- using R version 4.1.0 (2021-05-18)
- 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/2s] 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 ... [0s/0s] 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 ... [12s/12s] 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 ... [1s/1s] 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 ... [6s/7s] OK
- checking PDF version of manual ... OK
- DONE
Status: 1 NOTE
- using check arguments '--no-clean-on-error '