* using log directory 'd:/RCompile/CRANincoming/R-devel/AntibodyForests.Rcheck'
* using R Under development (unstable) (2025-01-15 r87581 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'AntibodyForests/DESCRIPTION' ... OK
* this is package 'AntibodyForests' version '1.0.0'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Daphne van Ginneken <daphne.v.ginneken@gmail.com>'

New submission

Possibly misspelled words in DESCRIPTION:
  AntibodyForests (3:9, 15:47)
  Intra (2:31)
  intra (14:5, 16:44)
* 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 'AntibodyForests' can be installed ... OK
* checking installed package size ... 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 ... 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 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 ... [24s] 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 ... WARNING
Variables with usage in Rd file 'small_vdj.Rd' but not in code:
  'small_vdj'

* 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 ... ERROR
Running examples in 'AntibodyForests-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Af_add_node_feature
> ### Title: Function to add node features to an AntibodyForests-object
> ### Aliases: Af_add_node_feature
> 
> ### ** Examples
> 
> af <- Af_add_node_feature(AntibodyForests::small_af, 
+                           feature.df = AntibodyForests::small_vdj, 
+                           feature.names = c("VDJ_dgene", "VDJ_jgene"))
Error: 'small_vdj' is not an exported object from 'namespace:AntibodyForests'
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [14s] OK
* checking PDF version of manual ... [29s] OK
* checking HTML version of manual ... OK
* DONE
Status: 1 ERROR, 1 WARNING, 1 NOTE