• using R Under development (unstable) (2025-10-20 r88955)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-15 (Debian 15.2.0-4) 15.2.0     GNU Fortran (Debian 15.2.0-4) 15.2.0
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8
• checking for file ‘malan/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘malan’ version ‘1.0.4’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [1s/2s] OK
• 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 whether package ‘malan’ can be installed ... OK See the install log for details.
• used C++ compiler: ‘g++-15 (Debian 15.2.0-4) 15.2.0’
• 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 ... [1s/1s] OK
• checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
• checking whether the package can be unloaded cleanly ... [1s/1s] OK
• checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
• checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
• checking loading without being on the library search path ... [1s/1s] 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 ... [7s/9s] OK
• checking Rd files ... [1s/1s] 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 ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking contents of ‘data’ directory ... OK
• checking data for non-ASCII characters ... [0s/0s] OK
• checking LazyData ... 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 ... [1s/1s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [9s/11s] OK   Running ‘testthat.R’ [9s/11s]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [18s/27s] OK
• checking PDF version of manual ... [7s/9s] OK
• checking HTML version of manual ... [2s/4s] NOTE Found the following HTML validation problems: calc_autosomal_genotype_probs.html:50:1 (calc_autosomal_genotype_probs.Rd:12): Warning: missing </ul> before </div> construct_M.html:54:1 (construct_M.Rd:14): Warning: missing </ul> before </div> generate_get_founder_haplotype_db.html:46:1 (generate_get_founder_haplotype_db.Rd:10): Warning: missing </ul> before </div> generate_get_founder_haplotype_ladder.html:50:1 (generate_get_founder_haplotype_ladder.Rd:12): Warning: missing </ul> before </div> get_individuals.html:46:1 (get_individuals.Rd:10): Warning: missing </ul> before </div> get_pedigree_as_graph.html:46:1 (get_pedigree_as_graph.Rd:10): Warning: missing </ul> before </div> get_pedigrees_tidy.html:46:1 (get_pedigrees_tidy.Rd:10): Warning: missing </ul> before </div> get_zero_haplotype_generator.html:46:1 (get_zero_haplotype_generator.Rd:10): Warning: missing </ul> before </div> load_haplotypes.html:62:1 (load_haplotypes.Rd:18): Warning: missing </ul> before </div> load_individuals.html:58:1 (load_individuals.Rd:16): Warning: missing </ul> before </div> meioses_generation_distribution.html:56:1 (meioses_generation_distribution.Rd:16): Warning: missing </ul> before </div> pedigree_size_generation.html:52:1 (pedigree_size_generation.Rd:13): Warning: missing </ul> before </div> plot.malan_pedigree.html:89:1 (plot.malan_pedigree.Rd:36): Warning: missing </ul> before </div> plot.malan_pedigreelist.html:52:1 (plot.malan_pedigreelist.Rd:12): Warning: missing </ul> before </div> population_size_generation.html:52:1 (population_size_generation.Rd:13): Warning: missing </ul> before </div> print.malan_pedigree.html:51:1 (print.malan_pedigree.Rd:12): Warning: missing </ul> before </div> print.malan_pedigreelist.html:52:1 (print.malan_pedigreelist.Rd:12): Warning: missing </ul> before </div> print.malan_population.html:52:1 (print.malan_population.Rd:12): Warning: missing </ul> before </div> print.malan_population_abort.html:51:1 (print.malan_population_abort.Rd:12): Warning: missing </ul> before </div> sample_autosomal_genotype.html:50:1 (sample_autosomal_genotype.Rd:12): Warning: missing </ul> before </div>
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 NOTE