* using log directory 'd:/Rcompile/CRANpkg/local/4.5/poppr.Rcheck'
* using R Under development (unstable) (2025-02-14 r87718 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'poppr/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'poppr' version '2.9.6'
* package encoding: UTF-8
* 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 whether package 'poppr' can be installed ... OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-windows-x86_64/poppr-00install.html' for details.
* used C compiler: 'gcc.exe (GCC) 13.3.0'
* checking installed package size ... OK
* checking package directory ... 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [4s] OK
* checking whether the package can be loaded with stated dependencies ... [4s] OK
* checking whether the package can be unloaded cleanly ... [4s] OK
* checking whether the namespace can be loaded with stated dependencies ... [4s] OK
* checking whether the namespace can be unloaded cleanly ... [4s] OK
* checking loading without being on the library search path ... [4s] OK
* checking whether startup messages can be suppressed ... [4s] 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] OK
* checking Rd files ... [2s] OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  MLG-accessors.Rd: genlight-class
  aboot.Rd: genind, genpop, genlight-class
  bitwise.dist.Rd: genlight-class, genind-class
  bitwise.ia.Rd: genlight-class
  bootgen-class.Rd: gen-class
  bruvo.boot.Rd: genind, boot.phylo, nancycats, nj, nodelabels, tab
  bruvo.dist.Rd: genind
  bruvo.msn.Rd: genind, nancycats
  bruvomat-methods.Rd: genind-class
  clonecorrect.Rd: genind-class
  coercion-methods.Rd: genind-class, splitStrata
  diss.dist.Rd: genind
  diversity_ci.Rd: genind
  filter_stats.Rd: genind, genlight
  fix_replen.Rd: genind
  genclone-class.Rd: genind-class, genlight-class
  genclone-method.Rd: genind-class
  genetic_distance.Rd: genind-class, dist.genpop
  genind2genalex.Rd: genind-class
  genotype_curve.Rd: genind-class
  ia.Rd: import2genind
  info_table.Rd: genind-class
  informloci.Rd: genind-class
  is.clone.Rd: genind-class, genlight-class
  missingno.Rd: genind-class, tab
  mlg.Rd: ggplot
  mlg.filter.Rd: genind-class
  pgen.Rd: strata
  plot_poppr_msn.Rd: genind-class, genlight-class
  poppr-package.Rd: genind-class, genlight-class
  poppr.Rd: tab, strata, last_plot
  poppr.amova.Rd: genind-class, genlight-class, strata, quasieuclid,
    lingoes, cailliez
  poppr.msn.Rd: genind, genlight, nancycats, nj, nodelabels, tab
  popsub.Rd: genind-class, genlight-class
  psex.Rd: strata
  read.genalex.Rd: genind, other, genind-class
  recode_polyploids.Rd: genind-class, genpop-class
  rraf.Rd: strata
  shufflepop.Rd: genind-class
  snpclone-coercion-methods.Rd: genlight-class
  snpclone-method.Rd: genlight-class
  test_replen.Rd: genind
  upgma.Rd: as.phylo
  win.ia.Rd: genlight-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 ... [4s] 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 pragmas in C/C++ headers and code ... OK
* checking compiled code ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [29s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [17s] OK
  Running 'test-all.R' [16s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [31s] OK
* checking PDF version of manual ... [26s] OK
* checking HTML version of manual ... [16s] OK
* DONE
Status: 1 NOTE