############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CNVgears.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CNVgears_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/CNVgears.Rcheck’ * using R version 4.4.0 beta (2024-04-14 r86421) * using platform: x86_64-apple-darwin20 * 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 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘CNVgears/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘CNVgears’ version ‘1.12.0’ * 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 ‘CNVgears’ can be installed ... OK * checking installed package size ... NOTE installed size is 5.2Mb sub-directories of 1Mb or more: data 1.4Mb extdata 3.6Mb * 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 ... NOTE Problems with news in ‘NEWS.md’: No news entries found. * checking code 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 whether startup messages can be suppressed ... 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 ... NOTE CNVresults_to_GRanges: no visible global function definition for ‘.’ CNVresults_to_GRanges: no visible binding for global variable ‘sample_ID’ CNVresults_to_GRanges: no visible binding for global variable ‘GT’ CNVresults_to_GRanges: no visible binding for global variable ‘meth_ID’ CNVresults_to_GRangesList: no visible binding for global variable ‘GRL’ DT_uniform_internal: no visible binding for global variable ‘chr’ DT_uniform_internal: no visible binding for global variable ‘start’ DT_uniform_internal: no visible binding for global variable ‘end’ DT_uniform_internal: no visible binding for global variable ‘CN’ DT_uniform_internal: no visible binding for global variable ‘GT’ DT_uniform_internal: no visible binding for global variable ‘P_ID’ DT_uniform_internal: no visible binding for global variable ‘last_P’ DT_uniform_internal: no visible binding for global variable ‘first_P’ DT_uniform_snps: no visible binding for global variable ‘pos’ DT_uniform_snps: no visible binding for global variable ‘chr’ DT_uniform_snps: no visible binding for global variable ‘start’ check_cnvrs: no visible binding for global variable ‘start’ check_cnvrs: no visible binding for global variable ‘end’ check_cnvrs: no visible binding for global variable ‘cnvr’ check_cnvrs: no visible binding for global variable ‘r_ID’ chr_st_en_etc: no visible binding for global variable ‘V1’ chr_st_en_etc: no visible global function definition for ‘.’ chr_st_en_etc: no visible binding for global variable ‘V2’ chr_st_en_etc: no visible binding for global variable ‘V3’ chr_uniform: no visible binding for global variable ‘chr’ cleaning_filter: no visible binding for global variable ‘sample_ID’ cleaning_filter: no visible binding for global variable ‘chr’ cleaning_filter: no visible binding for global variable ‘len’ cleaning_filter: no visible binding for global variable ‘NP’ cleaning_filter : filter_region: no visible binding for global variable ‘start’ cleaning_filter : filter_region: no visible binding for global variable ‘end’ cleaning_filter : filter_region: no visible binding for global variable ‘chr’ cnmops_to_CNVresults: no visible global function definition for ‘.’ cnmops_to_CNVresults: no visible binding for global variable ‘chr’ cnmops_to_CNVresults: no visible binding for global variable ‘start’ cnmops_to_CNVresults: no visible binding for global variable ‘end’ cnmops_to_CNVresults: no visible binding for global variable ‘sample_ID’ cnmops_to_CNVresults: no visible binding for global variable ‘CN’ cnvrs_create: no visible binding for global variable ‘start’ cnvrs_create: no visible binding for global variable ‘end’ cnvrs_create: no visible binding for global variable ‘chr’ cnvrs_create: no visible binding for global variable ‘cnvr’ cnvrs_create: no visible binding for global variable ‘arm_ID’ cnvrs_create: no visible binding for global variable ‘ix’ cnvrs_create: no visible binding for global variable ‘r_ID’ cnvrs_create: no visible binding for global variable ‘freq’ cnvrs_create: no visible binding for global variable ‘N’ cnvs_inheritance: no visible binding for global variable ‘role’ cnvs_inheritance: no visible binding for global variable ‘sample_ID’ cnvs_inheritance: no visible binding for global variable ‘fam_ID’ cnvs_inheritance: no visible binding for global variable ‘chr’ cnvs_inheritance: no visible binding for global variable ‘GT’ cnvs_inheritance: no visible binding for global variable ‘seg_ID’ cnvs_inheritance: no visible binding for global variable ‘inheritance’ cnvs_inheritance: no visible binding for global variable ‘start’ cnvs_inheritance: no visible binding for global variable ‘end’ cnvs_inheritance: no visible binding for global variable ‘copyratio’ cnvs_inheritance: no visible global function definition for ‘wilcox.test’ cnvs_inheritance: no visible global function definition for ‘sd’ cnvs_inheritance: no visible binding for global variable ‘mmmethod’ cnvs_inheritance: no visible binding for global variable ‘m_pval’ cnvs_inheritance: no visible binding for global variable ‘p_pval’ cnvs_inheritance: no visible global function definition for ‘p.adjust’ create_fill_CNVR: no visible binding for global variable ‘ix’ create_fill_CNVR: no visible binding for global variable ‘r_ID’ create_fill_CNVR: no visible binding for global variable ‘start’ create_fill_CNVR: no visible binding for global variable ‘end’ create_fill_CNVR: no visible binding for global variable ‘cnvr’ dupl_cnvrs: no visible binding for global variable ‘chr’ dupl_cnvrs: no visible binding for global variable ‘r_ID’ dupl_cnvrs: no visible binding for global variable ‘start’ dupl_cnvrs: no visible binding for global variable ‘end’ dupl_cnvrs: no visible binding for global variable ‘cnvr’ genic_load: no visible binding for global variable ‘gene_biotype’ genic_load: no visible binding for global variable ‘chr’ genic_load: no visible binding for global variable ‘start’ genic_load: no visible binding for global variable ‘ix’ genic_load: no visible binding for global variable ‘end’ genomic_locus: no visible binding for global variable ‘chr’ genomic_locus: no visible binding for global variable ‘start’ genomic_locus : match_band: no visible binding for global variable ‘chr’ genomic_locus : match_band: no visible binding for global variable ‘start’ genomic_locus : match_band: no visible binding for global variable ‘end’ genomic_locus: no visible binding for global variable ‘end’ genomic_locus: no visible binding for global variable ‘locus_start’ genomic_locus: no visible binding for global variable ‘locus_end’ genomic_locus: no visible binding for global variable ‘locus’ immuno_regions: no visible binding for global variable ‘chr’ immuno_regions: no visible binding for global variable ‘start’ immuno_regions: no visible binding for global variable ‘gene_biotype’ inter_res_merge: no visible binding for global variable ‘meth_ID’ inter_res_merge: no visible binding for global variable ‘len’ inter_res_merge: no visible binding for global variable ‘end’ inter_res_merge: no visible binding for global variable ‘start’ inter_res_merge: no visible binding for global variable ‘GT’ inter_res_merge: no visible global function definition for ‘.’ inter_res_merge: no visible binding for global variable ‘chr’ inter_res_merge: no visible binding for global variable ‘sample_ID’ inter_res_merge: no visible binding for global variable ‘CN’ inter_res_merge: no visible binding for global variable ‘arm_ID’ inter_res_merge: no visible binding for global variable ‘ix’ inter_res_merge: no visible binding for global variable ‘used’ inter_res_merge: no visible binding for global variable ‘outer_end’ inter_res_merge: no visible binding for global variable ‘outer_start’ inter_res_merge: no visible binding for global variable ‘seg_ID’ load_RDS: no visible binding for global variable ‘start’ load_RDS: no visible binding for global variable ‘end’ lrr_trio_plot: no visible binding for global variable ‘sample_ID’ lrr_trio_plot: no visible binding for global variable ‘fam_ID’ lrr_trio_plot: no visible binding for global variable ‘role’ lrr_trio_plot: no visible binding for global variable ‘start’ merge_calls: no visible binding for global variable ‘chr’ merge_calls: no visible binding for global variable ‘start’ merge_cnvrs: no visible binding for global variable ‘start’ merge_cnvrs: no visible binding for global variable ‘end’ merge_cnvrs: no visible binding for global variable ‘r_ID’ merge_cnvrs: no visible binding for global variable ‘cnvr’ pl: no visible binding for global variable ‘center’ pl: no visible binding for global variable ‘end’ pl: no visible binding for global variable ‘start’ pl: no visible binding for global variable ‘cr’ pl: no visible binding for global variable ‘copyratio’ pl: no visible binding for global variable ‘CN’ read_NGS_intervals : DT_uniform_internal: no visible binding for global variable ‘start’ read_NGS_intervals : DT_uniform_internal: no visible binding for global variable ‘end’ read_NGS_intervals : DT_uniform_internal: no visible binding for global variable ‘chr’ read_NGS_raw: no visible binding for global variable ‘chr’ read_NGS_raw: no visible binding for global variable ‘start’ read_NGS_raw: no visible binding for global variable ‘end’ read_NGS_raw: no visible binding for global variable ‘log2R’ read_NGS_raw: no visible binding for global variable ‘copyratio’ read_NGS_raw: no visible binding for global variable ‘P_ID’ read_NGS_raw: no visible binding for global variable ‘P_CN’ read_finalreport_raw: no visible binding for global variable ‘chr’ read_finalreport_raw: no visible binding for global variable ‘start’ read_finalreport_raw: no visible binding for global variable ‘log2R’ read_finalreport_raw: no visible global function definition for ‘.’ read_finalreport_raw: no visible binding for global variable ‘end’ read_finalreport_raw: no visible binding for global variable ‘BAF’ read_finalreport_raw: no visible binding for global variable ‘P_ID’ read_metadt: no visible binding for global variable ‘role’ read_metadt: no visible binding for global variable ‘sex’ read_results: no visible binding for global variable ‘sample_ID’ read_results: no visible binding for global variable ‘seg_ID’ read_results: no visible binding for global variable ‘meth_ID’ read_vcf: no visible binding for global variable ‘..end_vcf’ remove_cnvs: no visible binding for global variable ‘ix’ remove_cnvs: no visible binding for global variable ‘cnvr’ select_cnvs: no visible binding for global variable ‘sample_ID’ select_cnvs: no visible binding for global variable ‘GT’ select_cnvs: no visible binding for global variable ‘fam_ID’ select_cnvs: no visible binding for global variable ‘role’ select_cnvs: no visible binding for global variable ‘inheritance’ start_end: no visible binding for global variable ‘len’ start_end: no visible binding for global variable ‘end’ start_end: no visible binding for global variable ‘start’ start_end: no visible binding for global variable ‘outer_start’ summary.CNVresults: no visible binding for global variable ‘role’ summary.CNVresults: no visible binding for global variable ‘sample_ID’ summary.CNVresults: no visible binding for global variable ‘GT’ summary.CNVresults: no visible binding for global variable ‘len’ summary.CNVresults: no visible binding for global variable ‘NP’ summary.CNVresults: no visible global function definition for ‘pdf’ summary.CNVresults: no visible global function definition for ‘reorder’ summary.CNVresults: no visible binding for global variable ‘chr’ summary.CNVresults: no visible binding for global variable ‘CN’ summary.CNVresults: no visible global function definition for ‘dev.off’ summary.CNVresults: no visible global function definition for ‘.’ summary.CNVresults: no visible binding for global variable ‘n_cnvs’ summary.CNVresults: no visible global function definition for ‘head’ summary.CNVresults: no visible global function definition for ‘tail’ summary.CNVresults: no visible binding for global variable ‘mean_len’ trim_res: no visible binding for global variable ‘sample_ID’ trim_res: no visible binding for global variable ‘chr’ trim_res: no visible binding for global variable ‘start’ trim_res: no visible binding for global variable ‘end’ Undefined global functions or variables: . ..end_vcf BAF CN GRL GT N NP P_CN P_ID V1 V2 V3 arm_ID center chr cnvr copyratio cr dev.off end fam_ID first_P freq gene_biotype head inheritance ix last_P len locus locus_end locus_start log2R m_pval mean_len meth_ID mmmethod n_cnvs outer_end outer_start p.adjust p_pval pdf pos r_ID reorder role sample_ID sd seg_ID sex start tail used wilcox.test Consider adding importFrom("grDevices", "dev.off", "pdf") importFrom("stats", "end", "p.adjust", "reorder", "sd", "start", "wilcox.test") importFrom("utils", "head", "tail") to your NAMESPACE file. * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed inter_res_merge 10.200 0.175 10.524 read_vcf 9.051 0.313 9.505 cnmops_to_CNVresults 8.042 0.257 8.422 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc/meat/CNVgears.Rcheck/00check.log’ for details.