############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ZygosityPredictor.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ZygosityPredictor_1.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/ZygosityPredictor.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: aarch64-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 Ventura 13.6.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ZygosityPredictor/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ZygosityPredictor’ version ‘1.4.0’ * 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 ‘ZygosityPredictor’ 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 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 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 ZP_ov: no visible binding for global variable ‘status’ ZP_ov: no visible binding for global variable ‘eval_by’ ZP_ov: no visible binding for global variable ‘nconst’ ZP_ov: no visible binding for global variable ‘gene’ add_snps_to_matrices: no visible binding for global variable ‘mut_id’ add_snps_to_matrices: no visible binding for global variable ‘block_final’ add_snps_to_matrices: no visible binding for global variable ‘gt_final’ add_snps_to_matrices: no visible binding for global variable ‘.’ add_snps_to_matrices : : no visible binding for global variable ‘block_final’ add_snps_to_matrices : : no visible binding for global variable ‘mut_id’ aggregate_likelihoods: no visible binding for global variable ‘.’ aggregate_likelihoods : : no visible binding for global variable ‘mut_id’ aggregate_likelihoods : : no visible binding for global variable ‘gt’ aggregate_likelihoods : : no visible binding for global variable ‘lklhd’ aggregate_phasing : : no visible binding for global variable ‘mut_id’ aggregate_phasing : : no visible binding for global variable ‘p_same’ aggregate_phasing : : no visible binding for global variable ‘p_diff’ aggregate_phasing : : no visible binding for global variable ‘ep’ aggregate_phasing: no visible binding for global variable ‘comb’ aggregate_phasing: no visible binding for global variable ‘nconst’ aggregate_phasing: no visible binding for global variable ‘const’ aggregate_phasing: no visible binding for global variable ‘phasing’ aggregate_phasing: no visible binding for global variable ‘via’ aggregate_phasing: no visible binding for global variable ‘conf’ aggregate_phasing: no visible binding for global variable ‘unplausible’ aggregate_phasing: no visible binding for global variable ‘subclonal’ aggregate_phasing: no visible binding for global variable ‘wt_cp’ aggregate_phasing: no visible binding for global variable ‘min_poss_wt_cp’ aggregate_phasing: no visible binding for global variable ‘max_poss_wt_cp’ aggregate_phasing: no visible binding for global variable ‘score’ append_loglist: no visible binding for global variable ‘.’ bind_incdel_to_final_eval: no visible binding for global variable ‘status’ calc_genotype_likelihood_per_mut : : no visible binding for global variable ‘mapq’ calc_genotype_likelihood_per_mut : : no visible binding for global variable ‘.’ calc_genotype_likelihood_per_mut : : no visible binding for global variable ‘qual’ calc_genotype_likelihood_per_mut : : no visible binding for global variable ‘processed_bq’ calc_genotype_likelihood_per_mut : : no visible binding for global variable ‘processed_mapq’ calc_genotype_likelihood_per_mut : : no visible binding for global variable ‘aggregated_qual’ cigar_element: no visible binding for global variable ‘.’ classify_combination: no visible binding for global variable ‘baseq1’ classify_combination: no visible binding for global variable ‘baseq2’ classify_combination: no visible binding for global variable ‘mapq1’ classify_combination: no visible binding for global variable ‘mapq2’ classify_combination: no visible binding for global variable ‘pb1’ classify_combination: no visible binding for global variable ‘mq1’ classify_combination: no visible binding for global variable ‘pb2’ classify_combination: no visible binding for global variable ‘mq2’ classify_combination: no visible binding for global variable ‘ppos1’ classify_combination: no visible binding for global variable ‘ppos2’ classify_combination: no visible binding for global variable ‘p_result’ classify_combination: no visible binding for global variable ‘prob_sum’ classify_combination: no visible binding for global variable ‘origin’ eval_lost_in_tumor: no visible binding for global variable ‘gene’ eval_lost_in_tumor: no visible binding for global variable ‘pre_info’ eval_lost_in_tumor: no visible binding for global variable ‘wt_cp’ eval_one_mut: no visible binding for global variable ‘gene’ eval_one_mut: no visible binding for global variable ‘n_mut’ eval_one_mut: no visible binding for global variable ‘vn_status’ eval_one_mut: no visible binding for global variable ‘conf’ eval_one_mut: no visible binding for global variable ‘pre_info’ eval_one_mut: no visible binding for global variable ‘wt_cp’ eval_one_mut: no visible binding for global variable ‘eval_by’ eval_one_mut_affects_all: no visible binding for global variable ‘vn_status’ eval_one_mut_affects_all: no visible binding for global variable ‘.’ eval_one_mut_affects_all: no visible binding for global variable ‘mut_id’ eval_one_mut_affects_all: no visible binding for global variable ‘gene’ eval_one_mut_affects_all: no visible binding for global variable ‘n_mut’ eval_one_mut_affects_all: no visible binding for global variable ‘conf’ eval_one_mut_affects_all: no visible binding for global variable ‘eval_by’ eval_one_mut_affects_all: no visible binding for global variable ‘wt_cp’ eval_phasing_new: no visible binding for global variable ‘score’ eval_phasing_new: no visible binding for global variable ‘wt_cp’ eval_phasing_new: no visible binding for global variable ‘.’ eval_phasing_new: no visible binding for global variable ‘p_comb’ eval_phasing_new: no visible binding for global variable ‘comb’ eval_phasing_new: no visible binding for global variable ‘gene’ eval_phasing_new: no visible binding for global variable ‘phasing’ eval_rare_case: no visible binding for global variable ‘.’ find_unplaus_issues: no visible binding for global variable ‘unplausible’ find_unplaus_issues: no visible binding for global variable ‘comb’ find_unplaus_issues: no visible binding for global variable ‘.’ gene_ov: no visible binding for global variable ‘gene’ gene_ov: no visible binding for global variable ‘vn_status’ gene_ov: no visible binding for global variable ‘pre_info’ gene_ov: no visible binding for global variable ‘purity’ gene_ov: no visible binding for global variable ‘nconst’ gene_ov: no visible binding for global variable ‘conf’ gene_ov: no visible binding for global variable ‘xsq_diff’ gene_ov: no visible binding for global variable ‘xsq_same’ gene_ov: no visible binding for global variable ‘v_same’ gene_ov: no visible binding for global variable ‘v_diff’ gene_ov: no visible binding for global variable ‘phasing’ get_next_path: no visible binding for global variable ‘.’ get_xy_index: no visible binding for global variable ‘.’ loadVcf: no visible binding for global variable ‘.’ load_snps: no visible binding for global variable ‘.’ load_snps: no visible binding for global variable ‘QUAL’ load_snps: no visible binding for global variable ‘gt’ load_snps: no visible binding for global variable ‘mut_id’ make_mut_template: no visible global function definition for ‘expand_grid’ make_mut_template: no visible binding for global variable ‘.’ merge_sCNAs: no visible binding for global variable ‘all_imb’ merge_sCNAs: no visible binding for global variable ‘gt_cna’ merge_sCNAs: no visible binding for global variable ‘seg_id’ parse_cigar: no visible binding for global variable ‘.’ perform_copy_number_phasing : : no visible binding for global variable ‘seg_id’ perform_copy_number_phasing : : no visible binding for global variable ‘mut_id2’ perform_copy_number_phasing : : no visible binding for global variable ‘mut_id1’ perform_copy_number_phasing : : no visible binding for global variable ‘llr’ perform_indirect_phasing: no visible binding for global variable ‘af’ perform_indirect_phasing: no visible binding for global variable ‘tcn’ perform_indirect_phasing: no visible binding for global variable ‘chr’ perform_indirect_phasing: no visible binding for global variable ‘pos’ perform_indirect_phasing: no visible binding for global variable ‘ref’ perform_indirect_phasing: no visible binding for global variable ‘alt’ perform_indirect_phasing: no visible binding for global variable ‘mut_id’ perform_indirect_phasing: no visible binding for global variable ‘REF’ perform_indirect_phasing: no visible binding for global variable ‘ALT’ perform_indirect_phasing: no visible binding for global variable ‘gt_final’ phase: no visible binding for global variable ‘comb’ phase: no visible binding for global variable ‘ncomb’ phase_combination: no visible binding for global variable ‘purity’ phase_combination: no visible binding for global variable ‘printLog’ predict_zygosity: no visible binding for global variable ‘n_mut’ predict_zygosity: no visible binding for global variable ‘conf’ predict_zygosity: no visible binding for global variable ‘eval_by’ predict_zygosity: no visible binding for global variable ‘wt_cp_range’ predict_zygosity: no visible binding for global variable ‘phasing’ predict_zygosity: no visible binding for global variable ‘eval_time_s’ predict_zygosity_genewise: no visible binding for global variable ‘vn_status’ prepare_germline_variants: no visible binding for global variable ‘all_imb’ prepare_germline_variants: no visible binding for global variable ‘gt_cna’ prepare_germline_variants: no visible binding for global variable ‘seg_id’ prepare_germline_variants: no visible binding for global variable ‘vn_status’ prioritize_combination: no visible binding for global variable ‘.’ prioritize_combination : : no visible binding for global variable ‘.’ prioritize_combination: no visible binding for global variable ‘m’ prioritize_combination: no visible binding for global variable ‘n’ prioritize_combination: no visible binding for global variable ‘n1’ prioritize_combination: no visible binding for global variable ‘n2’ remove_duplicated_variants: no visible binding for global variable ‘chr’ remove_duplicated_variants: no visible binding for global variable ‘pos’ remove_duplicated_variants: no visible binding for global variable ‘n’ remove_duplicated_variants : : no visible binding for global variable ‘chr’ remove_duplicated_variants : : no visible binding for global variable ‘pos’ remove_duplicated_variants : : no visible binding for global variable ‘.’ remove_duplicated_variants : : no visible binding for global variable ‘mut_id’ vm: no visible binding for global variable ‘.’ Undefined global functions or variables: . ALT QUAL REF af aggregated_qual all_imb alt baseq1 baseq2 block_final chr comb conf const ep eval_by eval_time_s expand_grid gene gt gt_cna gt_final lklhd llr m mapq mapq1 mapq2 max_poss_wt_cp min_poss_wt_cp mq1 mq2 mut_id mut_id1 mut_id2 n n1 n2 n_mut ncomb nconst origin p_comb p_diff p_result p_same pb1 pb2 phasing pos ppos1 ppos2 pre_info printLog prob_sum processed_bq processed_mapq purity qual ref score seg_id status subclonal tcn unplausible v_diff v_same via vn_status wt_cp wt_cp_range xsq_diff xsq_same * 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 data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... 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: 1 NOTE See ‘/Users/biocbuild/bbs-3.19-bioc/meat/ZygosityPredictor.Rcheck/00check.log’ for details.