bounds
---
Backtrace:
▆
1. └─IrregLong::iiw.weights(...)
2. └─IrregLong::iiw(...)
3. ├─stats::predict(phfit, type = "lp", newdata = data)
4. └─survival:::predict.coxph(phfit, type = "lp", newdata = data)
5. └─stats::delete.response(Terms)
6. └─stats (local) off(a$specials[[i]])
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Irreglong-vignette.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘Irreglong-vignette.Rmd’
SUMMARY: processing the following file failed:
‘Irreglong-vignette.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc