* using log directory ‘/srv/hornik/tmp/CRAN/TopArtCalc.Rcheck’ * using R Under development (unstable) (2024-05-20 r86569) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 18.1.4 (1) Debian flang-new version 18.1.4 (1) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘TopArtCalc/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘TopArtCalc’ version ‘1.1.5’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [1s/2s] NOTE Maintainer: ‘Marco Rheinnecker ’ New submission Non-FOSS package license (file LICENSE) Possibly misspelled words in DESCRIPTION: HRD (23:135) NGS (23:148) WES (3:57) Package has a VignetteBuilder field but no prebuilt vignette index. The Title field should be in title case. Current version is: ‘Package for calculation of TOP-ART score for WGS/WES sample’ In title case that is: ‘Package for Calculation of TOP-ART Score for WGS/WES Sample’ The Date field is over a month old. * checking package namespace information ... OK * checking package dependencies ... NOTE Vignette dependency required without any vignettes:: ‘knitr’ * 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 ‘TopArtCalc’ can be installed ... [24s/24s] OK * checking package directory ... OK * checking for future file timestamps ... 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 ... [8s/8s] OK * checking whether the package can be loaded with stated dependencies ... [8s/8s] OK * checking whether the package can be unloaded cleanly ... [8s/8s] OK * checking whether the namespace can be loaded with stated dependencies ... [7s/7s] OK * checking whether the namespace can be unloaded cleanly ... [8s/8s] OK * checking loading without being on the library search path ... [8s/8s] 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 ... [32s/32s] NOTE check_input_data: no visible binding for global variable ‘.’ check_input_data: no visible binding for global variable ‘width’ check_input_data: no visible binding for global variable ‘seqnames’ check_input_data: no visible binding for global variable ‘start’ check_input_data: no visible binding for global variable ‘ref’ check_input_data: no visible binding for global variable ‘alt’ check_input_data: no visible global function definition for ‘all_of’ create_gene_overview: no visible binding for global variable ‘score’ create_gene_overview: no visible binding for global variable ‘gene’ create_output_message: no visible binding for global variable ‘key’ create_output_message: no visible binding for global variable ‘value’ create_output_message: no visible binding for global variable ‘mes’ create_output_message: no visible global function definition for ‘head’ create_output_message: no visible binding for global variable ‘.’ create_output_message : : no visible binding for global variable ‘gene’ create_output_message : : no visible binding for global variable ‘.’ create_output_message: no visible global function definition for ‘bind_rows’ create_output_message: no visible global function definition for ‘desc’ create_output_message: no visible binding for global variable ‘score’ create_output_message: no visible binding for global variable ‘gene’ create_output_message: no visible binding for global variable ‘gene_info’ create_output_message: no visible binding for global variable ‘phasing_info’ create_output_message: no visible binding for global variable ‘chr’ create_output_message: no visible binding for global variable ‘pos’ create_output_message: no visible binding for global variable ‘af’ create_output_message: no visible binding for global variable ‘tcn’ create_output_message: no visible binding for global variable ‘cna_type’ create_output_message: no visible binding for global variable ‘aff_cp’ create_output_message: no visible binding for global variable ‘pre_info’ estimate_germline_score: no visible binding for global variable ‘.’ estimate_germline_score: no visible binding for global variable ‘gene’ estimate_germline_score: no visible binding for global variable ‘ACMG_class’ estimate_signature_score: no visible global function definition for ‘run_YAPSA_signature_analysis’ estimate_signature_score: no visible binding for global variable ‘exposure’ estimate_signature_score: no visible binding for global variable ‘sig’ estimate_signature_score: no visible binding for global variable ‘lower’ estimate_signature_score: no visible binding for global variable ‘upper’ estimate_signature_score: no visible binding for global variable ‘conf’ estimate_somatic_score: no visible binding for global variable ‘gene’ estimate_somatic_score: no visible binding for global variable ‘origin’ estimate_somatic_score: no visible binding for global variable ‘is_som’ Undefined global functions or variables: . ACMG_class af aff_cp all_of alt bind_rows chr cna_type conf desc exposure gene gene_info head is_som key lower mes origin phasing_info pos pre_info ref run_YAPSA_signature_analysis score seqnames sig start tcn upper value width Consider adding importFrom("stats", "start") importFrom("utils", "head") to your NAMESPACE file. * checking Rd files ... [0s/0s] 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 examples ... [11s/11s] OK * checking PDF version of manual ... [3s/2s] OK * checking HTML version of manual ... [0s/0s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 3 NOTEs