############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:tidybulk.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings tidybulk_1.8.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/tidybulk.Rcheck’ * using R version 4.2.1 (2022-06-23) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘tidybulk/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘tidybulk’ version ‘1.8.2’ * 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 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 ‘.’ .adjust_abundance_se: no visible binding for global variable ‘x’ .aggregate_duplicates_se: no visible binding for global variable ‘.’ .as_SummarizedExperiment: no visible binding for global variable ‘.’ .cluster_elements_se: no visible binding for global variable ‘.’ .deconvolve_cellularity_se: no visible binding for global variable ‘X_cibersort’ .deconvolve_cellularity_se: no visible binding for global variable ‘.’ .describe_transcript: no visible binding for global variable ‘.’ .describe_transcript_SE: no visible binding for global variable ‘.’ .describe_transcript_SE: no visible binding for global variable ‘transcript’ .describe_transcript_SE: no visible binding for global variable ‘description’ .get_bibliography: no visible binding for global variable ‘.’ .identify_abundant_se: no visible binding for global variable ‘.’ .impute_missing_abundance_se: no visible binding for global variable ‘.’ .keep_abundant: no visible binding for global variable ‘.abundant’ .keep_variable_se: no visible binding for global variable ‘.’ .pivot_sample: no visible binding for global variable ‘.’ .pivot_transcript: no visible binding for global variable ‘.’ .reduce_dimensions_se: no visible binding for global variable ‘.’ .rotate_dimensions_se: no visible binding for global variable ‘.’ .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 ‘.’ .scale_abundance_se: no visible binding for global variable ‘x’ .test_differential_abundance_se: no visible binding for global variable ‘.’ .test_differential_cellularity: no visible binding for global variable ‘X_cibersort’ .test_differential_cellularity: no visible binding for global variable ‘.’ .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_stratification_cellularity: no visible binding for global variable ‘X_cibersort’ .test_stratification_cellularity: no visible binding for global variable ‘.’ .test_stratification_cellularity_SE: no visible binding for global variable ‘X_cibersort’ .test_stratification_cellularity_SE: no visible binding for global variable ‘.’ .test_stratification_cellularity_SE: no visible binding for global variable ‘.cell_type’ .tidybulk_se: no visible binding for global variable ‘.’ .tidybulk_se: no visible binding for global variable ‘feature’ add_scaled_counts_bulk.calcNormFactor: no visible binding for global variable ‘transcript’ add_scaled_counts_bulk.get_low_expressed: no visible binding for global variable ‘transcript’ add_scaled_counts_bulk.get_low_expressed: no visible binding for global variable ‘.’ 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’ as_matrix: no visible binding for global variable ‘variable’ 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 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 ‘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_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_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_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’ initialise_tt_internals: no visible binding for global variable ‘.’ 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’ 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’ symbol_to_entrez: no visible binding for global variable ‘transcript_upper’ symbol_to_entrez: no visible binding for global variable ‘.’ 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 ‘.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 global function definition for ‘egsea’ 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_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 ‘.’ adjust_abundance,RangedSummarizedExperiment: no visible binding for global variable ‘x’ adjust_abundance,SummarizedExperiment: no visible binding for global variable ‘.’ adjust_abundance,SummarizedExperiment: no visible binding for global variable ‘x’ aggregate_duplicates,RangedSummarizedExperiment: no visible binding for global variable ‘.’ aggregate_duplicates,SummarizedExperiment: no visible binding for global variable ‘.’ as_SummarizedExperiment,spec_tbl_df: no visible binding for global variable ‘.’ as_SummarizedExperiment,tbl_df: no visible binding for global variable ‘.’ as_SummarizedExperiment,tidybulk: no visible binding for global variable ‘.’ cluster_elements,RangedSummarizedExperiment: no visible binding for global variable ‘.’ cluster_elements,SummarizedExperiment: no visible binding for global variable ‘.’ deconvolve_cellularity,RangedSummarizedExperiment: no visible binding for global variable ‘.’ deconvolve_cellularity,SummarizedExperiment: no visible binding for global variable ‘.’ describe_transcript,RangedSummarizedExperiment: no visible binding for global variable ‘.’ 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 ‘.’ describe_transcript,SummarizedExperiment: no visible binding for global variable ‘transcript’ describe_transcript,SummarizedExperiment: no visible binding for global variable ‘description’ describe_transcript,spec_tbl_df: no visible binding for global variable ‘.’ describe_transcript,tbl_df: no visible binding for global variable ‘.’ describe_transcript,tidybulk: no visible binding for global variable ‘.’ get_bibliography,RangedSummarizedExperiment: no visible binding for global variable ‘.’ get_bibliography,SummarizedExperiment: no visible binding for global variable ‘.’ get_bibliography,spec_tbl_df: no visible binding for global variable ‘.’ get_bibliography,tbl: no visible binding for global variable ‘.’ get_bibliography,tbl_df: no visible binding for global variable ‘.’ get_bibliography,tidybulk: no visible binding for global variable ‘.’ identify_abundant,RangedSummarizedExperiment: no visible binding for global variable ‘.’ identify_abundant,SummarizedExperiment: no visible binding for global variable ‘.’ impute_missing_abundance,RangedSummarizedExperiment: no visible binding for global variable ‘.’ impute_missing_abundance,SummarizedExperiment: no visible binding for global variable ‘.’ 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’ keep_variable,RangedSummarizedExperiment: no visible binding for global variable ‘.’ keep_variable,SummarizedExperiment: no visible binding for global variable ‘.’ pivot_sample,RangedSummarizedExperiment: no visible binding for global variable ‘.’ pivot_sample,SummarizedExperiment: no visible binding for global variable ‘.’ pivot_transcript,RangedSummarizedExperiment: no visible binding for global variable ‘.’ pivot_transcript,SummarizedExperiment: no visible binding for global variable ‘.’ reduce_dimensions,RangedSummarizedExperiment: no visible binding for global variable ‘.’ reduce_dimensions,SummarizedExperiment: no visible binding for global variable ‘.’ rotate_dimensions,RangedSummarizedExperiment: no visible binding for global variable ‘.’ rotate_dimensions,SummarizedExperiment: no visible binding for global variable ‘.’ scale_abundance,RangedSummarizedExperiment: no visible binding for global variable ‘.’ scale_abundance,RangedSummarizedExperiment: no visible binding for global variable ‘x’ scale_abundance,SummarizedExperiment: no visible binding for global variable ‘.’ 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_abundance,RangedSummarizedExperiment: no visible binding for global variable ‘.’ test_differential_abundance,SummarizedExperiment: no visible binding for global variable ‘.’ 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,spec_tbl_df: no visible binding for global variable ‘.’ test_differential_cellularity,tbl_df: no visible binding for global variable ‘X_cibersort’ test_differential_cellularity,tbl_df: no visible binding for global variable ‘.’ test_differential_cellularity,tidybulk: no visible binding for global variable ‘X_cibersort’ test_differential_cellularity,tidybulk: no visible binding for global variable ‘.’ 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_stratification_cellularity,RangedSummarizedExperiment: no visible binding for global variable ‘X_cibersort’ test_stratification_cellularity,RangedSummarizedExperiment: no visible binding for global variable ‘.’ 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 ‘.’ 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,spec_tbl_df: no visible binding for global variable ‘.’ test_stratification_cellularity,tbl_df: no visible binding for global variable ‘X_cibersort’ test_stratification_cellularity,tbl_df: no visible binding for global variable ‘.’ test_stratification_cellularity,tidybulk: no visible binding for global variable ‘X_cibersort’ test_stratification_cellularity,tidybulk: no visible binding for global variable ‘.’ tidybulk,RangedSummarizedExperiment: no visible binding for global variable ‘.’ tidybulk,RangedSummarizedExperiment: no visible binding for global variable ‘feature’ tidybulk,SummarizedExperiment: no visible binding for global variable ‘.’ tidybulk,SummarizedExperiment: no visible binding for global variable ‘feature’ Undefined global functions or variables: (Intercept) . .abundance_scaled .abundant .cell_type .feature .proportion Component Component value EPIC GeneID NUL Status X_cibersort Y abundance buildCustomIdx buildIdx cell_type cell_type_proportions cluster cluster kmeans correlation counts cov_data ct_data data_base description egsea element ensembl_id entrez feature fit geneID genes gs_cat item1 library_size__ m med multiplier my_n n_aggr name nf pathway prop rc read count ref_genome rotated dimensions sample 1 sample 2 sample a sample b sample_idx samples sdev seurat_clusters surv_test temp term test tot tot_filt transcript transcript_upper tt_columns value variable web_page x Consider adding importFrom("base", "sample") importFrom("stats", "kmeans") to your NAMESPACE file. * checking Rd files ... NOTE prepare_Rd: remove_redundancy-methods.Rd:136-138: Dropping empty section \details * 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 test_differential_cellularity-methods 11.608 0.100 11.708 test_stratification_cellularity-methods 6.623 0.036 6.660 test_differential_abundance-methods 6.545 0.112 6.656 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ 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: 2 NOTEs See ‘/home/biocbuild/bbs-3.15-bioc/meat/tidybulk.Rcheck/00check.log’ for details.