- 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