• using R Under development (unstable) (2023-09-21 r85192)
• using platform: x86_64-pc-linux-gnu
• R was compiled by
      clang version 17.0.1
      flang-new version 17.0.1
• running under: Fedora Linux 36 (Workstation Edition)
• using session charset: UTF-8
• using option ‘--no-stop-on-test-error’
• checking for file ‘PhylogeneticEM/DESCRIPTION’ ... OK
• this is package ‘PhylogeneticEM’ version ‘1.6.0’
• 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 whether package ‘PhylogeneticEM’ can be installed ... [90s/92s] OK
  See the install log for details.
• used C compiler: ‘clang version 17.0.1’
• used C++ compiler: ‘clang version 17.0.1’
• 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 R files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... OK
• checking whether the package can be loaded with stated dependencies ... OK
• checking whether the package can be unloaded cleanly ... OK
• checking whether the namespace can be loaded with stated dependencies ... OK
• checking whether the namespace can be unloaded cleanly ... OK
• checking loading without being on the library search path ... 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 ... [56s/74s] OK
• checking Rd files ... 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 ... NOTE
  Documented arguments not in \usage in documentation object 'allocate_subset_node.simulate':
    ‘node:’ ‘array:’ ‘value:’
  
  Documented arguments not in \usage in documentation object 'check_data':
    ‘trait_correlation_threshold’
  
  Documented arguments not in \usage in documentation object 'compute_E.simple':
    ‘sim’ ‘Sigma’ ‘Sigma_YY_inv’
  
  Documented arguments not in \usage in documentation object 'compute_expectations.BM':
    ‘phylo:’
  
  Documented arguments not in \usage in documentation object 'compute_expectations.scOU':
    ‘phylo:’
  
  Documented arguments not in \usage in documentation object 'compute_gauss_lasso':
    ‘Yp’
  
  Documented arguments not in \usage in documentation object 'compute_log_likelihood.simple':
    ‘Y_data’ ‘Sigma_YY_inv’
  
  Documented arguments not in \usage in documentation object 'compute_mahalanobis_distance.simple':
    ‘Y_data’ ‘Sigma_YY_inv’
  
  Documented arguments not in \usage in documentation object 'compute_residuals.simple':
    ‘Y_data’ ‘Sigma_YY_inv’
  
  Documented arguments not in \usage in documentation object 'equivalent_shifts_values':
    ‘shifts’ ‘beta_0’
  
  Documented arguments not in \usage in documentation object 'extract.variance_covariance':
    ‘what:’ ‘miss;’
  
  Documented arguments not in \usage in documentation object 'find_shift_values':
    ‘m_Y’
  
  Documented arguments not in \usage in documentation object 'go_back_to_original_process':
    ‘phy_original:’ ‘known.selection.strength:’ ‘sBM_variance:’ ‘params:’
  
  Documented arguments not in \usage in documentation object 'init.parsimonyCost':
    ‘phylo’
  
  Documented arguments not in \usage in documentation object 'init.simulate.OU':
    ‘phy:’ ‘p:’
  
  Documented arguments not in \usage in documentation object 'init.simulate.StateAndExp':
    ‘phy:’ ‘p:’
  
  Documented arguments not in \usage in documentation object 'is.in.ranges':
    ‘params’
  
  Documented arguments not in \usage in documentation object 'merge_params_independent':
    ‘params_split:’
  
  Documented arguments not in \usage in documentation object 'penalty_pBIC':
    ‘C’
  
  Documented arguments not in \usage in documentation object 'segmentation.OU.specialCase.lasso':
    ‘conditional_law_X’ ‘selection.strength’
  
  Documented arguments not in \usage in documentation object 'segmentation.OU.specialCase.same_shifts':
    ‘conditional_law_X’ ‘selection.strength’
  
  Functions with \usage entries need to have the appropriate \alias
  entries, and all their arguments documented.
  The \usage entries must correspond to syntactically valid R code.
  See chapter ‘Writing R documentation files’ in the ‘Writing R
  Extensions’ manual.
  S3 methods shown with full name in documentation object 'qr.solve_exact':
    ‘qr.solve_exact’
  
  The \usage entries for S3 methods should use the \method markup and not
  their full name.
  See chapter ‘Writing R documentation files’ in the ‘Writing R
  Extensions’ manual.
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking contents of ‘data’ directory ... OK
• checking data for non-ASCII characters ... 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 ... [8s/20s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [70s/173s] OK
    Running ‘testthat_EM.R’ [5s/12s]
    Running ‘testthat_core.R’ [11s/31s]
    Running ‘testthat_independent.R’ [5s/13s]
    Running ‘testthat_shifts.R’ [12s/30s]
    Running ‘testthat_upward.R’ [15s/34s]
    Running ‘testthat_utilities.R’ [22s/52s]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes in ‘inst/doc’ ... OK
• checking re-building of vignette outputs ... [39s/532s] OK
• checking PDF version of manual ... [14s/23s] OK
• checking HTML version of manual ... [8s/11s] OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE

Status: 1 NOTE