- using R Under development (unstable) (2024-11-06 r87293)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
Debian clang version 19.1.2 (2)
Debian flang-new version 19.1.2 (2)
- 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: ‘Debian clang version 19.1.2 (2)’
- 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 ... [4s/6s] OK
- checking whether the package can be loaded with stated dependencies ... [4s/6s] OK
- checking whether the package can be unloaded cleanly ... [4s/5s] OK
- checking whether the namespace can be loaded with stated dependencies ... [4s/6s] OK
- checking whether the namespace can be unloaded cleanly ... [5s/6s] OK
- checking loading without being on the library search path ... [5s/6s] OK
- checking whether startup messages can be suppressed ... [4s/6s] 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 ... [41s/50s] OK
- checking Rd files ... [1s/2s] 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 ... [5s/7s] 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 ... [17s/20s] OK
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [20s/25s] OK
Running ‘test-all.R’ [20s/25s]
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [12s/16s] OK
- checking PDF version of manual ... [10s/14s] OK
- checking HTML version of manual ... [6s/10s] OK
- checking for non-standard things in the check directory ... OK
- DONE
Status: 1 NOTE