* using log directory 'd:/RCompile/CRANincoming/R-devel/seAMLess.Rcheck'
* using R Under development (unstable) (2024-11-03 r87286 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'seAMLess/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'seAMLess' version '0.1.1'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'E Onur Karakaslar <eonurkara@gmail.com>'

New submission

Package was archived on CRAN

Possibly misspelled words in DESCRIPTION:
  Deconvolution (3:44)
  Myeloid (5:65)
  Transcriptomics (3:22)
  transcriptomic (5:27)

CRAN repository db overrides:
  X-CRAN-Comment: Archived on 2023-05-07 as requires archived package
    'ggtern'.

Suggests or Enhances not in mainstream repositories:
  xbioc, MuSiC, seAMLessData
Availability using Additional_repositories specification:
  xbioc          yes   https://eonurk.github.io/drat/
  MuSiC          yes   https://eonurk.github.io/drat/
  seAMLessData   yes   https://eonurk.github.io/drat/

Found the following (possibly) invalid URLs:
  URL: https://eonurk.github.io/
    From: README.md
    Status: 404
    Message: Not Found

The Description field contains
  https://www.nature.com/articles/s41698-024-00596-9.
Please enclose URLs in angle brackets (<...>).
* checking package namespace information ... OK
* checking package dependencies ... INFO
Packages suggested but not available for checking:
  'xbioc', 'MuSiC', 'seAMLessData'
* 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 'seAMLess' can be installed ... OK
* checking installed package size ... OK
* 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 ... NOTE
'library' or 'require' call to 'xbioc' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
cli: no visible global function definition for 'OptionParser'
cli: no visible global function definition for 'add_option'
cli: no visible global function definition for 'parse_args'
main: no visible binding for global variable 'scRef'
main: no visible global function definition for 'write.table'
Undefined global functions or variables:
  OptionParser add_option parse_args scRef write.table
Consider adding
  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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... OK
* checking PDF version of manual ... [14s] OK
* checking HTML version of manual ... OK
* DONE
Status: 3 NOTEs