* using log directory 'd:/RCompile/CRANincoming/R-devel/rags2ridges.Rcheck'
* using R Under development (unstable) (2023-10-10 r85312 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 12.2.0
    GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'rags2ridges/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'rags2ridges' version '2.2.7'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Carel F.W. Peeters <carel.peeters@wur.nl>'

Found the following (possibly) invalid URLs:
  URL: https://support.posit.co/hc/en-us/articles/200486498-Package-Development-Prerequisites
    From: README.md
    Status: 403
    Message: Forbidden
* 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 'rags2ridges' can be installed ... OK
* used C++ compiler: 'g++.exe (GCC) 12.2.0'
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking 'build' directory ... 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 ... [20s] NOTE
Found if() conditions comparing class() to string:
File 'rags2ridges/R/rags2ridges.R': if (class(verbose) != "logical") ...
File 'rags2ridges/R/rags2ridges.R': if (class(type) != "character") ...
File 'rags2ridges/R/rags2ridges.R': if (class(fraction) != "numeric") ...
File 'rags2ridges/R/rags2ridges.R': if (class(const) != "numeric") ...
File 'rags2ridges/R/rags2ridges.R': if (class(verbose) != "logical") ...
File 'rags2ridges/R/rags2ridges.R': if (class(lambdaMin) != "numeric") ...
File 'rags2ridges/R/rags2ridges.R': if (class(lambdaMax) != "numeric") ...
File 'rags2ridges/R/rags2ridges.R': if (class(step) != "numeric") ...
File 'rags2ridges/R/rags2ridges.R': if (class(graph) != "logical") ...
File 'rags2ridges/R/rags2ridges.R': if (class(verbose) != "logical") ...
File 'rags2ridges/R/rags2ridges.R': if (class(lambdaMin) != "numeric") ...
File 'rags2ridges/R/rags2ridges.R': if (class(lambdaMax) != "numeric") ...
File 'rags2ridges/R/rags2ridges.R': if (class(step) != "numeric") ...
File 'rags2ridges/R/rags2ridges.R': if (class(graph) != "logical") ...
File 'rags2ridges/R/rags2ridges.R': if (class(fold) != "numeric" & class(fold) != "integer") ...
File 'rags2ridges/R/rags2ridges.R': if (class(lambdaMin) != "numeric") ...
File 'rags2ridges/R/rags2ridges.R': if (class(lambdaMax) != "numeric") ...
File 'rags2ridges/R/rags2ridges.R': if (class(lambdaInit) != "numeric") ...
File 'rags2ridges/R/rags2ridges.R': if (class(fold) != "numeric" & class(fold) != "integer") ...
File 'rags2ridges/R/rags2ridges.R': if (class(verbose) != "logical") ...
File 'rags2ridges/R/rags2ridges.R': if (class(lambdaMin) != "numeric") ...
File 'rags2ridges/R/rags2ridges.R': if (class(lambdaMax) != "numeric") ...
File 'rags2ridges/R/rags2ridges.R': if (class(step) != "numeric") ...
File 'rags2ridges/R/rags2ridges.R': if (class(Iaids) != "logical") ...
File 'rags2ridges/R/rags2ridges.R': if (class(vertical) != "logical") ...
File 'rags2ridges/R/rags2ridges.R': if (vertical & (class(value) != "numeric")) ...
File 'rags2ridges/R/rags2ridges.R': if (class(main) != "character") ...
File 'rags2ridges/R/rags2ridges.R': if (class(nOutput) != "logical") ...
File 'rags2ridges/R/rags2ridges.R': if (class(id) != "numeric" & class(id) != "integer") ...
File 'rags2ridges/R/rags2ridges.R': if (class(nPerm) != "numeric" & class(nPerm) != "integer") ...
File 'rags2ridges/R/rags2ridges.R': if (class(lambdaMin) != "numeric") ...
File 'rags2ridges/R/rags2ridges.R': if (class(lambdaMax) != "numeric") ...
File 'rags2ridges/R/rags2ridges.R': if (class(lambdaInit) != "numeric") ...
File 'rags2ridges/R/rags2ridges.R': if (class(ncpus) != "numeric" & class(ncpus) != "integer") ...
File 'rags2ridges/R/rags2ridges.R': if (class(id) != "numeric" & class(id) != "integer") ...
File 'rags2ridges/R/rags2ridges.R': if (class(nPerm) != "numeric" & class(nPerm) != "integer") ...
File 'rags2ridges/R/rags2ridges.R': if (class(lambda) != "numeric") ...
File 'rags2ridges/R/rags2ridges.R': if (class(lowCiThres) != "numeric") ...
File 'rags2ridges/R/rags2ridges.R': if (class(ncpus) != "numeric" & class(ncpus) != "integer") ...
File 'rags2ridges/R/rags2ridges.R': if (class(verbose) != "logical") ...
File 'rags2ridges/R/rags2ridges.R': if (class(top) != "numeric") ...
File 'rags2ridges/R/rags2ridges.R': if (class(absValueCut) != "numeric") ...
File 'rags2ridges/R/rags2ridges.R': if (class(FDRcut) != "numeric") ...
File 'rags2ridges/R/rags2ridges.R': if (class(verbose) != "logical") ...
File 'rags2ridges/R/rags2ridges.R': if (class(precision) != "logical") ...
File 'rags2ridges/R/rags2ridges.R': if (class(Mtest) != "numeric") ...
File 'rags2ridges/R/rags2ridges.R': if (class(Mref) != "numeric") ...
File 'rags2ridges/R/rags2ridges.R': if (class(symmetric) != "logical") ...
File 'rags2ridges/R/rags2ridges.R': if (class(diag) != "logical") ...
File 'rags2ridges/R/rags2ridges.R': if (class(nameExt) != "character") ...
File 'rags2ridges/R/rags2ridges.R': if (class(dir) != "character") ...
File 'rags2ridges/R/rags2ridges.R': if (class(verbose) != "logical") ...
File 'rags2ridges/R/rags2ridges.R': if (class(lambdaMin) != "numeric") ...
File 'rags2ridges/R/rags2ridges.R': if (class(lambdaMax) != "numeric") ...
File 'rags2ridges/R/rags2ridges.R': if (class(step) != "numeric") ...
File 'rags2ridges/R/rags2ridges.R': if (class(plotType) != "character") ...
File 'rags2ridges/R/rags2ridges.R': if (class(diag) != "logical") ...
File 'rags2ridges/R/rags2ridges.R': if (class(vertical) != "logical") ...
File 'rags2ridges/R/rags2ridges.R': if (class(value) != "numeric") ...
File 'rags2ridges/R/rags2ridges.R': if (class(lowColor) != "character") ...
File 'rags2ridges/R/rags2ridges.R': if (class(highColor) != "character") ...
File 'rags2ridges/R/rags2ridges.R': if (class(textsize) != "numeric") ...
File 'rags2ridges/R/rags2ridges.R': if (class(diag) != "logical") ...
File 'rags2ridges/R/rags2ridges.R': if (class(legend) != "logical") ...
File 'rags2ridges/R/rags2ridges.R': if (class(main) != "character") ...
File 'rags2ridges/R/rags2ridges.R': if (class(Vsize) != "numeric") ...
File 'rags2ridges/R/rags2ridges.R': if (class(Vcex) != "numeric") ...
File 'rags2ridges/R/rags2ridges.R': if (class(Vcolor) != "character") ...
File 'rags2ridges/R/rags2ridges.R': if (class(VBcolor) != "character") ...
File 'rags2ridges/R/rags2ridges.R': if (class(VLcolor) != "character") ...
File 'rags2ridges/R/rags2ridges.R': if (class(prune) != "logical") ...
File 'rags2ridges/R/rags2ridges.R': if (class(legend) != "logical") ...
File 'rags2ridges/R/rags2ridges.R': if (class(main) != "character") ...
File 'rags2ridges/R/rags2ridges.R': if (class(cut) != "numeric") ...
File 'rags2ridges/R/rags2ridges.R': if (class(scale) != "numeric") ...
File 'rags2ridges/R/rags2ridges.R': if (class(pEcolor) != "character") ...
File 'rags2ridges/R/rags2ridges.R': if (class(nEcolor) != "character") ...
File 'rags2ridges/R/rags2ridges.R': if (class(label) != "character") ...
File 'rags2ridges/R/rags2ridges.R': if (class(Lcex) != "numeric") ...
File 'rags2ridges/R/rags2ridges.R': if (class(PTcex) != "numeric") ...
File 'rags2ridges/R/rags2ridges.R': if (class(as.table) != "logical") ...
File 'rags2ridges/R/rags2ridges.R': if (class(node1) != "numeric") ...
File 'rags2ridges/R/rags2ridges.R': if (class(node2) != "numeric") ...
File 'rags2ridges/R/rags2ridges.R': if (class(neiExpansions) != "numeric") ...
File 'rags2ridges/R/rags2ridges.R': if (class(graph) != "logical") ...
File 'rags2ridges/R/rags2ridges.R': if (class(verbose) != "logical") ...
File 'rags2ridges/R/rags2ridges.R': if (class(nrPaths) != "numeric") ...
File 'rags2ridges/R/rags2ridges.R': if (class(nodecol) != "character") ...
File 'rags2ridges/R/rags2ridges.R': if (class(Vsize) != "numeric") ...
File 'rags2ridges/R/rags2ridges.R': if (class(Vcex) != "numeric") ...
File 'rags2ridges/R/rags2ridges.R': if (class(VBcolor) != "character") ...
File 'rags2ridges/R/rags2ridges.R': if (class(VLcolor) != "character") ...
File 'rags2ridges/R/rags2ridges.R': if (class(all.edges) != "logical") ...
File 'rags2ridges/R/rags2ridges.R': if (class(prune) != "logical") ...
File 'rags2ridges/R/rags2ridges.R': if (class(legend) != "logical") ...
File 'rags2ridges/R/rags2ridges.R': if (class(main) != "character") ...
File 'rags2ridges/R/rags2ridges.R': if (class(scale) != "numeric") ...
File 'rags2ridges/R/rags2ridges.R': if (class(Lcex) != "numeric") ...
File 'rags2ridges/R/rags2ridges.R': if (class(PTcex) != "numeric") ...
File 'rags2ridges/R/rags2ridges.R': if (class(dir) != "character") ...
File 'rags2ridges/R/rags2ridges.R': if (class(nOutput) != "logical") ...
File 'rags2ridges/R/rags2ridges.R': if (class(verbose) != "logical") ...
File 'rags2ridges/R/rags2ridges.R': if (class(Vsize) != "numeric") ...
File 'rags2ridges/R/rags2ridges.R': if (class(Vcex) != "numeric") ...
File 'rags2ridges/R/rags2ridges.R': if (class(Vcolor) != "character") ...
File 'rags2ridges/R/rags2ridges.R': if (class(VBcolor) != "character") ...
File 'rags2ridges/R/rags2ridges.R': if (class(VLcolor) != "character") ...
File 'rags2ridges/R/rags2ridges.R': if (class(main) != "character") ...
File 'rags2ridges/R/rags2ridges.R': if (class(Vsize) != "numeric") ...
File 'rags2ridges/R/rags2ridges.R': if (class(Vcex) != "numeric") ...
File 'rags2ridges/R/rags2ridges.R': if (class(Vcolor) != "character") ...
File 'rags2ridges/R/rags2ridges.R': if (class(VBcolor) != "character") ...
File 'rags2ridges/R/rags2ridges.R': if (class(VLcolor) != "character") ...
File 'rags2ridges/R/rags2ridges.R': if (class(P1color) != "character") ...
File 'rags2ridges/R/rags2ridges.R': if (class(P2color) != "character") ...
File 'rags2ridges/R/rags2ridges.R': if (class(main) != "character") ...
File 'rags2ridges/R/rags2ridgesDepr.R': if (class(verbose) != "logical") ...
File 'rags2ridges/R/rags2ridgesDepr.R': if (class(lambdaMin) != "numeric") ...
File 'rags2ridges/R/rags2ridgesDepr.R': if (class(lambdaMax) != "numeric") ...
File 'rags2ridges/R/rags2ridgesDepr.R': if (class(step) != "numeric") ...
File 'rags2ridges/R/rags2ridgesDepr.R': if (class(digitLoss) != "logical") ...
File 'rags2ridges/R/rags2ridgesDepr.R': if (class(rlDist) != "logical") ...
File 'rags2ridges/R/rags2ridgesDepr.R': if (class(vertical) != "logical") ...
File 'rags2ridges/R/rags2ridgesDepr.R': if (class(main) != "logical") ...
File 'rags2ridges/R/rags2ridgesDepr.R': if (class(nOutput) != "logical") ...
File 'rags2ridges/R/rags2ridgesDepr.R': if (class(value) != "numeric") ...
File 'rags2ridges/R/rags2ridgesDepr.R': if (class(verbose) != "logical") ...
File 'rags2ridges/R/rags2ridgesDepr.R': if (class(lambdaMin) != "numeric") ...
File 'rags2ridges/R/rags2ridgesDepr.R': if (class(lambdaMax) != "numeric") ...
File 'rags2ridges/R/rags2ridgesDepr.R': if (class(step) != "numeric") ...
File 'rags2ridges/R/rags2ridgesDepr.R': if (class(cor) != "logical") ...
File 'rags2ridges/R/rags2ridgesDepr.R': if (class(graph) != "logical") ...
File 'rags2ridges/R/rags2ridgesDepr.R': if (class(lambdaMin) != "numeric") ...
File 'rags2ridges/R/rags2ridgesDepr.R': if (class(lambdaMax) != "numeric") ...
File 'rags2ridges/R/rags2ridgesDepr.R': if (class(lambdaInit) != "numeric") ...
File 'rags2ridges/R/rags2ridgesDepr.R': if (class(cor) != "logical") ...
Use inherits() (or maybe is()) instead.
* 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 ... NOTE
Documented arguments not in \usage in Rd file 'dot-armaRidgeP.Rd':
  'alpha'

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 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [32s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [21s] OK
  Running 'testthat.R' [20s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... [19s] OK
* checking HTML version of manual ... [10s] OK
* DONE
Status: 3 NOTEs