* using log directory 'd:/RCompile/CRANincoming/R-devel/MethScope.Rcheck'
* using R Under development (unstable) (2025-11-20 r89043 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 '1.0.2'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Hongxiang Fu <fhx@seas.upenn.edu>'

New submission

Possibly misspelled words in DESCRIPTION:
  MRMPs (9:75)
  Methylation (9:53)
  Methylome (2:42)

Package has a VignetteBuilder field but no prebuilt vignette index.

The Description field should not start with the package name,
  'This package' or similar.

Size of tarball: 95506258 bytes
* 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 'MethScope' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 14.3.0'
* checking installed package size ... INFO
  installed size is 91.3Mb
  sub-directories of 1Mb or more:
    R         1.1Mb
    extdata  88.8Mb
    help      1.2Mb
* checking package directory ... OK
* checking for future file timestamps ... 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 ... WARNING
Registration problem:
  call to '"yame_summary_cfunc"' with 2 parameters, expected 3:
   .Call("yame_summary_cfunc", query_fn, knowledge_fn)
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
* checking R code for possible problems ... [13s] NOTE
GenerateReference: no visible global function definition for
  'write.table'
PlotConfusion: no visible binding for global variable 'Predicted'
PlotConfusion: no visible binding for global variable 'Actual'
PlotConfusion: no visible binding for global variable 'Freq'
PlotF1: no visible global function definition for 'reorder'
PlotF1: no visible binding for global variable 'Class'
PlotF1: no visible binding for global variable 'F1_Score'
PlotUMAP: no visible binding for global variable 'conf'
PlotUMAP_fixedwindow: no visible binding for global variable 'conf'
PredictCellType: no visible global function definition for 'predict'
nnls_deconv: no visible binding for global variable 'var'
Undefined global functions or variables:
  Actual Class F1_Score Freq Predicted conf predict reorder var
  write.table
Consider adding
  importFrom("stats", "predict", "reorder", "var")
  importFrom("utils", "write.table")
to your NAMESPACE file.
* 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 R/sysdata.rda ... WARNING
  Warning: large data file saved inefficiently:
                size ASCII compress
  sysdata.rda 10.2Mb FALSE     none
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
              old_size new_size compress
  sysdata.rda   10.2Mb    1.0Mb       xz
* 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 files in 'vignettes' ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  'MethScope-MRMP.Rmd' 'MethScope-Tutorial.Rmd'
* checking examples ... ERROR
Running examples in 'MethScope-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: PredictCellType
> ### Title: Predict cell type annotation from the trained model
> ### Aliases: PredictCellType
> 
> ### ** Examples
> 
> # Use the example.cg file included in the package
> reference_pattern <- system.file("extdata", "Liu2021_MouseBrain.cm", package = "MethScope")
> example_file <- system.file("extdata", "example.cg", package = "MethScope")
> result <- GenerateInput(example_file,reference_pattern)
Error in GenerateInput(example_file, reference_pattern) : 
  Testing sequencing data does not support Windows.
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... WARNING
Directory 'inst/doc' does not exist.
Package vignettes without corresponding single PDF/HTML:
  'MethScope-MRMP.Rmd'
  'MethScope-Tutorial.Rmd'
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... [12s] OK
* checking HTML version of manual ... OK
* DONE
Status: 1 ERROR, 4 WARNINGs, 2 NOTEs