##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:tidybulk.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings tidybulk_1.11.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/tidybulk.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘tidybulk/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘tidybulk’ version ‘1.11.1’
* 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 ‘.’
.aggregate_duplicates_se: no visible binding for global variable
  ‘group_name’
.aggregate_duplicates_se: no visible binding for global variable
  ‘group’
.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
  ‘.contrasts’
.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 ‘.’
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’
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 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’
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 ‘.’
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,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 ‘.’
aggregate_duplicates,SummarizedExperiment: no visible binding for
  global variable ‘group_name’
aggregate_duplicates,SummarizedExperiment: no visible binding for
  global variable ‘group’
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,SummarizedExperiment: no visible binding for global variable
  ‘.’
Undefined global functions or variables:
  (Intercept) . .abundance_scaled .abundant .cell_type .contrasts
  .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 group group_name gs_cat item1
  library_size__ m med multiplier my_n n_aggr name nf nulldist 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:144-146: 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 ... ERROR
Running examples in ‘tidybulk-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: test_differential_cellularity
> ### Title: Add differential tissue composition information to a tbl
> ### Aliases: test_differential_cellularity
> ###   test_differential_cellularity,spec_tbl_df-method
> ###   test_differential_cellularity,tbl_df-method
> ###   test_differential_cellularity,tidybulk-method
> ###   test_differential_cellularity,SummarizedExperiment-method
> ###   test_differential_cellularity,RangedSummarizedExperiment-method
> 
> ### ** Examples
> 
> 
>  # Regular regression
> 	test_differential_cellularity(
+ 	 tidybulk::se_mini ,
+ 	    . ~ condition,
+ 	    cores = 1
+ 	)
# A tibble: 22 × 7
   .cell_type                   cell_t…¹ estim…² estim…³ std.e…⁴ stati…⁵ p.val…⁶
   <chr>                        <list>     <dbl>   <dbl>   <dbl>   <dbl>   <dbl>
 1 cibersort.B.cells.naive      <tibble>   -2.37   1.54    1.05    1.47   0.142 
 2 cibersort.B.cells.memory     <tibble>   -2.75   0.821   0.962   0.853  0.393 
 3 cibersort.Plasma.cells       <tibble>   NA     NA      NA      NA     NA     
 4 cibersort.T.cells.CD8        <tibble>   NA     NA      NA      NA     NA     
 5 cibersort.T.cells.CD4.naive  <tibble>   NA     NA      NA      NA     NA     
 6 cibersort.T.cells.CD4.memor… <tibble>   -3.81   1.93    0.900   2.14   0.0324
 7 cibersort.T.cells.CD4.memor… <tibble>   NA     NA      NA      NA     NA     
 8 cibersort.T.cells.follicula… <tibble>   -6.01   0.677   0.835   0.811  0.417 
 9 cibersort.T.cells.regulator… <tibble>   NA     NA      NA      NA     NA     
10 cibersort.T.cells.gamma.del… <tibble>   NA     NA      NA      NA     NA     
# … with 12 more rows, and abbreviated variable names ¹​cell_type_proportions,
#   ²​`estimate_(Intercept)`, ³​estimate_conditionTRUE, ⁴​std.error_conditionTRUE,
#   ⁵​statistic_conditionTRUE, ⁶​p.value_conditionTRUE
> 
> 	# Cox regression - multiple
> 
> tidybulk::se_mini |>
+ 
+ 	# Test
+ 	test_differential_cellularity(
+ 	    survival::Surv(days, dead) ~ .,
+ 	    cores = 1
+ 	)
Killed
* 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:
    suppressPackageStartupMessages(library(tidybulk))
  ========================================
  
  
  Attaching package: 'tidybulk'
  
  The following object is masked from 'package:stats':
  
      filter
  
  > 
  > test_check("tidybulk")
  Coefficients not estimable: conditionTRUE 
  Coefficients not estimable: conditionTRUE 
  Killed
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘comparison_with_base_R.Rmd’ using ‘UTF-8’... OK
  ‘introduction.Rmd’ using ‘UTF-8’... OK
  ‘manuscript_differential_transcript_abundance.Rmd’ using ‘UTF-8’... OK
  ‘manuscript_transcriptional_signatures.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘comparison_with_base_R.Rmd’ using knitr
--- finished re-building ‘comparison_with_base_R.Rmd’

--- re-building ‘introduction.Rmd’ using knitr
Killed
--- re-building ‘manuscript_differential_transcript_abundance.Rmd’ using knitr
Killed
--- re-building ‘manuscript_transcriptional_signatures.Rmd’ using knitr
--- finished re-building ‘manuscript_transcriptional_signatures.Rmd’

SUMMARY: processing the following files failed:
  ‘introduction.Rmd’ ‘manuscript_differential_transcript_abundance.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 3 ERRORs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/tidybulk.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL tidybulk
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/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 '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 Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

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)
========================================
tidybulk version 1.11.1
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")
Coefficients not estimable: conditionTRUE 
Coefficients not estimable: conditionTRUE 
Killed