* using log directory 'd:/Rcompile/CRANpkg/local/4.5/DrugSim2DR.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'DrugSim2DR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DrugSim2DR' version '0.1.1'
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'DrugSim2DR' can be installed ... OK
* checking installed package size ... 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 ... [3s] OK
* checking whether the package can be loaded with stated dependencies ... [3s] OK
* checking whether the package can be unloaded cleanly ... [3s] OK
* checking whether the namespace can be loaded with stated dependencies ... [2s] OK
* checking whether the namespace can be unloaded cleanly ... [3s] OK
* checking loading without being on the library search path ... [3s] 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 ... [8s] OK
* checking Rd files ... [0s] OK
* checking Rd metadata ... 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 ... [2s] 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 ... [13s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [9s] ERROR
Error(s) in re-building vignettes:
--- re-building 'DrugSim2DR.Rmd' using rmarkdown

Quitting from DrugSim2DR.Rmd:107-115 [unnamed-chunk-7]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! error in evaluating the argument 'x' in selecting a method for function 'as.matrix': subscript out of bounds
---
Backtrace:
     ▆
  1. ├─DrugSim2DR::plotDrugstructure("DB00780")
  2. │ ├─sp::plot(sdfset)
  3. │ └─sp::plot(sdfset)
  4. │   └─ChemmineR (local) .local(x, ...)
  5. │     └─ChemmineR::plotStruc(sdf = x[[i]], main = print_cid[i], ...)
  6. │       ├─base::cbind(...)
  7. │       ├─base::as.matrix(bonds(sdf, type = "bonds")[, -1])
  8. │       └─ChemmineR::bonds(sdf, type = "bonds")
  9. │         └─ChemmineR (local) .bonds(x, type)
 10. └─base (local) `<fn>`(`<sbscOOBE>`)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'DrugSim2DR.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'as.matrix': subscript out of bounds
--- failed re-building 'DrugSim2DR.Rmd'

SUMMARY: processing the following file failed:
  'DrugSim2DR.Rmd'

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [20s] OK
* checking HTML version of manual ... [2s] OK
* DONE
Status: 1 ERROR