* using log directory ‘/srv/hornik/tmp/CRAN_pretest/rPDBapi.Rcheck’
* using R Under development (unstable) (2026-03-06 r89561)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 21.1.8 (3+b1)
    Debian flang version 21.1.8 (3+b1)
* running under: Debian GNU/Linux forky/sid
* using session charset: UTF-8
* current time: 2026-03-07 13:14:07 UTC
* checking for file ‘rPDBapi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rPDBapi’ version ‘3.0.1’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [4s/6s] NOTE
Maintainer: ‘Selcuk Korkmaz <selcukorkmaz@gmail.com>’

Days since last update: 0

Possibly misspelled words in DESCRIPTION:
  RCSB (10:45)
  bioinformatics (15:26)
* 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 serialization versions ... OK
* checking whether package ‘rPDBapi’ can be installed ... [3s/3s] OK
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
* checking loading without being on the library search path ... [1s/1s] 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 ... [5s/5s] OK
* checking Rd files ... [0s/0s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [2s/3s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [2s/2s] OK
  Running ‘testthat.R’ [2s/2s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [17s/33s] ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘rPDBapi-structural-bioinformatics.Rmd’ using rmarkdown

Quitting from rPDBapi-structural-bioinformatics.Rmd:880-897 [r3dmol-view]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `loadNamespace()`:
! there is no package called 'shiny'
---
Backtrace:
     ▆
  1. ├─... %>% r3d$m_zoom_to()
  2. ├─r3d$m_zoom_to(.)
  3. │ └─r3dmol:::callJS()
  4. │   ├─base::Filter(function(x) !is.symbol(x), as.list(parent.frame(1)))
  5. │   │ ├─base::unlist(lapply(x, f))
  6. │   │ └─base::lapply(x, f)
  7. │   ├─base::as.list(parent.frame(1))
  8. │   └─base::as.list.environment(parent.frame(1))
  9. ├─r3d$m_set_style(., style = r3d$m_style_cartoon(color = "spectrum"))
 10. │ └─r3dmol:::callJS()
 11. │   ├─base::Filter(function(x) !is.symbol(x), as.list(parent.frame(1)))
 12. │   │ ├─base::unlist(lapply(x, f))
 13. │   │ └─base::lapply(x, f)
 14. │   ├─base::as.list(parent.frame(1))
 15. │   └─base::as.list.environment(parent.frame(1))
 16. ├─r3d$m_add_model(., data = saved_structure$path, format = "pdb")
 17. │ └─r3dmol:::callJS()
 18. └─base::loadNamespace(x)
 19.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
 20.     └─base (local) withOneRestart(expr, restarts[[1L]])
 21.       └─base (local) doWithOneRestart(return(expr), restart)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'rPDBapi-structural-bioinformatics.Rmd' failed with diagnostics:
there is no package called 'shiny'
--- failed re-building ‘rPDBapi-structural-bioinformatics.Rmd’

SUMMARY: processing the following file failed:
  ‘rPDBapi-structural-bioinformatics.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [3s/3s] OK
* checking HTML version of manual ... [2s/2s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR, 1 NOTE