* using log directory ‘/srv/hornik/tmp/CRAN_pretest/MethScope.Rcheck’
* using R Under development (unstable) (2025-11-20 r89043)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 21.1.5 (1)
    Debian flang version 21.1.5 (1)
* running under: Debian GNU/Linux forky/sid
* using session charset: UTF-8
* checking for file ‘MethScope/DESCRIPTION’ ... OK
* this is package ‘MethScope’ version ‘1.0.1’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [3s/5s] 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: 95506260 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 executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MethScope’ can be installed ... [13s/13s] WARNING
Found the following significant warnings:
  bgzf.c:646:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result]
See ‘/srv/hornik/tmp/CRAN_pretest/MethScope.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 21.1.5 (1)’
* 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 ... [2s/2s] OK
* checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the package can be unloaded cleanly ... [2s/2s] OK
* checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the namespace can be unloaded cleanly ... [2s/2s] OK
* checking loading without being on the library search path ... [2s/2s] 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 ... [10s/10s] 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 ... [0s/0s] 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 ... NOTE
File ‘MethScope/libs/MethScope.so’:
  Found ‘stdout’, possibly from ‘stdout’ (C)
    Object: ‘summary.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘MethScope-MRMP.Rmd’ ‘MethScope-Tutorial.Rmd’
* checking examples ... [35s/35s] NOTE
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
PredictCellType 15.36  0.787  16.157
GenerateInput   15.26  0.804  16.073
* 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 ... [4s/4s] OK
* checking PDF version of manual ... [3s/3s] OK
* checking HTML version of manual ... [0s/0s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 4 WARNINGs, 4 NOTEs