Last updated on 2026-10-24 06:51:08 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.1.2 | 6.13 | 74.90 | 81.03 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.1.2 | 4.99 | 57.59 | 62.58 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.1.2 | 54.43 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 0.1.2 | 54.49 | OK | |||
| r-devel-windows-x86_64 | 0.1.2 | 9.00 | 93.00 | 102.00 | OK | |
| r-patched-linux-x86_64 | 0.1.2 | 6.35 | 56.98 | 63.33 | OK | |
| r-release-linux-x86_64 | 0.1.2 | 6.22 | 57.68 | 63.90 | OK | |
| r-release-macos-arm64 | 0.1.2 | 2.00 | 18.00 | 20.00 | OK | |
| r-release-macos-x86_64 | 0.1.2 | 5.00 | 58.00 | 63.00 | OK | |
| r-release-windows-x86_64 | 0.1.2 | 8.00 | 75.00 | 83.00 | OK | |
| r-oldrel-macos-arm64 | 0.1.2 | 2.00 | 17.00 | 19.00 | OK | |
| r-oldrel-macos-x86_64 | 0.1.2 | 4.00 | 63.00 | 67.00 | OK | |
| r-oldrel-windows-x86_64 | 0.1.2 | 12.00 | 87.00 | 99.00 | OK |
Version: 0.1.2
Check: examples
Result: ERROR
Running examples in ‘collett-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: step_s
> ### Title: Utilities
> ### Aliases: step_s as.data.frame.survfit as.data.frame.summary.survfit
> ### predict_coxph_tt predict_coxph_tv plot_coxph_functional
>
> ### ** Examples
>
> step_s(data.frame(g=c(1,1), a=1:2, b=4:5), a, b)
g a b
1 1 0 1
2 1 1 1
3 1 1 4
4 1 2 4
5 1 2 5
> step_s(data.frame(g=c(2,2), a=3:4, b=6:7), a, b)
g a b
1 2 0 1
2 2 3 1
3 2 3 6
4 2 4 6
5 2 4 7
> step_s(data.frame(g=c(1,1,2,2), a=1:4, b=4:7), a, b, group=g)
g a b
1 1 0 1
2 1 1 1
3 1 1 4
4 1 2 4
5 1 2 5
6 2 0 1
7 2 3 1
8 2 3 6
9 2 4 6
10 2 4 7
> library(survival)
Attaching package: ‘survival’
The following objects are masked from ‘package:collett’:
bladder, kidney, lung, myeloma, ovarian
> library(tinyplot)
> sfit1 = survfit(Surv(time,status)~rx, data=survival::colon,
+ subset=etype==1)
> with(as.data.frame(sfit1),
+ tinyplot::plt(surv~time|strata,ymin=lower,ymax=upper,type="ribbon"))
> library(survival)
> library(tinyplot)
> sfit1 = survfit(Surv(time,status)~rx, data=survival::colon,
+ subset=etype==1)
> with(as.data.frame(sfit1, type="expanded"),
+ tinyplot::plt(surv~time|strata,ymin=lower,ymax=upper,type="ribbon"))
> library(splines)
> library(tinyplot)
> fit1 = coxph(Surv(time,status)~tt(treat),data=breast_rfs,
+ tt=function(x,t,...) x*cbind(1,t))
> fit2 = coxph(Surv(time,status)~tt(treat),data=breast_rfs,
+ tt=function(x,t,...) x*ns(t,df=4,intercept=TRUE))
> times = seq(0,2500,len=301L)
> df1 = transform(predict_coxph_tt(fit1,times,se.fit=TRUE),
+ lower=exp(fitted-1.96*se.fit),
+ upper=exp(fitted+1.96*se.fit),
+ fitted=exp(fitted),
+ model="linear",times=times)
> df2 = transform(predict_coxph_tt(fit2,times,se.fit=TRUE),
+ lower=exp(fitted-1.96*se.fit),
+ upper=exp(fitted+1.96*se.fit),
+ fitted=exp(fitted),
+ model="ns",times=times)
> with(rbind(df1,df2),
+ plt(fitted ~ times | model, ymin=lower, ymax=upper, type="ribbon",
+ xlab="Time since diagnosis (days)",
+ ylab="Hazard ratio comparing treated with untreated"))
> with(subset(breast_rfs,status==1), rug(time))
> library(survival)
> liver = transform(collett::liverbase, lbr=NULL)
> liver = tmerge(liver, liver, id=patient, status=event(time,status))
> liver = tmerge(liver,
+ rbind(with(collett::liverbase, data.frame(patient,tstart=0,lbr)),
+ with(collett::lbrdata0, data.frame(patient,tstart=time,lbr))),
+ id=patient, lbr = tdc(tstart,lbr))
> fit3 = coxph(Surv(tstart,tstop,status)~lbr+treat,liver)
> predict_coxph_tv(fit3,data=subset(liver,patient %in% c(1,7)),
+ id="patient")
Error in a$specials[[i]] : subscript out of bounds
Calls: predict_coxph_tv ... survfit.coxph -> model.matrix.coxph -> delete.response -> off
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc