* using log directory 'd:/RCompile/CRANincoming/R-devel/ANPreg.Rcheck'
* using R Under development (unstable) (2024-02-08 r85876 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'ANPreg/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ANPreg' version '1.0.0'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Daniele Cuntrera <daniele.cuntrera@unipa.it>'

New submission

Possibly misspelled words in DESCRIPTION:
  ANP (4:57, 16:26)
  Augugliaro (18:68)
  Cuntrera (18:54)
  Karush (17:86)
  Muggeo (18:86)
  gaussian (16:98)

The Title field should be in title case. Current version is:
'Estimate a Penalized Linear Model and Gaussian Graphical Model using the Adaptive Non-Convex penalty function (ANP)'
In title case that is:
'Estimate a Penalized Linear Model and Gaussian Graphical Model using the Adaptive Non-Convex Penalty Function (ANP)'
* 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 'ANPreg' 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 R 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 ... NOTE
interp_coeff: no visible binding for global variable 'p'
Undefined global functions or variables:
  p
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... WARNING
Unknown package 'pLM' in Rd xrefs
Missing link or links in Rd file 'plot.pLM.cv.Rd':
  'summary.pLM.cv'

See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'checkKKT'
Undocumented S4 classes:
  'pLM.cv' 'pLM' 'pGGM'
Undocumented S4 methods:
  generic 'BIC' and siglist 'pLM'
  generic 'checkKKT' and siglist 'pGGM'
  generic 'coef' and siglist 'pGGM'
  generic 'coef' and siglist 'pLM'
  generic 'plot' and siglist 'pGGM'
  generic 'plot' and siglist 'pLM'
  generic 'plot' and siglist 'pLM.cv'
  generic 'predict' and siglist 'pLM'
  generic 'print' and siglist 'pGGM'
  generic 'print' and siglist 'pLM'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... WARNING
Functions or methods with usage in Rd file 'BIC.pLM.Rd' but not in code:
  'BIC.pLM'

Functions or methods with usage in Rd file 'checkKKT.pGGM.Rd' but not in code:
  'checkKKT.pGGM'

Functions or methods with usage in Rd file 'coef.pGGM.Rd' but not in code:
  'coef.pGGM'

Functions or methods with usage in Rd file 'coef.pLM.Rd' but not in code:
  'coef.pLM'

Functions or methods with usage in Rd file 'plot.pGGM.Rd' but not in code:
  'plot.pGGM'

Functions or methods with usage in Rd file 'plot.pLM.Rd' but not in code:
  'plot.pLM'

Functions or methods with usage in Rd file 'predict.pLM.Rd' but not in code:
  'predict.pLM'

Functions or methods with usage in Rd file 'print.pGGM.Rd' but not in code:
  'print.pGGM'

Functions or methods with usage in Rd file 'print.pLM.Rd' but not in code:
  'print.pLM'

Functions or methods with usage in Rd file 'show.pGGM.Rd' but not in code:
  'show.pGGM'

Functions or methods with usage in Rd file 'show.pLM.Rd' but not in code:
  'show.pLM'

Functions or methods with usage in Rd file 'show.pLM.cv.Rd' but not in code:
  'show'

Codoc mismatches from Rd file 'plot.pLM.cv.Rd':
plot
  Code: function(x, y, ...)
  Docs: function(x, ...)
  Argument names in code not in docs:
    y
  Mismatches in argument names:
    Position: 2 Code: y Docs: ...

* checking Rd \usage sections ... WARNING
Objects in \usage without \alias in Rd file 'coef.pLM.Rd':
  'coef.pLM'

Objects in \usage without \alias in Rd file 'plot.pLM.cv.Rd':
  'plot'

Objects in \usage without \alias in Rd file 'show.pLM.cv.Rd':
  'show'

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 examples ... OK
* checking PDF version of manual ... [22s] OK
* checking HTML version of manual ... OK
* DONE
Status: 4 WARNINGs, 2 NOTEs