* using log directory ‘/srv/hornik/tmp/CRAN/BayesQuantify.Rcheck’ * using R Under development (unstable) (2023-11-16 r85542) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 17.0.4 (1) Debian flang-new version 17.0.4 (1) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘BayesQuantify/DESCRIPTION’ ... OK * this is package ‘BayesQuantify’ version ‘1.0.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/6s] NOTE Maintainer: ‘Sihan Liu ’ New submission Possibly misspelled words in DESCRIPTION: ACMG (3:9, 7:18, 11:8) BayesQuantify (15:8) ClinGen (9:62) The Title field should be in title case. Current version is: ‘An R package for quantifying the strength of evidence for ACMG/AMP criteria using a Bayesian framework’ In title case that is: ‘An R Package for Quantifying the Strength of Evidence for ACMG/AMP Criteria using a Bayesian Framework’ * 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 ‘BayesQuantify’ can be installed ... [8s/8s] OK * checking package directory ... OK * checking for future file timestamps ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... NOTE Non-standard file/directory found at top level: ‘BayesQuantify_1.0.0.pdf’ * 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 ... [2s/2s] OK * checking whether the package can be loaded with stated dependencies ... [2s/2s] OK * checking whether the package can be unloaded cleanly ... [2s/2s] OK * checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK * checking whether the namespace can be unloaded cleanly ... [2s/2s] OK * checking loading without being on the library search path ... [2s/2s] 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 ... [11s/11s] NOTE multi_plot: no visible binding for global variable ‘Gene’ multi_plot: no visible binding for global variable ‘sum.n.’ multi_plot: no visible binding for global variable ‘Classification’ multi_plot: no visible binding for global variable ‘Classification_3’ multi_plot: no visible binding for global variable ‘Consequence’ multi_plot: no visible binding for global variable ‘n.x’ multi_plot: no visible binding for global variable ‘n.y’ multi_plot: no visible binding for global variable ‘percent.x’ multi_plot: no visible binding for global variable ‘percent.y’ plot_lr: no visible binding for global variable ‘test_cutoff’ plot_lr: no visible binding for global variable ‘Posterior’ plot_lr: no visible binding for global variable ‘Posterior1’ Undefined global functions or variables: Classification Classification_3 Consequence Gene Posterior Posterior1 n.x n.y percent.x percent.y sum.n. test_cutoff * checking Rd files ... [0s/0s] OK * checking Rd metadata ... OK * checking Rd line widths ... NOTE Rd file 'LR.Rd': \examples lines wider than 100 characters: truth_set <- VCI_data[VCI_data$VUS_class != "Hot" & VCI_data$VUS_class != "Warm" & VCI_data$VUS_class != "Tepid" & VCI_data$VUS_class ! ... [TRUNCATED] Rd file 'get_lr_threshold.Rd': \examples lines wider than 100 characters: local_bootstrapped_lr(ClinVar2020_AJHG_Pejaver_data, "PrimateAI_score", 0.1, 10, 100, 0.1, "test_dir") Rd file 'local_bootstrapped_lr.Rd': \examples lines wider than 100 characters: local_bootstrapped_lr(ClinVar2020_AJHG_Pejaver_data, "PrimateAI_score", 0.1, 10, 100, 0.1, "test_dir") Rd file 'lr_CI.Rd': \examples lines wider than 100 characters: local_bootstrapped_lr(ClinVar2020_AJHG_Pejaver_data, "PrimateAI_score", 0.1, 30, 100, 0.1, "test_dir") Rd file 'plot_lr.Rd': \examples lines wider than 100 characters: # local_bootstrapped_lr(ClinVar2020_AJHG_Pejaver_data, "PrimateAI_score", 0.1, 30, 100, 0.1, "test_dir") These lines will be truncated in the PDF manual. * 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 ... [1s/1s] 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 ... [30m/30m] NOTE Examples with CPU (user + system) or elapsed time > 5s user system elapsed LR 836.432 18.566 855.074 lr_CI 504.536 0.008 504.567 local_bootstrapped_lr 185.213 0.012 185.234 get_lr_threshold 184.895 0.004 184.909 local_lr 25.223 0.028 25.251 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking re-building of vignette outputs ... [3s/3s] OK * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [0s/0s] NOTE Found the following HTML validation problems: VUS_classify.html:19:1 (VUS_classify.Rd:5): Warning: missing before
    VUS_classify.html:43:1 (VUS_classify.Rd:15): Warning: discarding unexpected * checking for non-standard things in the check directory ... NOTE Found the following files/directories: ‘test_dir’ * checking for detritus in the temp directory ... OK * DONE Status: 7 NOTEs