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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD check --install=check:tidybulk.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings tidybulk_1.17.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/tidybulk.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘tidybulk/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘tidybulk’ version ‘1.17.0’
* 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 loading without being on the library search path ... 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 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 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 ... 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     60.316  0.539  60.953
test_differential_cellularity-methods   15.625  0.080  15.730
test_stratification_cellularity-methods  9.012  0.060   9.086
deconvolve_cellularity-methods           6.995  0.051   7.058
adjust_abundance-methods                 6.514  0.224   6.751
* 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:
    'test-tximeta_GRnges_IRanges.R:3:1', 'test-tximeta_GRnges_IRanges.R:19:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-bulk_methods.R:1526:3'): Add reduced dimensions UMAP - no object ──
  magrittr::extract2(pull(res, UMAP1), 1) not equal to -2.12.
  1/1 mismatches
  [1] -1.91 - -2.12 == 0.209
  ── Failure ('test-bulk_methods_SummarizedExperiment.R:736:3'): gene over representation ──
  ncol(res) not equal to 10.
  1/1 mismatches
  [1] 13 - 10 == 3
  
  [ FAIL 2 | WARN 47 | SKIP 3 | PASS 223 ]
  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, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/tidybulk.Rcheck/00check.log’
for details.