* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/raymolecule.Rcheck’
* using R Under development (unstable) (2023-12-09 r85665)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 13.2.1 20231011 (Red Hat 13.2.1-4)
    GNU Fortran (GCC) 13.2.1 20231011 (Red Hat 13.2.1-4)
* running under: Fedora Linux 38 (Workstation Edition)
* using session charset: UTF-8
* checking for file ‘raymolecule/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘raymolecule’ 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 ‘raymolecule’ can be installed ... 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 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 ... 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 ... NOTE
Documented arguments not in \usage in Rd file 'onb_from_w.Rd':
  ‘v’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... OK
* checking examples with --run-donttest ... ERROR
Running examples in ‘raymolecule-Ex.R’ failed
The error most likely occurred in:

> ### Name: generate_atom_scene
> ### Title: Build Scene (atoms only)
> ### Aliases: generate_atom_scene
> 
> ### ** Examples
> 
> #Generate a scene with caffeine molecule with just the atoms
> ## No test: 
> get_example_molecule("caffeine") %>%
+   read_sdf() %>%
+   generate_atom_scene() %>%
+   render_model(samples=256,sample_method="sobol_blue")
> 
> #Generate a rayvertex scene, using toon shading
> shiny_toon_material = rayvertex::material_list(type="toon_phong",
+                                                toon_levels=3,
+                                                toon_outline_width=0.1)
> get_example_molecule("caffeine") %>%
+   read_sdf() %>%
+   generate_atom_scene(pathtrace=FALSE, material_vertex = shiny_toon_material) %>%
+   render_model(background="white")
Error in scene$vertices[, 1] : incorrect number of dimensions
Calls: %>% -> render_model
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
* checking for new files in some other directories ... OK
* DONE

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

Command exited with non-zero status 1
Time 0:29.18, 116.59 + 5.52