############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:primirTSS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings primirTSS_1.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/primirTSS.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘primirTSS/DESCRIPTION’ ... OK * this is package ‘primirTSS’ version ‘1.18.0’ * 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 hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘primirTSS’ can be installed ... 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 dependencies in R code ... WARNING '::' or ':::' import not declared from: 'magrittr' * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE check_DHS_df: no visible binding for global variable ‘can_tss’ check_DHS_df: no visible binding for global variable ‘new_info’ check_DHS_s: no visible binding for global variable ‘dhs_p1’ check_DHS_s: no visible binding for global variable ‘dhs_p2’ eponine_score: no visible binding for global variable ‘previous’ eponine_score: no visible binding for global variable ‘histone_p1_flank’ eponine_score: no visible binding for global variable ‘histone_p2_flank’ eponine_score: no visible binding for global variable ‘tss_p1’ eponine_score: no visible binding for global variable ‘tss_p2’ find_nearest_peak: no visible binding for global variable ‘mir_name’ find_nearest_peak: no visible binding for global variable ‘start1’ find_nearest_peak: no visible binding for global variable ‘end1’ mir_tf: no visible binding for global variable ‘arrow’ mir_tf: no visible binding for global variable ‘seqname’ mir_tf: no visible binding for global variable ‘TF’ mir_tf: no visible binding for global variable ‘TF_class’ phast_score: no visible binding for global variable ‘loci’ phast_score: no visible binding for global variable ‘eponine_rank’ phast_score: no visible binding for global variable ‘phast_rank’ phast_score: no visible binding for global variable ‘e_p_rank’ phast_score_plot: no visible binding for global variable ‘loci’ plot_primiRNA_track: no visible binding for global variable ‘predicted_tss’ plot_primiRNA_track: no visible binding for global variable ‘symbol_name’ plot_primiRNA_track: no visible binding for global variable ‘stem_loop_p1’ plot_primiRNA_track: no visible binding for global variable ‘stem_loop_p2’ plot_primiRNA_track: no visible binding for global variable ‘gene_id’ plot_primiRNA_track: no visible binding for global variable ‘gene_p1’ plot_primiRNA_track: no visible binding for global variable ‘gene_p2’ plot_primiRNA_track: no visible binding for global variable ‘tss_p1’ plot_primiRNA_track: no visible binding for global variable ‘tss_p2’ require_fa: no visible binding for global variable ‘arrow’ tss_filter: no visible binding for global variable ‘gene_id’ tss_filter: no visible binding for global variable ‘new_info’ tss_filter: no visible binding for global variable ‘predicted_tss’ tss_filter: no visible binding for global variable ‘tss_type’ Undefined global functions or variables: TF TF_class arrow can_tss dhs_p1 dhs_p2 e_p_rank end1 eponine_rank gene_id gene_p1 gene_p2 histone_p1_flank histone_p2_flank loci mir_name new_info phast_rank predicted_tss previous seqname start1 stem_loop_p1 stem_loop_p2 symbol_name tss_p1 tss_p2 tss_type * checking Rd files ... 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 R/sysdata.rda ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 1 NOTE See ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/primirTSS.Rcheck/00check.log’ for details.