############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:tidybulk.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings tidybulk_1.15.5.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/tidybulk.Rcheck’ * using R Under development (unstable) (2024-01-16 r85808) * 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 ‘tidybulk/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘tidybulk’ version ‘1.15.5’ * 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 ‘tidybulk’ 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 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 .adjust_abundance_se: no visible binding for global variable ‘x’ .aggregate_duplicates_se: no visible binding for global variable ‘group_name’ .aggregate_duplicates_se: no visible binding for global variable ‘group’ .deconvolve_cellularity_se: no visible binding for global variable ‘X_cibersort’ .describe_transcript_SE: no visible binding for global variable ‘transcript’ .describe_transcript_SE: no visible binding for global variable ‘description’ .identify_abundant: no visible binding for global variable ‘.abundant’ .keep_abundant: no visible binding for global variable ‘.abundant’ .pivot_sample: no visible binding for global variable ‘.’ .quantile_normalise_abundance: no visible binding for global variable ‘x’ .quantile_normalise_abundance_se: no visible binding for global variable ‘x’ .scale_abundance: no visible binding for global variable ‘x’ .scale_abundance: no visible binding for global variable ‘multiplier’ .scale_abundance_se: no visible binding for global variable ‘x’ .test_differential_abundance_se: no visible binding for global variable ‘.contrasts’ .test_differential_abundance_se: no visible binding for global variable ‘action’ .test_differential_cellularity: no visible binding for global variable ‘X_cibersort’ .test_differential_cellularity_se: no visible binding for global variable ‘X_cibersort’ .test_differential_cellularity_se: no visible binding for global variable ‘cell_type’ .test_differential_cellularity_se: no visible binding for global variable ‘prop’ .test_differential_cellularity_se: no visible binding for global variable ‘.cell_type’ .test_gene_enrichment_SE: no visible global function definition for ‘buildCustomIdx’ .test_gene_enrichment_SE: no visible global function definition for ‘buildIdx’ .test_gene_enrichment_SE: no visible global function definition for ‘egsea’ .test_gene_enrichment_SE: no visible binding for global variable ‘pathway’ .test_gene_enrichment_SE: no visible binding for global variable ‘data_base’ .test_gene_enrichment_SE: no visible binding for global variable ‘web_page’ .test_gene_overrepresentation: no visible binding for global variable ‘my_do_test’ .test_gene_overrepresentation_SE: no visible binding for global variable ‘my_do_test’ .test_gene_rank: no visible global function definition for ‘with_groups’ .test_gene_rank: no visible global function definition for ‘desc’ .test_gene_rank_SE: no visible global function definition for ‘desc’ .test_stratification_cellularity: no visible binding for global variable ‘X_cibersort’ .test_stratification_cellularity_SE: no visible binding for global variable ‘X_cibersort’ .test_stratification_cellularity_SE: no visible binding for global variable ‘.cell_type’ add_scaled_counts_bulk.calcNormFactor: no visible binding for global variable ‘transcript’ aggregate_duplicated_transcripts_DT: no visible binding for global variable ‘.abundance_scaled’ aggregate_duplicated_transcripts_bulk: no visible binding for global variable ‘.abundance_scaled’ aggregate_duplicated_transcripts_bulk: no visible binding for global variable ‘n_aggr’ aggregate_duplicated_transcripts_bulk: no visible global function definition for ‘where’ as_matrix: no visible binding for global variable ‘variable’ call_core: no visible binding for global variable ‘nulldist’ change_reserved_column_names: no visible binding for global variable ‘.’ check_if_duplicated_genes: no visible binding for global variable ‘transcript’ check_if_duplicated_genes: no visible binding for global variable ‘read count’ counts_scaled_exist_SE: no visible binding for global variable ‘tt_columns’ counts_scaled_exist_SE: no visible binding for global variable ‘.’ create_tt_from_bam_sam_bulk: no visible binding for global variable ‘.’ create_tt_from_bam_sam_bulk: no visible binding for global variable ‘temp’ create_tt_from_bam_sam_bulk: no visible binding for global variable ‘Status’ create_tt_from_bam_sam_bulk: no visible binding for global variable ‘counts’ create_tt_from_bam_sam_bulk: no visible binding for global variable ‘GeneID’ create_tt_from_bam_sam_bulk: no visible binding for global variable ‘genes’ create_tt_from_bam_sam_bulk: no visible binding for global variable ‘samples’ create_tt_from_bam_sam_bulk: no visible binding for global variable ‘transcript’ eliminate_sparse_transcripts: no visible global function definition for ‘add_count’ eliminate_sparse_transcripts: no visible binding for global variable ‘my_n’ entrez_over_to_gsea: no visible binding for global variable ‘gs_cat’ entrez_over_to_gsea: no visible binding for global variable ‘test’ entrez_over_to_gsea: no visible binding for global variable ‘geneID’ entrez_rank_to_gsea: no visible binding for global variable ‘gs_cat’ entrez_rank_to_gsea: no visible binding for global variable ‘.’ entrez_rank_to_gsea: no visible binding for global variable ‘entrez_gene’ entrez_rank_to_gsea: no visible binding for global variable ‘fit’ error_if_duplicated_genes: no visible binding for global variable ‘transcript’ error_if_duplicated_genes: no visible binding for global variable ‘read count’ error_if_duplicated_genes: no visible global function definition for ‘desc’ error_if_log_transformed: no visible binding for global variable ‘m’ fill_NA_matrix_with_factor_colwise: no visible binding for global variable ‘.’ fill_NA_using_formula: no visible binding for global variable ‘NUL’ fill_NA_using_formula: no visible binding for global variable ‘ct_data’ fill_NA_using_formula: no visible binding for global variable ‘library_size__’ fill_NA_using_formula: no visible binding for global variable ‘cov_data’ filter_genes_on_condition: no visible binding for global variable ‘.feature’ get_abundance_norm_if_exists: no visible binding for global variable ‘.abundance_scaled’ get_adjusted_counts_for_unwanted_variation_bulk: no visible binding for global variable ‘.’ get_adjusted_counts_for_unwanted_variation_bulk: no visible global function definition for ‘all_of’ get_assay_scaled_if_exists_SE: no visible binding for global variable ‘tt_columns’ get_assay_scaled_if_exists_SE: no visible binding for global variable ‘.abundance_scaled’ get_cell_type_proportions: no visible binding for global variable ‘.’ get_clusters_SNN_bulk: no visible binding for global variable ‘seurat_clusters’ get_clusters_SNN_bulk_SE: no visible binding for global variable ‘.’ get_clusters_SNN_bulk_SE: no visible binding for global variable ‘seurat_clusters’ get_clusters_kmeans_bulk: no visible binding for global variable ‘.’ get_clusters_kmeans_bulk: no visible binding for global variable ‘cluster’ get_clusters_kmeans_bulk: no visible binding for global variable ‘cluster kmeans’ get_clusters_kmeans_bulk_SE: no visible binding for global variable ‘.’ get_clusters_kmeans_bulk_SE: no visible binding for global variable ‘cluster’ get_differential_transcript_abundance_bulk: no visible binding for global variable ‘.’ get_differential_transcript_abundance_bulk_SE: no visible binding for global variable ‘.’ get_differential_transcript_abundance_bulk_voom: no visible binding for global variable ‘.’ get_differential_transcript_abundance_bulk_voom_SE: no visible binding for global variable ‘.’ get_differential_transcript_abundance_deseq2: no visible binding for global variable ‘counts’ get_differential_transcript_abundance_deseq2: no visible binding for global variable ‘.’ get_differential_transcript_abundance_deseq2_SE: no visible binding for global variable ‘.’ get_differential_transcript_abundance_glmmSeq: no visible global function definition for ‘eliminate_random_effects’ get_differential_transcript_abundance_glmmSeq: no visible binding for global variable ‘tagwise.dispersion’ get_differential_transcript_abundance_glmmSeq: no visible binding for global variable ‘.’ get_differential_transcript_abundance_glmmSeq_SE: no visible binding for global variable ‘tagwise.dispersion’ get_differential_transcript_abundance_glmmSeq_SE: no visible binding for global variable ‘.’ get_reduced_dimensions_MDS_bulk: no visible binding for global variable ‘Component’ get_reduced_dimensions_MDS_bulk: no visible binding for global variable ‘Component value’ get_reduced_dimensions_MDS_bulk_SE: no visible binding for global variable ‘Component’ get_reduced_dimensions_MDS_bulk_SE: no visible binding for global variable ‘Component value’ get_reduced_dimensions_PCA_bulk: no visible binding for global variable ‘sdev’ get_reduced_dimensions_PCA_bulk: no visible binding for global variable ‘name’ get_reduced_dimensions_PCA_bulk: no visible binding for global variable ‘value’ get_reduced_dimensions_PCA_bulk: no visible binding for global variable ‘x’ get_reduced_dimensions_PCA_bulk_SE: no visible binding for global variable ‘sdev’ get_reduced_dimensions_PCA_bulk_SE: no visible binding for global variable ‘name’ get_reduced_dimensions_PCA_bulk_SE: no visible binding for global variable ‘value’ get_reduced_dimensions_PCA_bulk_SE: no visible binding for global variable ‘x’ get_reduced_dimensions_TSNE_bulk: no visible binding for global variable ‘Y’ get_reduced_dimensions_TSNE_bulk_SE: no visible binding for global variable ‘Y’ get_reduced_dimensions_UMAP_bulk_SE: no visible binding for global variable ‘x’ get_rotated_dimensions: no visible binding for global variable ‘value’ get_rotated_dimensions: no visible binding for global variable ‘rotated dimensions’ get_scaled_counts_bulk: no visible binding for global variable ‘med’ get_scaled_counts_bulk: no visible binding for global variable ‘tot_filt’ get_scaled_counts_bulk: no visible binding for global variable ‘nf’ get_scaled_counts_bulk: no visible binding for global variable ‘.’ get_scaled_counts_bulk: no visible binding for global variable ‘tot’ get_symbol_from_ensembl: no visible binding for global variable ‘ensembl_id’ get_symbol_from_ensembl: no visible binding for global variable ‘transcript’ get_symbol_from_ensembl: no visible binding for global variable ‘ref_genome’ get_tt_columns: no visible binding for global variable ‘tt_columns’ glmerCore: no visible global function definition for ‘coef’ glmerCore: no visible global function definition for ‘vcov’ glmerCore: no visible global function definition for ‘AIC’ glmerCore: no visible global function definition for ‘logLik’ glmerCore: no visible global function definition for ‘anova’ glmerCore: no visible global function definition for ‘predict’ glmmSeq: no visible global function definition for ‘update.formula’ glmmTMB_to_confidence_intervals_random_effects: no visible binding for global variable ‘group_id’ glmmTMB_to_confidence_intervals_random_effects: no visible binding for global variable ‘parameter’ glmmTMB_to_confidence_intervals_random_effects: no visible binding for global variable ‘CI’ glmmTMB_to_confidence_intervals_random_effects: no visible binding for global variable ‘lower’ glmmTMB_to_confidence_intervals_random_effects: no visible binding for global variable ‘upper’ glmmTMBcore: no visible global function definition for ‘coef’ glmmTMBcore: no visible global function definition for ‘vcov’ glmmTMBcore: no visible global function definition for ‘AIC’ glmmTMBcore: no visible global function definition for ‘logLik’ glmmTMBcore: no visible global function definition for ‘anova’ glmmTMBcore: no visible global function definition for ‘predict’ initialise_tt_internals: no visible binding for global variable ‘.’ lmer_to_confidence_intervals_random_effects: no visible binding for global variable ‘group_id’ lmer_to_confidence_intervals_random_effects: no visible binding for global variable ‘parameter’ lmer_to_confidence_intervals_random_effects: no visible binding for global variable ‘CI’ lmer_to_confidence_intervals_random_effects: no visible binding for global variable ‘lower’ lmer_to_confidence_intervals_random_effects: no visible binding for global variable ‘upper’ memorise_methods_used: no visible binding for global variable ‘.’ multivariable_differential_tissue_composition: no visible binding for global variable ‘.’ multivariable_differential_tissue_composition: no visible binding for global variable ‘.cell_type’ multivariable_differential_tissue_composition: no visible binding for global variable ‘term’ multivariable_differential_tissue_composition_SE: no visible binding for global variable ‘.’ multivariable_differential_tissue_composition_SE: no visible binding for global variable ‘.cell_type’ multivariable_differential_tissue_composition_SE: no visible binding for global variable ‘term’ remove_redundancy_elements_though_reduced_dimensions: no visible binding for global variable ‘sample b’ remove_redundancy_elements_though_reduced_dimensions: no visible binding for global variable ‘sample a’ remove_redundancy_elements_though_reduced_dimensions: no visible binding for global variable ‘sample 1’ remove_redundancy_elements_though_reduced_dimensions: no visible binding for global variable ‘sample 2’ remove_redundancy_elements_though_reduced_dimensions_SE: no visible binding for global variable ‘sample b’ remove_redundancy_elements_though_reduced_dimensions_SE: no visible binding for global variable ‘sample a’ remove_redundancy_elements_though_reduced_dimensions_SE: no visible binding for global variable ‘sample 1’ remove_redundancy_elements_though_reduced_dimensions_SE: no visible binding for global variable ‘sample 2’ remove_redundancy_elements_through_correlation: no visible binding for global variable ‘rc’ remove_redundancy_elements_through_correlation: no visible binding for global variable ‘transcript’ remove_redundancy_elements_through_correlation: no visible binding for global variable ‘correlation’ remove_redundancy_elements_through_correlation: no visible binding for global variable ‘item1’ remove_redundancy_elements_through_correlation_SE: no visible binding for global variable ‘abundance’ remove_redundancy_elements_through_correlation_SE: no visible binding for global variable ‘transcript’ remove_redundancy_elements_through_correlation_SE: no visible binding for global variable ‘element’ remove_redundancy_elements_through_correlation_SE: no visible binding for global variable ‘feature’ remove_redundancy_elements_through_correlation_SE: no visible binding for global variable ‘rc’ remove_redundancy_elements_through_correlation_SE: no visible binding for global variable ‘correlation’ remove_redundancy_elements_through_correlation_SE: no visible binding for global variable ‘item1’ rowwise.tidybulk: no visible binding for global variable ‘.data’ run_epic: no visible global function definition for ‘EPIC’ run_llsr: no visible binding for global variable ‘X_cibersort’ scale_design: no visible binding for global variable ‘value’ scale_design: no visible binding for global variable ‘sample_idx’ scale_design: no visible binding for global variable ‘(Intercept)’ select_closest_pairs: no visible binding for global variable ‘sample 1’ select_closest_pairs: no visible binding for global variable ‘sample 2’ subset_tibble_output: no visible binding for global variable ‘.’ symbol_to_entrez: no visible binding for global variable ‘transcript_upper’ symbol_to_entrez: no visible binding for global variable ‘entrez’ test_differential_cellularity: no visible binding for global variable ‘X_cibersort’ test_differential_cellularity_: no visible binding for global variable ‘cell_type’ test_differential_cellularity_: no visible binding for global variable ‘prop’ test_differential_cellularity_: no visible binding for global variable ‘.’ test_differential_cellularity_: no visible binding for global variable ‘.cell_type’ test_gene_enrichment_bulk_EGSEA: no visible global function definition for ‘buildCustomIdx’ test_gene_enrichment_bulk_EGSEA: no visible global function definition for ‘buildIdx’ test_gene_enrichment_bulk_EGSEA: no visible binding for global variable ‘pathway’ test_gene_enrichment_bulk_EGSEA: no visible binding for global variable ‘data_base’ test_gene_enrichment_bulk_EGSEA: no visible binding for global variable ‘web_page’ test_gene_enrichment_bulk_EGSEA: no visible global function definition for ‘egsea’ test_stratification_cellularity: no visible binding for global variable ‘X_cibersort’ test_stratification_cellularity_: no visible binding for global variable ‘.cell_type’ tidybulk_to_SummarizedExperiment: no visible binding for global variable ‘.’ univariable_differential_tissue_composition: no visible binding for global variable ‘.proportion’ univariable_differential_tissue_composition: no visible binding for global variable ‘.cell_type’ univariable_differential_tissue_composition: no visible binding for global variable ‘cell_type_proportions’ univariable_differential_tissue_composition: no visible binding for global variable ‘surv_test’ univariable_differential_tissue_composition_SE: no visible binding for global variable ‘.proportion’ univariable_differential_tissue_composition_SE: no visible binding for global variable ‘.cell_type’ univariable_differential_tissue_composition_SE: no visible binding for global variable ‘cell_type_proportions’ univariable_differential_tissue_composition_SE: no visible binding for global variable ‘surv_test’ univariable_differential_tissue_stratification: no visible binding for global variable ‘.cell_type’ univariable_differential_tissue_stratification: no visible binding for global variable ‘cell_type_proportions’ univariable_differential_tissue_stratification: no visible binding for global variable ‘surv_test’ univariable_differential_tissue_stratification_SE: no visible binding for global variable ‘.cell_type’ univariable_differential_tissue_stratification_SE: no visible binding for global variable ‘cell_type_proportions’ univariable_differential_tissue_stratification_SE: no visible binding for global variable ‘surv_test’ adjust_abundance,RangedSummarizedExperiment: no visible binding for global variable ‘x’ adjust_abundance,SummarizedExperiment: no visible binding for global variable ‘x’ aggregate_duplicates,RangedSummarizedExperiment: no visible binding for global variable ‘group_name’ aggregate_duplicates,RangedSummarizedExperiment: no visible binding for global variable ‘group’ aggregate_duplicates,SummarizedExperiment: no visible binding for global variable ‘group_name’ aggregate_duplicates,SummarizedExperiment: no visible binding for global variable ‘group’ describe_transcript,RangedSummarizedExperiment: no visible binding for global variable ‘transcript’ describe_transcript,RangedSummarizedExperiment: no visible binding for global variable ‘description’ describe_transcript,SummarizedExperiment: no visible binding for global variable ‘transcript’ describe_transcript,SummarizedExperiment: no visible binding for global variable ‘description’ identify_abundant,spec_tbl_df: no visible binding for global variable ‘.abundant’ identify_abundant,tbl_df: no visible binding for global variable ‘.abundant’ identify_abundant,tidybulk: no visible binding for global variable ‘.abundant’ keep_abundant,spec_tbl_df: no visible binding for global variable ‘.abundant’ keep_abundant,tbl_df: no visible binding for global variable ‘.abundant’ keep_abundant,tidybulk: no visible binding for global variable ‘.abundant’ pivot_sample,RangedSummarizedExperiment: no visible binding for global variable ‘.’ pivot_sample,SummarizedExperiment: no visible binding for global variable ‘.’ quantile_normalise_abundance,RangedSummarizedExperiment: no visible binding for global variable ‘x’ quantile_normalise_abundance,SummarizedExperiment: no visible binding for global variable ‘x’ quantile_normalise_abundance,spec_tbl_df: no visible binding for global variable ‘x’ quantile_normalise_abundance,tbl_df: no visible binding for global variable ‘x’ quantile_normalise_abundance,tidybulk: no visible binding for global variable ‘x’ scale_abundance,RangedSummarizedExperiment: no visible binding for global variable ‘x’ scale_abundance,SummarizedExperiment: no visible binding for global variable ‘x’ scale_abundance,spec_tbl_df: no visible binding for global variable ‘x’ scale_abundance,spec_tbl_df: no visible binding for global variable ‘multiplier’ scale_abundance,tbl_df: no visible binding for global variable ‘x’ scale_abundance,tbl_df: no visible binding for global variable ‘multiplier’ scale_abundance,tidybulk: no visible binding for global variable ‘x’ scale_abundance,tidybulk: no visible binding for global variable ‘multiplier’ test_differential_cellularity,RangedSummarizedExperiment: no visible binding for global variable ‘X_cibersort’ test_differential_cellularity,RangedSummarizedExperiment: no visible binding for global variable ‘cell_type’ test_differential_cellularity,RangedSummarizedExperiment: no visible binding for global variable ‘prop’ test_differential_cellularity,RangedSummarizedExperiment: no visible binding for global variable ‘.cell_type’ test_differential_cellularity,SummarizedExperiment: no visible binding for global variable ‘X_cibersort’ test_differential_cellularity,SummarizedExperiment: no visible binding for global variable ‘cell_type’ test_differential_cellularity,SummarizedExperiment: no visible binding for global variable ‘prop’ test_differential_cellularity,SummarizedExperiment: no visible binding for global variable ‘.cell_type’ test_differential_cellularity,spec_tbl_df: no visible binding for global variable ‘X_cibersort’ test_differential_cellularity,tbl_df: no visible binding for global variable ‘X_cibersort’ test_differential_cellularity,tidybulk: no visible binding for global variable ‘X_cibersort’ test_gene_enrichment,RangedSummarizedExperiment: no visible global function definition for ‘buildCustomIdx’ test_gene_enrichment,RangedSummarizedExperiment: no visible global function definition for ‘buildIdx’ test_gene_enrichment,RangedSummarizedExperiment: no visible global function definition for ‘egsea’ test_gene_enrichment,RangedSummarizedExperiment: no visible binding for global variable ‘pathway’ test_gene_enrichment,RangedSummarizedExperiment: no visible binding for global variable ‘data_base’ test_gene_enrichment,RangedSummarizedExperiment: no visible binding for global variable ‘web_page’ test_gene_enrichment,SummarizedExperiment: no visible global function definition for ‘buildCustomIdx’ test_gene_enrichment,SummarizedExperiment: no visible global function definition for ‘buildIdx’ test_gene_enrichment,SummarizedExperiment: no visible global function definition for ‘egsea’ test_gene_enrichment,SummarizedExperiment: no visible binding for global variable ‘pathway’ test_gene_enrichment,SummarizedExperiment: no visible binding for global variable ‘data_base’ test_gene_enrichment,SummarizedExperiment: no visible binding for global variable ‘web_page’ test_gene_overrepresentation,RangedSummarizedExperiment: no visible binding for global variable ‘my_do_test’ test_gene_overrepresentation,SummarizedExperiment: no visible binding for global variable ‘my_do_test’ test_gene_overrepresentation,spec_tbl_df: no visible binding for global variable ‘my_do_test’ test_gene_overrepresentation,tbl_df: no visible binding for global variable ‘my_do_test’ test_gene_overrepresentation,tidybulk: no visible binding for global variable ‘my_do_test’ test_gene_rank,RangedSummarizedExperiment: no visible global function definition for ‘desc’ test_gene_rank,SummarizedExperiment: no visible global function definition for ‘desc’ test_gene_rank,spec_tbl_df: no visible global function definition for ‘with_groups’ test_gene_rank,spec_tbl_df: no visible global function definition for ‘desc’ test_gene_rank,tbl_df: no visible global function definition for ‘with_groups’ test_gene_rank,tbl_df: no visible global function definition for ‘desc’ test_gene_rank,tidybulk: no visible global function definition for ‘with_groups’ test_gene_rank,tidybulk: no visible global function definition for ‘desc’ test_stratification_cellularity,RangedSummarizedExperiment: no visible binding for global variable ‘X_cibersort’ test_stratification_cellularity,RangedSummarizedExperiment: no visible binding for global variable ‘.cell_type’ test_stratification_cellularity,SummarizedExperiment: no visible binding for global variable ‘X_cibersort’ test_stratification_cellularity,SummarizedExperiment: no visible binding for global variable ‘.cell_type’ test_stratification_cellularity,spec_tbl_df: no visible binding for global variable ‘X_cibersort’ test_stratification_cellularity,tbl_df: no visible binding for global variable ‘X_cibersort’ test_stratification_cellularity,tidybulk: no visible binding for global variable ‘X_cibersort’ Undefined global functions or variables: (Intercept) . .abundance_scaled .abundant .cell_type .contrasts .data .feature .proportion AIC CI Component Component value EPIC GeneID NUL Status X_cibersort Y abundance action add_count all_of anova buildCustomIdx buildIdx cell_type cell_type_proportions cluster cluster kmeans coef correlation counts cov_data ct_data data_base desc description egsea element eliminate_random_effects ensembl_id entrez entrez_gene feature fit geneID genes group group_id group_name gs_cat item1 library_size__ logLik lower m med multiplier my_do_test my_n n_aggr name nf nulldist parameter pathway predict prop rc read count ref_genome rotated dimensions sample 1 sample 2 sample a sample b sample_idx samples sdev seurat_clusters surv_test tagwise.dispersion temp term test tot tot_filt transcript transcript_upper tt_columns update.formula upper value variable vcov web_page where with_groups x Consider adding importFrom("base", "sample") importFrom("stats", "AIC", "anova", "coef", "kmeans", "logLik", "predict", "update.formula", "vcov") 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 ... NOTE Documented arguments not in \usage in Rd file 'get_reduced_dimensions_UMAP_bulk.Rd': ‘log_transform’ Documented arguments not in \usage in Rd file 'get_reduced_dimensions_UMAP_bulk_SE.Rd': ‘.abundance’ ‘.feature’ ‘.element’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 test_differential_abundance-methods 72.359 0.726 82.938 test_differential_cellularity-methods 23.302 0.306 27.708 test_stratification_cellularity-methods 13.409 0.150 16.030 deconvolve_cellularity-methods 10.028 0.148 11.696 adjust_abundance-methods 8.448 0.264 10.073 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. ├─utils::head(...) 5. ├─dplyr::pull(...) 6. ├─tidybulk::test_differential_abundance(...) 7. ├─tidybulk::test_differential_abundance(...) 8. │ └─... %>% ... 9. └─purrr::when(...) 10. └─base::eval(dots[[i]][[action]], env, env) 11. └─base::eval(dots[[i]][[action]], env, env) 12. └─tidybulk:::get_differential_transcript_abundance_glmmSeq(...) 13. └─stats::model.matrix(...) [ FAIL 2 | WARN 46 | SKIP 3 | PASS 222 ] Error: Test failures Execution halted * 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 ERROR, 2 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc/meat/tidybulk.Rcheck/00check.log’ for details.