* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/rnmamod.Rcheck’
* using R Under development (unstable) (2026-06-19 r90183)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
    GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
* running under: Fedora Linux 40 (Workstation Edition)
* using session charset: UTF-8
* current time: 2026-06-20 09:22:56 UTC
* checking for file ‘rnmamod/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rnmamod’ version ‘0.5.0’
* 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 ‘rnmamod’ can be installed ... [22s/23s] OK
* checking package directory ... OK
* checking ‘build’ 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 ... 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 whether startup messages can be suppressed ... 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 ... [39s/39s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [17s/17s] OK
* checking examples with --run-donttest ... ERROR
Running examples in ‘rnmamod-Ex.R’ failed
The error most likely occurred in:

> ### Name: comp_clustering
> ### Title: End-user-ready results for comparison dissimilarity and
> ###   hierarchical clustering (Comparisons' comparability for transitivity
> ###   evaluation)
> ### Aliases: comp_clustering
> 
> ### ** Examples
> 
> ## No test: 
> # Fictional dataset
> data_set <- data.frame(Trial_name = as.character(1:7),
+                       arm1 = c("1", "1", "1", "1", "1", "2", "2"),
+                       arm2 = c("2", "2", "2", "3", "3", "3", "3"),
+                       sample = c(140, 145, 150, 40, 45, 75, 80),
+                       age = c(18, 18, 18, 48, 48, 35, 35),
+                       blinding = factor(c("yes", "yes", "yes", "no", "no", "no", "no")))
> 
> # Obtain comparison dissimilarities (informative = TRUE)
> comp_clustering(input = data_set,
+                 drug_names = c("A", "B", "C"),
+                 threshold = 0.13,  # General research setting
+                 informative = TRUE,
+                 get_plots = TRUE)
- 3 observed comparisons (0 single-study comparisons)
- Dropped characteristics: none
Error in as.character.factor(X[[i]], ...) : malformed factor
Calls: comp_clustering ... unlist -> URapply -> lapply -> FUN -> as.character.factor
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [40s/40s]
 [40s/40s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [31s/32s] OK
* checking PDF version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* checking for new files in some other directories ... OK
* DONE

Status: 1 ERROR
See
  ‘/data/blackswan/ripley/R/packages/tests-devel/rnmamod.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 3:58.77, 216.65 + 20.02