• using R version 4.2.0 beta (2022-04-07 r82126)
  • using platform: x86_64-apple-darwin17.0 (64-bit)
  • using session charset: UTF-8
  • checking for file ‘phylosamp/DESCRIPTION’ ... OK
  • checking extension type ... Package
  • this is package ‘phylosamp’ version ‘0.1.6’
  • 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 whether package ‘phylosamp’ can be installed ... [2s/3s] OK
  • 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 dependencies in R code ... NOTE
    Namespaces in Imports field not imported from:
      ‘RColorBrewer’ ‘cowplot’ ‘ggplot2’ ‘reshape2’
      All declared Imports should be used.
  • checking S3 generic/method consistency ... OK
  • checking replacement functions ... OK
  • checking foreign function calls ... OK
  • checking R code for possible problems ... [2s/2s] OK
  • checking Rd files ... [1s/1s] OK
  • checking Rd metadata ... 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 ... OK
  • checking LazyData ... OK
  • checking data for ASCII and uncompressed saves ... 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 ... [17s/18s] OK
      Running ‘test-exp_links.R’ [1s/1s]
      Running ‘test-falsediscoveryrate.R’ [1s/1s]
      Running ‘test-gen_dists.R’ [1s/1s]
      Running ‘test-get_optim_roc.R’ [1s/1s]
      Running ‘test-obs_pairs_mtml.R’ [1s/1s]
      Running ‘test-obs_pairs_mtsl.R’ [1s/1s]
      Running ‘test-obs_pairs_stsl.R’ [1s/1s]
      Running ‘test-prob_trans_mtml.R’ [1s/1s]
      Running ‘test-prob_trans_mtsl.R’ [1s/1s]
      Running ‘test-prob_trans_stsl.R’ [1s/1s]
      Running ‘test-samplesize.R’ [1s/1s]
      Running ‘test-sens_spec_calc.R’ [1s/1s]
      Running ‘test-sens_spec_roc.R’ [1s/1s]
      Running ‘test-true_pairs.R’ [1s/1s]
      Running ‘test-true_pairs_mtml.R’ [1s/1s]
      Running ‘test-true_pairs_mtsl.R’ [1s/1s]
      Running ‘test-true_pairs_stsl.R’ [1s/1s]
      Running ‘test-truediscoveryrate.R’ [1s/1s]
  • checking for unstated dependencies in vignettes ... OK
  • checking package vignettes in ‘inst/doc’ ... OK
  • checking running R code from vignettes ... [2s/2s] NONE
      ‘V1_FalseDicoveryRate.Rmd’ using ‘UTF-8’... [0s/0s] OK
      ‘V2_SampleSize.Rmd’ using ‘UTF-8’... [0s/0s] OK
      ‘V3_SensitivitySpecificity.Rmd’ using ‘UTF-8’... [0s/0s] OK
      ‘V4_FullExamples.Rmd’ using ‘UTF-8’... [0s/0s] OK
  • checking re-building of vignette outputs ... [7s/8s] OK
  • checking PDF version of manual ... OK
  • DONE
    Status: 1 NOTE
  • using check arguments '--no-clean-on-error '