• using R Under development (unstable) (2024-12-19 r87451)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-14 (Debian 14.2.0-8) 14.2.0     GNU Fortran (Debian 14.2.0-8) 14.2.0
• running under: Debian GNU/Linux trixie/sid
• 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 executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking serialization versions ... OK
• checking whether package ‘poppr’ can be installed ... OK See the install log for details.
• used C compiler: ‘gcc-14 (Debian 14.2.0-8) 14.2.0’
• 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 code files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... [3s/4s] OK
• checking whether the package can be loaded with stated dependencies ... [4s/4s] OK
• checking whether the package can be unloaded cleanly ... [3s/3s] OK
• checking whether the namespace can be loaded with stated dependencies ... [3s/3s] OK
• checking whether the namespace can be unloaded cleanly ... [3s/4s] OK
• checking loading without being on the library search path ... [3s/3s] OK
• checking whether startup messages can be suppressed ... [3s/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 ... [27s/32s] OK
• checking Rd files ... [1s/1s] OK
• checking Rd metadata ... OK
• checking Rd line widths ... 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 ... [3s/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 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 sizes of PDF files under ‘inst/doc’ ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [11s/15s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [13s/15s] OK   Running ‘test-all.R’ [13s/15s]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [8s/11s] OK
• checking PDF version of manual ... [7s/10s] OK
• checking HTML version of manual ... [3s/6s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 NOTE