* using log directory 'd:/RCompile/CRANincoming/R-devel/cxreg.Rcheck'
* using R Under development (unstable) (2025-07-24 r88447 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'cxreg/DESCRIPTION' ... OK
* this is package 'cxreg' version '1.0.0'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Younghoon Kim <yk748@cornell.edu>'

New submission

Possibly misspelled words in DESCRIPTION:
  glmnet (9:25)
  pathwise (10:19)

Package has a VignetteBuilder field but no prebuilt vignette index.

Found the following (possibly) invalid URLs:
  URL: https://arxiv.org/abs/2401
    From: man/cxreg-package.Rd
    Status: 404
    Message: Not Found

Found the following (possibly) invalid DOIs:
  DOI: arXiv:2401.11128
    From: man/predict.classo.Rd
    Message: Invalid DOI

The Title field should be in title case. Current version is:
  'Complex-valued lasso and complex-valued graphical lasso'
In title case that is:
  'Complex-Valued Lasso and Complex-Valued Graphical Lasso'
* 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 ... NOTE
Found the following hidden files and directories:
  .github
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.

CRAN-pack does not know about
  .github
* checking for portable file names ... OK
* checking whether package 'cxreg' can be installed ... OK
* used Fortran compiler: 'GNU Fortran (GCC) 14.2.0'
* used C++ compiler: 'g++.exe (GCC) 14.2.0'
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
Non-standard files/directories found at top level:
  'README.Rmd' 'cxreg-ref.bib' 'paper.Rmd'
* 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 ... WARNING
plot:
  function(x, ...)
plot.cglasso:
  function(x, index, type, label)
See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
dft.X: no visible global function definition for 'mvfft'
plot.cglasso: no visible global function definition for
  'colorRampPalette'
predict.classo: no visible global function definition for 'check_dots'
Undefined global functions or variables:
  check_dots colorRampPalette mvfft
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("stats", "mvfft")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) cglasso.Rd:30: Lost braces; missing escapes or markup?
    30 | \deqn{D^{-1/2}(\arg\min_{\Theta}\textrm{Tr}[\hat{R}\hat{\Theta}]-\log\det\Theta + \sum_{i\neq j}|\Theta_{ij}|)D^{-1/2}} for the given D. If type is \code{II}, the algorithm solves CGLASSO-II in the reference. It is for each iterative classo with covariate update, the squared-root of scale matrix D^{-1/2} is multiplied. Please refer to the equation (5.2) in the reference for the details.}
       |                                                                                                                                                                                                                                                                                                            ^
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented data sets:
  'cglasso_example' 'classo_example'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'buildPredmat.Rd'
  'outlist' 'lambda' 'x' 'foldid' 'alignment'

Undocumented arguments in Rd file 'buildPredmat.default.Rd'
  'outlist' 'lambda' 'x' 'foldid' 'alignment'

Undocumented arguments in Rd file 'cglasso.Rd'
  '...'

Undocumented arguments in Rd file 'classo.Rd'
  '...'

Undocumented arguments in Rd file 'classo.path.Rd'
  'maxit' '...'

Undocumented arguments in Rd file 'cv.classo.Rd'
  'type.measure'

Undocumented arguments in Rd file 'dft.X.Rd'
  'X' 'j' 'm'

Undocumented arguments in Rd file 'fixm.Rd'
  'v' 'n'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking usage of KIND in Fortran files ... OK
* checking files in 'vignettes' ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  'cxreg.Rmd' 'cxreg.pdf' 'cxreg_refs.bib'
Files named as vignettes but with no recognized vignette engine:
   'vignettes/cxreg.Rmd'
(Is a VignetteBuilder field missing?)
* checking examples ... [23s] OK
* checking package vignettes ... NOTE
Package has 'vignettes' subdirectory but apparently no vignettes.
Perhaps the 'VignetteBuilder' information is missing from the
DESCRIPTION file?
* checking PDF version of manual ... [13s] OK
* checking HTML version of manual ... OK
* DONE
Status: 4 WARNINGs, 6 NOTEs