* using log directory 'd:/RCompile/CRANincoming/R-devel/MethScope.Rcheck'
* using R Under development (unstable) (2025-12-02 r89085 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.3.0
    GNU Fortran (GCC) 14.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'MethScope/DESCRIPTION' ... OK
* this is package 'MethScope' version '1.0.0'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Hongxiang Fu <fhx@seas.upenn.edu>'

New submission

Possibly misspelled words in DESCRIPTION:
  MRMPs (14:98)
  Methylation (14:76)
  Methylome (2:42)
  NNLS (14:362)
  XGBoost (14:342)
  YAME (14:254)
  deconvolution (14:145, 14:367)
  methylation (14:40)
  methylomes (14:446)
* 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 serialization versions ... OK
* checking whether package 'MethScope' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 14.3.0'
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Author field differs from that derived from Authors@R
  Author:    'Hongxiang Fu [aut, cre] (ORCID: <https://orcid.org/0000-0002-9873-8606>), Wanding Zhou [cph, fnd]'
  Authors@R: 'Hongxiang Fu [aut, cre] (ORCID: <https://orcid.org/0000-0002-9873-8606>), Wanding Zhou [cph, fnd], The SAMtools/HTSlib authors [ctb, cph] (BGZF components; see inst/COPYRIGHTS), Attractive Chaos [ctb, cph] (Author and copyright holder of khash.h (klib, MIT license))'

* 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 ... [19s] 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
Codoc mismatches from Rd file 'GenerateReference.Rd':
GenerateReference
  Code: function(binary_file, min_CG = 50, output_path = NULL)
  Docs: function(binary_file, min_CG = 50, output_path =
                 "./patterns.txt")
  Mismatches in argument default values:
    Name: 'output_path' Code: NULL Docs: "./patterns.txt"

Codoc mismatches from Rd file 'PlotConfusion.Rd':
PlotConfusion
  Code: function(prediction_result, actual_label, log2 = FALSE)
  Docs: function(prediction_result, actual_label, log2 = F)
  Mismatches in argument default values:
    Name: 'log2' Code: FALSE Docs: F

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking R/sysdata.rda ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... NONE
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... OK
  Running 'spelling.R'
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... [19s] OK
* checking HTML version of manual ... OK
* DONE
Status: 1 WARNING, 2 NOTEs