* using log directory 'd:/RCompile/CRANincoming/R-devel/RCNA.Rcheck'
* using R Under development (unstable) (2024-11-24 r87369 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 'RCNA/DESCRIPTION' ... OK
* this is package 'RCNA' version '1.0'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Matt Bradley <mbradley@emmes.com>'

New submission

Possibly misspelled words in DESCRIPTION:
  GC (9:69)
  RCNA (2:49)
  karyotype (10:54)
  quantile (10:32, 11:61)
* 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 'RCNA' 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 ... NOTE
Non-standard file/directory found at top level:
  'output'
* 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 ... 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 ... ERROR
Running examples in 'RCNA-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: correct_gc_bias
> ### Title: correct_gc_bias: Estimate and correct GC bias in coverage
> ### Aliases: correct_gc_bias correct_gc_bias.default
> ###   correct_gc_bias.RCNA_object
> 
> ### ** Examples
> 
> ## Run GC-bias estimation and correction on example object
> # See example_obj for more information on example
> # Create output directory
> dir.create(file.path("output", "gc"), recursive = TRUE)
> # Estimate and correct GC bias, append results
> correct_gc_analysisObj <- correct_gc_bias(example_obj)
Error in { : task 1 failed - "cannot open the connection"
Calls: correct_gc_bias ... correct_gc_bias.RCNA_object -> %dopar% -> <Anonymous>
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... [16s] OK
* checking HTML version of manual ... OK
* DONE
Status: 1 ERROR, 2 NOTEs