- using R Under development (unstable) (2026-04-15 r89882)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
clang version 22.1.3 (https://github.com/llvm/llvm-project e9846648fd6183ee6d8cbdb4502213fcf902a211)
flang version 22.1.3 (https://github.com/llvm/llvm-project e9846648fd6183ee6d8cbdb4502213fcf902a211)
- running under: Fedora Linux 42 (Workstation Edition)
- using session charset: UTF-8
* current time: 2026-04-15 09:23:43 UTC
- using option ‘--no-stop-on-test-error’
- checking for file ‘cohorttools/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘cohorttools’ version ‘0.1.7’
- package encoding: UTF-8
- checking package namespace information ... OK
- checking package dependencies ... OK
- 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 ‘cohorttools’ can be installed ... [22s/59s] OK
See the install log for details.
- checking installed package size ... 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 code files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... [6s/14s] OK
- checking whether the package can be loaded with stated dependencies ... [6s/16s] OK
- checking whether the package can be unloaded cleanly ... [6s/14s] OK
- checking whether the namespace can be loaded with stated dependencies ... [6s/14s] OK
- checking whether the namespace can be unloaded cleanly ... [6s/19s] OK
- checking loading without being on the library search path ... [7s/20s] 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 ... [30s/80s] 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 examples ... [7s/18s] ERROR
Running examples in ‘cohorttools-Ex.R’ failed
The error most likely occurred in:
> ### Name: boxesLx
> ### Title: Boxes plot summarizing Lexis object
> ### Aliases: boxesLx
>
> ### ** Examples
>
> library(DiagrammeR)
> library(survival)
> library(Epi)
> library(mstate)
Attaching package: ‘mstate’
The following objects are masked from ‘package:Epi’:
absorbing, paths
> data(ebmt3)
> bmt <- Lexis(exit = list(tft = rfstime/365.25),
+ exit.status = factor(rfsstat, labels = c("Tx", "RD")),
+ data = ebmt3)
NOTE: entry.status has been set to "Tx" for all.
NOTE: entry is assumed to be 0 on the tft timescale.
> bmtr <- cutLexis(bmt, cut = bmt$prtime/365.25, precursor.states = "Tx",
+ new.state = "PR")
>
> summary(bmtr)
Transitions:
To
From Tx PR RD Records: Events: Risk time: Persons:
Tx 577 1169 458 2204 1627 2439.43 2204
PR 0 786 383 1169 383 3173.03 1169
Sum 577 1955 841 3373 2010 5612.46 2204
> kk<-boxesLx(bmtr)
Error in lv.1$Transitions[1:lv.len, " Persons:"] :
subscript out of bounds
Calls: boxesLx
Execution halted
- checking PDF version of manual ... [7s/15s] OK
- checking HTML 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