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### Running command:
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###   /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_1.16.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/tidybulk.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 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘tidybulk/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘tidybulk’ version ‘1.16.0’
* 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 ‘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 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
.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_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’
aggregate_duplicated_transcripts_DT: no visible binding for global
  variable ‘.abundance_scaled’
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_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_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_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 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,spec_tbl_df: no visible binding for global
  variable ‘x’
quantile_normalise_abundance,SummarizedExperiment: 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,spec_tbl_df: no visible binding for global variable ‘x’
scale_abundance,spec_tbl_df: no visible binding for global variable
  ‘multiplier’
scale_abundance,SummarizedExperiment: no visible binding for global
  variable ‘x’
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,spec_tbl_df: no visible binding for
  global variable ‘X_cibersort’
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,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,spec_tbl_df: 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,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,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,SummarizedExperiment: 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,spec_tbl_df: no visible binding for
  global variable ‘X_cibersort’
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,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:
  . .abundance_scaled .abundant .cell_type .contrasts .data .feature
  .proportion (Intercept) abundance action add_count AIC all_of anova
  buildCustomIdx buildIdx cell_type cell_type_proportions CI cluster
  cluster kmeans coef Component Component value correlation counts
  cov_data ct_data data_base desc description egsea element ensembl_id
  entrez entrez_gene EPIC feature fit geneID 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 NUL 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 Status 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 X_cibersort Y
Consider adding
  importFrom("base", "sample")
  importFrom("stats", "AIC", "anova", "coef", "kmeans", "logLik",
             "predict", "update.formula", "vcov")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) remove_redundancy-methods.Rd:158-175: Lost braces
   158 | select_closest_pairs = function(df) {
       |                                     ^
checkRd: (-1) remove_redundancy-methods.Rd:161-171: Lost braces
   161 |                 while (df |> nrow() > 0) {
       |                                          ^
checkRd: (-1) rotate_dimensions-methods.Rd:126-134: Lost braces
   126 |         rotation = function(m, d) {
       |                                   ^
* 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 17.744   0.14  17.891
* 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-mac-arm64/meat/tidybulk.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL tidybulk
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘tidybulk’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Note: wrong number of arguments to 'expm1' 
Note: wrong number of arguments to 'expm1' 
Note: wrong number of arguments to 'expm1' 
Note: wrong number of arguments to 'expm1' 
Note: wrong number of arguments to 'expm1' 
Note: wrong number of arguments to 'expm1' 
Note: wrong number of arguments to 'expm1' 
Note: wrong number of arguments to 'floor' 
Note: wrong number of arguments to 'floor' 
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (tidybulk)

R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(tidybulk)
Loading required package: ttservice
========================================
tidybulk version 1.16.0
If you use TIDYBULK in published research, please cite:

Mangiola et al. tidybulk: an R tidy framework for modular 
transcriptomic data analysis. Genome Biology 2021.

This message can be suppressed by:
  suppressPackageStartupMessages(library(tidybulk))
========================================


Attaching package: 'tidybulk'

The following object is masked from 'package:stats':

    filter

> 
> test_check("tidybulk")
Found 2 batches
Using null model in ComBat-seq.
Adjusting for 1 covariate(s) or covariate level(s)
Estimating dispersions
Fitting the GLM model
Apply shrinkage - computing posterior estimates for parameters
Using 100 random genes for Monte Carlo integration
Adjusting the data
Time difference of 2.521167 secs
Time difference of 2.473539 secs
Performing PCA
Read the 251 x 50 data matrix successfully!
Using no_dims = 2, perplexity = 30.000000, and theta = 0.500000
Computing input similarities...
Building tree...
Done in 0.01 seconds (sparsity = 0.490437)!
Learning embedding...
Iteration 50: error is 56.758633 (50 iterations in 0.02 seconds)
Iteration 100: error is 57.392975 (50 iterations in 0.02 seconds)
Iteration 150: error is 55.912913 (50 iterations in 0.02 seconds)
Iteration 200: error is 58.518611 (50 iterations in 0.02 seconds)
Iteration 250: error is 57.302387 (50 iterations in 0.02 seconds)
Iteration 300: error is 0.830613 (50 iterations in 0.01 seconds)
Iteration 350: error is 0.781404 (50 iterations in 0.01 seconds)
Iteration 400: error is 0.776612 (50 iterations in 0.01 seconds)
Iteration 450: error is 0.775445 (50 iterations in 0.01 seconds)
Iteration 500: error is 0.771984 (50 iterations in 0.01 seconds)
Iteration 550: error is 0.771300 (50 iterations in 0.01 seconds)
Iteration 600: error is 0.770335 (50 iterations in 0.01 seconds)
Iteration 650: error is 0.768922 (50 iterations in 0.01 seconds)
Iteration 700: error is 0.770392 (50 iterations in 0.01 seconds)
Iteration 750: error is 0.770681 (50 iterations in 0.01 seconds)
Iteration 800: error is 0.769506 (50 iterations in 0.01 seconds)
Iteration 850: error is 0.768152 (50 iterations in 0.01 seconds)
Iteration 900: error is 0.768142 (50 iterations in 0.01 seconds)
Iteration 950: error is 0.767525 (50 iterations in 0.01 seconds)
Iteration 1000: error is 0.768302 (50 iterations in 0.01 seconds)
Fitting performed in 0.27 seconds.
Coefficients not estimable: conditionTRUE 
Coefficients not estimable: conditionTRUE 
Time difference of 2.225028 secs
Time difference of 1.959905 secs
Found 2 batches
Using null model in ComBat-seq.
Adjusting for 1 covariate(s) or covariate level(s)
Estimating dispersions
Fitting the GLM model
Apply shrinkage - computing posterior estimates for parameters
Using 100 random genes for Monte Carlo integration
Adjusting the data
Found 2 batches
Using null model in ComBat-seq.
Adjusting for 1 covariate(s) or covariate level(s)
Estimating dispersions
Fitting the GLM model
Apply shrinkage - computing posterior estimates for parameters
Using 100 random genes for Monte Carlo integration
Adjusting the data
[ FAIL 0 | WARN 46 | SKIP 3 | PASS 225 ]

══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• empty test (3): 'test-bulk_methods.R:1067:1',
  'test-tximeta_GRnges_IRanges.R:3:1', 'test-tximeta_GRnges_IRanges.R:19:1'

[ FAIL 0 | WARN 46 | SKIP 3 | PASS 225 ]
> 
> proc.time()
   user  system elapsed 
 83.735   2.188  85.967