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### Running command:
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###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:tidybulk.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings tidybulk_1.7.1.tar.gz
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/tidybulk.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'tidybulk/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'tidybulk' version '1.7.1'
* 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 whether package 'tidybulk' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.adjust_abundance_se: no visible binding for global variable '.'
.adjust_abundance_se: no visible binding for global variable 'x'
.aggregate_duplicates_se: no visible binding for global variable '.'
.as_SummarizedExperiment: no visible binding for global variable '.'
.cluster_elements_se: no visible binding for global variable '.'
.deconvolve_cellularity_se: no visible binding for global variable
  'X_cibersort'
.deconvolve_cellularity_se: no visible binding for global variable '.'
.describe_transcript: no visible binding for global variable '.'
.describe_transcript_SE: no visible binding for global variable '.'
.describe_transcript_SE: no visible binding for global variable
  'transcript'
.describe_transcript_SE: no visible binding for global variable
  'description'
.get_bibliography: no visible binding for global variable '.'
.identify_abundant_se: no visible binding for global variable '.'
.keep_abundant: no visible binding for global variable '.abundant'
.keep_variable_se: no visible binding for global variable '.'
.pivot_sample: no visible binding for global variable '.'
.pivot_transcript: no visible binding for global variable '.'
.reduce_dimensions_se: no visible binding for global variable '.'
.rotate_dimensions_se: no visible binding for global variable '.'
.scale_abundance: no visible binding for global variable 'x'
.scale_abundance: no visible binding for global variable 'multiplier'
.scale_abundance_se: no visible binding for global variable '.'
.scale_abundance_se: no visible binding for global variable 'x'
.test_differential_abundance_se: no visible binding for global variable
  '.'
.test_differential_cellularity: no visible binding for global variable
  'X_cibersort'
.test_differential_cellularity: no visible binding for global variable
  '.'
.test_differential_cellularity_se: no visible binding for global
  variable 'X_cibersort'
.test_differential_cellularity_se: no visible binding for global
  variable 'cell_type'
.test_differential_cellularity_se: no visible binding for global
  variable 'prop'
.test_differential_cellularity_se: no visible binding for global
  variable '.cell_type'
.test_gene_enrichment_SE: no visible global function definition for
  'buildCustomIdx'
.test_gene_enrichment_SE: no visible global function definition for
  'buildIdx'
.test_gene_enrichment_SE: no visible global function definition for
  'egsea'
.test_gene_enrichment_SE: no visible binding for global variable
  'pathway'
.test_gene_enrichment_SE: no visible binding for global variable
  'data_base'
.test_gene_enrichment_SE: no visible binding for global variable
  'web_page'
.test_stratification_cellularity: no visible binding for global
  variable 'X_cibersort'
.test_stratification_cellularity: no visible binding for global
  variable '.'
.test_stratification_cellularity_SE: no visible binding for global
  variable 'X_cibersort'
.test_stratification_cellularity_SE: no visible binding for global
  variable '.'
.test_stratification_cellularity_SE: no visible binding for global
  variable '.cell_type'
.tidybulk_se: no visible binding for global variable '.'
.tidybulk_se: no visible binding for global variable 'feature'
add_scaled_counts_bulk.calcNormFactor: no visible binding for global
  variable 'transcript'
add_scaled_counts_bulk.get_low_expressed: no visible binding for global
  variable 'transcript'
add_scaled_counts_bulk.get_low_expressed: no visible binding for global
  variable '.'
aggregate_duplicated_transcripts_DT: no visible binding for global
  variable '.abundance_scaled'
aggregate_duplicated_transcripts_bulk: no visible binding for global
  variable '.abundance_scaled'
aggregate_duplicated_transcripts_bulk: no visible binding for global
  variable 'n_aggr'
as_matrix: no visible binding for global variable 'variable'
change_reserved_column_names: no visible binding for global variable
  '.'
check_if_duplicated_genes: no visible binding for global variable
  'transcript'
check_if_duplicated_genes: no visible binding for global variable 'read
  count'
counts_scaled_exist_SE: no visible binding for global variable
  'tt_columns'
counts_scaled_exist_SE: no visible binding for global variable '.'
create_tt_from_bam_sam_bulk: no visible binding for global variable '.'
create_tt_from_bam_sam_bulk: no visible binding for global variable
  'temp'
create_tt_from_bam_sam_bulk: no visible binding for global variable
  'Status'
create_tt_from_bam_sam_bulk: no visible binding for global variable
  'counts'
create_tt_from_bam_sam_bulk: no visible binding for global variable
  'GeneID'
create_tt_from_bam_sam_bulk: no visible binding for global variable
  'genes'
create_tt_from_bam_sam_bulk: no visible binding for global variable
  'samples'
create_tt_from_bam_sam_bulk: no visible binding for global variable
  'transcript'
eliminate_sparse_transcripts: no visible binding for global variable
  'my_n'
entrez_over_to_gsea: no visible binding for global variable 'gs_cat'
entrez_over_to_gsea: no visible binding for global variable 'test'
entrez_over_to_gsea: no visible binding for global variable 'geneID'
entrez_rank_to_gsea: no visible binding for global variable 'gs_cat'
entrez_rank_to_gsea: no visible binding for global variable 'fit'
error_if_duplicated_genes: no visible binding for global variable
  'transcript'
error_if_duplicated_genes: no visible binding for global variable 'read
  count'
error_if_log_transformed: no visible binding for global variable 'm'
fill_NA_using_formula: no visible binding for global variable 'ct_data'
fill_NA_using_formula: no visible binding for global variable
  'cov_data'
filter_genes_on_condition: no visible binding for global variable
  '.feature'
get_abundance_norm_if_exists: no visible binding for global variable
  '.abundance_scaled'
get_adjusted_counts_for_unwanted_variation_bulk: no visible binding for
  global variable '.'
get_assay_scaled_if_exists_SE: no visible binding for global variable
  'tt_columns'
get_assay_scaled_if_exists_SE: no visible binding for global variable
  '.abundance_scaled'
get_cell_type_proportions: no visible binding for global variable '.'
get_clusters_SNN_bulk: no visible binding for global variable
  'seurat_clusters'
get_clusters_SNN_bulk_SE: no visible binding for global variable '.'
get_clusters_SNN_bulk_SE: no visible binding for global variable
  'seurat_clusters'
get_clusters_kmeans_bulk: no visible binding for global variable '.'
get_clusters_kmeans_bulk: no visible binding for global variable
  'cluster'
get_clusters_kmeans_bulk: no visible binding for global variable
  'cluster kmeans'
get_clusters_kmeans_bulk_SE: no visible binding for global variable '.'
get_clusters_kmeans_bulk_SE: no visible binding for global variable
  'cluster'
get_differential_transcript_abundance_bulk: no visible binding for
  global variable '.'
get_differential_transcript_abundance_bulk_SE: no visible binding for
  global variable '.'
get_differential_transcript_abundance_bulk_voom: no visible binding for
  global variable '.'
get_differential_transcript_abundance_bulk_voom_SE: no visible binding
  for global variable '.'
get_differential_transcript_abundance_deseq2: no visible binding for
  global variable 'counts'
get_differential_transcript_abundance_deseq2: no visible binding for
  global variable '.'
get_differential_transcript_abundance_deseq2_SE: no visible binding for
  global variable '.'
get_reduced_dimensions_MDS_bulk: no visible binding for global variable
  'Component'
get_reduced_dimensions_MDS_bulk: no visible binding for global variable
  'Component value'
get_reduced_dimensions_MDS_bulk_SE: no visible binding for global
  variable 'Component'
get_reduced_dimensions_MDS_bulk_SE: no visible binding for global
  variable 'Component value'
get_reduced_dimensions_PCA_bulk: no visible binding for global variable
  'sdev'
get_reduced_dimensions_PCA_bulk: no visible binding for global variable
  'name'
get_reduced_dimensions_PCA_bulk: no visible binding for global variable
  'value'
get_reduced_dimensions_PCA_bulk: no visible binding for global variable
  'x'
get_reduced_dimensions_PCA_bulk_SE: no visible binding for global
  variable 'sdev'
get_reduced_dimensions_PCA_bulk_SE: no visible binding for global
  variable 'name'
get_reduced_dimensions_PCA_bulk_SE: no visible binding for global
  variable 'value'
get_reduced_dimensions_PCA_bulk_SE: no visible binding for global
  variable 'x'
get_reduced_dimensions_TSNE_bulk: no visible binding for global
  variable 'Y'
get_reduced_dimensions_TSNE_bulk_SE: no visible binding for global
  variable 'Y'
get_reduced_dimensions_UMAP_bulk_SE: no visible binding for global
  variable 'x'
get_rotated_dimensions: no visible binding for global variable 'value'
get_rotated_dimensions: no visible binding for global variable 'rotated
  dimensions'
get_scaled_counts_bulk: no visible binding for global variable 'med'
get_scaled_counts_bulk: no visible binding for global variable
  'tot_filt'
get_scaled_counts_bulk: no visible binding for global variable 'nf'
get_scaled_counts_bulk: no visible binding for global variable '.'
get_scaled_counts_bulk: no visible binding for global variable 'tot'
get_symbol_from_ensembl: no visible binding for global variable
  'ensembl_id'
get_symbol_from_ensembl: no visible binding for global variable
  'transcript'
get_symbol_from_ensembl: no visible binding for global variable
  'ref_genome'
get_tt_columns: no visible binding for global variable 'tt_columns'
initialise_tt_internals: no visible binding for global variable '.'
memorise_methods_used: no visible binding for global variable '.'
multivariable_differential_tissue_composition: no visible binding for
  global variable '.'
multivariable_differential_tissue_composition: no visible binding for
  global variable '.cell_type'
multivariable_differential_tissue_composition: no visible binding for
  global variable 'term'
multivariable_differential_tissue_composition_SE: no visible binding
  for global variable '.'
multivariable_differential_tissue_composition_SE: no visible binding
  for global variable '.cell_type'
multivariable_differential_tissue_composition_SE: no visible binding
  for global variable 'term'
remove_redundancy_elements_though_reduced_dimensions: no visible
  binding for global variable 'sample b'
remove_redundancy_elements_though_reduced_dimensions: no visible
  binding for global variable 'sample a'
remove_redundancy_elements_though_reduced_dimensions: no visible
  binding for global variable 'sample 1'
remove_redundancy_elements_though_reduced_dimensions: no visible
  binding for global variable 'sample 2'
remove_redundancy_elements_though_reduced_dimensions_SE: no visible
  binding for global variable 'sample b'
remove_redundancy_elements_though_reduced_dimensions_SE: no visible
  binding for global variable 'sample a'
remove_redundancy_elements_though_reduced_dimensions_SE: no visible
  binding for global variable 'sample 1'
remove_redundancy_elements_though_reduced_dimensions_SE: no visible
  binding for global variable 'sample 2'
remove_redundancy_elements_through_correlation: no visible binding for
  global variable 'rc'
remove_redundancy_elements_through_correlation: no visible binding for
  global variable 'transcript'
remove_redundancy_elements_through_correlation: no visible binding for
  global variable 'correlation'
remove_redundancy_elements_through_correlation: no visible binding for
  global variable 'item1'
remove_redundancy_elements_through_correlation_SE: no visible binding
  for global variable 'abundance'
remove_redundancy_elements_through_correlation_SE: no visible binding
  for global variable 'transcript'
remove_redundancy_elements_through_correlation_SE: no visible binding
  for global variable 'element'
remove_redundancy_elements_through_correlation_SE: no visible binding
  for global variable 'feature'
remove_redundancy_elements_through_correlation_SE: no visible binding
  for global variable 'rc'
remove_redundancy_elements_through_correlation_SE: no visible binding
  for global variable 'correlation'
remove_redundancy_elements_through_correlation_SE: no visible binding
  for global variable 'item1'
run_epic: no visible global function definition for 'EPIC'
run_llsr: no visible binding for global variable 'X_cibersort'
scale_design: no visible binding for global variable 'value'
scale_design: no visible binding for global variable 'sample_idx'
scale_design: no visible binding for global variable '(Intercept)'
select_closest_pairs: no visible binding for global variable 'sample 1'
select_closest_pairs: no visible binding for global variable 'sample 2'
symbol_to_entrez: no visible binding for global variable
  'transcript_upper'
symbol_to_entrez: no visible binding for global variable '.'
symbol_to_entrez: no visible binding for global variable 'entrez'
test_differential_cellularity: no visible binding for global variable
  'X_cibersort'
test_differential_cellularity_: no visible binding for global variable
  'cell_type'
test_differential_cellularity_: no visible binding for global variable
  'prop'
test_differential_cellularity_: no visible binding for global variable
  '.cell_type'
test_gene_enrichment_bulk_EGSEA: no visible global function definition
  for 'buildCustomIdx'
test_gene_enrichment_bulk_EGSEA: no visible global function definition
  for 'buildIdx'
test_gene_enrichment_bulk_EGSEA: no visible global function definition
  for 'egsea'
test_gene_enrichment_bulk_EGSEA: no visible binding for global variable
  'pathway'
test_gene_enrichment_bulk_EGSEA: no visible binding for global variable
  'data_base'
test_gene_enrichment_bulk_EGSEA: no visible binding for global variable
  'web_page'
test_stratification_cellularity: no visible binding for global variable
  'X_cibersort'
test_stratification_cellularity_: no visible binding for global
  variable '.cell_type'
tidybulk_to_SummarizedExperiment: no visible binding for global
  variable '.'
univariable_differential_tissue_composition: no visible binding for
  global variable '.proportion'
univariable_differential_tissue_composition: no visible binding for
  global variable '.cell_type'
univariable_differential_tissue_composition: no visible binding for
  global variable 'cell_type_proportions'
univariable_differential_tissue_composition: no visible binding for
  global variable 'surv_test'
univariable_differential_tissue_composition_SE: no visible binding for
  global variable '.proportion'
univariable_differential_tissue_composition_SE: no visible binding for
  global variable '.cell_type'
univariable_differential_tissue_composition_SE: no visible binding for
  global variable 'cell_type_proportions'
univariable_differential_tissue_composition_SE: no visible binding for
  global variable 'surv_test'
univariable_differential_tissue_stratification: no visible binding for
  global variable '.cell_type'
univariable_differential_tissue_stratification: no visible binding for
  global variable 'cell_type_proportions'
univariable_differential_tissue_stratification: no visible binding for
  global variable 'surv_test'
univariable_differential_tissue_stratification_SE: no visible binding
  for global variable '.cell_type'
univariable_differential_tissue_stratification_SE: no visible binding
  for global variable 'cell_type_proportions'
univariable_differential_tissue_stratification_SE: no visible binding
  for global variable 'surv_test'
adjust_abundance,RangedSummarizedExperiment: no visible binding for
  global variable '.'
adjust_abundance,RangedSummarizedExperiment: no visible binding for
  global variable 'x'
adjust_abundance,SummarizedExperiment: no visible binding for global
  variable '.'
adjust_abundance,SummarizedExperiment: no visible binding for global
  variable 'x'
aggregate_duplicates,RangedSummarizedExperiment: no visible binding for
  global variable '.'
aggregate_duplicates,SummarizedExperiment: no visible binding for
  global variable '.'
as_SummarizedExperiment,spec_tbl_df: no visible binding for global
  variable '.'
as_SummarizedExperiment,tbl_df: no visible binding for global variable
  '.'
as_SummarizedExperiment,tidybulk: no visible binding for global
  variable '.'
cluster_elements,RangedSummarizedExperiment: no visible binding for
  global variable '.'
cluster_elements,SummarizedExperiment: no visible binding for global
  variable '.'
deconvolve_cellularity,RangedSummarizedExperiment: no visible binding
  for global variable '.'
deconvolve_cellularity,SummarizedExperiment: no visible binding for
  global variable '.'
describe_transcript,RangedSummarizedExperiment: no visible binding for
  global variable '.'
describe_transcript,RangedSummarizedExperiment: no visible binding for
  global variable 'transcript'
describe_transcript,RangedSummarizedExperiment: no visible binding for
  global variable 'description'
describe_transcript,SummarizedExperiment: no visible binding for global
  variable '.'
describe_transcript,SummarizedExperiment: no visible binding for global
  variable 'transcript'
describe_transcript,SummarizedExperiment: no visible binding for global
  variable 'description'
describe_transcript,spec_tbl_df: no visible binding for global variable
  '.'
describe_transcript,tbl_df: no visible binding for global variable '.'
describe_transcript,tidybulk: no visible binding for global variable
  '.'
get_bibliography,RangedSummarizedExperiment: no visible binding for
  global variable '.'
get_bibliography,SummarizedExperiment: no visible binding for global
  variable '.'
get_bibliography,spec_tbl_df: no visible binding for global variable
  '.'
get_bibliography,tbl: no visible binding for global variable '.'
get_bibliography,tbl_df: no visible binding for global variable '.'
get_bibliography,tidybulk: no visible binding for global variable '.'
identify_abundant,RangedSummarizedExperiment: no visible binding for
  global variable '.'
identify_abundant,SummarizedExperiment: no visible binding for global
  variable '.'
keep_abundant,spec_tbl_df: no visible binding for global variable
  '.abundant'
keep_abundant,tbl_df: no visible binding for global variable
  '.abundant'
keep_abundant,tidybulk: no visible binding for global variable
  '.abundant'
keep_variable,RangedSummarizedExperiment: no visible binding for global
  variable '.'
keep_variable,SummarizedExperiment: no visible binding for global
  variable '.'
pivot_sample,RangedSummarizedExperiment: no visible binding for global
  variable '.'
pivot_sample,SummarizedExperiment: no visible binding for global
  variable '.'
pivot_transcript,RangedSummarizedExperiment: no visible binding for
  global variable '.'
pivot_transcript,SummarizedExperiment: no visible binding for global
  variable '.'
reduce_dimensions,RangedSummarizedExperiment: no visible binding for
  global variable '.'
reduce_dimensions,SummarizedExperiment: no visible binding for global
  variable '.'
rotate_dimensions,RangedSummarizedExperiment: no visible binding for
  global variable '.'
rotate_dimensions,SummarizedExperiment: no visible binding for global
  variable '.'
scale_abundance,RangedSummarizedExperiment: no visible binding for
  global variable '.'
scale_abundance,RangedSummarizedExperiment: no visible binding for
  global variable 'x'
scale_abundance,SummarizedExperiment: no visible binding for global
  variable '.'
scale_abundance,SummarizedExperiment: no visible binding for global
  variable 'x'
scale_abundance,spec_tbl_df: no visible binding for global variable 'x'
scale_abundance,spec_tbl_df: no visible binding for global variable
  'multiplier'
scale_abundance,tbl_df: no visible binding for global variable 'x'
scale_abundance,tbl_df: no visible binding for global variable
  'multiplier'
scale_abundance,tidybulk: no visible binding for global variable 'x'
scale_abundance,tidybulk: no visible binding for global variable
  'multiplier'
test_differential_abundance,RangedSummarizedExperiment: no visible
  binding for global variable '.'
test_differential_abundance,SummarizedExperiment: no visible binding
  for global variable '.'
test_differential_cellularity,RangedSummarizedExperiment: no visible
  binding for global variable 'X_cibersort'
test_differential_cellularity,RangedSummarizedExperiment: no visible
  binding for global variable 'cell_type'
test_differential_cellularity,RangedSummarizedExperiment: no visible
  binding for global variable 'prop'
test_differential_cellularity,RangedSummarizedExperiment: no visible
  binding for global variable '.cell_type'
test_differential_cellularity,SummarizedExperiment: no visible binding
  for global variable 'X_cibersort'
test_differential_cellularity,SummarizedExperiment: no visible binding
  for global variable 'cell_type'
test_differential_cellularity,SummarizedExperiment: no visible binding
  for global variable 'prop'
test_differential_cellularity,SummarizedExperiment: no visible binding
  for global variable '.cell_type'
test_differential_cellularity,spec_tbl_df: no visible binding for
  global variable 'X_cibersort'
test_differential_cellularity,spec_tbl_df: no visible binding for
  global variable '.'
test_differential_cellularity,tbl_df: no visible binding for global
  variable 'X_cibersort'
test_differential_cellularity,tbl_df: no visible binding for global
  variable '.'
test_differential_cellularity,tidybulk: no visible binding for global
  variable 'X_cibersort'
test_differential_cellularity,tidybulk: no visible binding for global
  variable '.'
test_gene_enrichment,RangedSummarizedExperiment: no visible global
  function definition for 'buildCustomIdx'
test_gene_enrichment,RangedSummarizedExperiment: no visible global
  function definition for 'buildIdx'
test_gene_enrichment,RangedSummarizedExperiment: no visible global
  function definition for 'egsea'
test_gene_enrichment,RangedSummarizedExperiment: no visible binding for
  global variable 'pathway'
test_gene_enrichment,RangedSummarizedExperiment: no visible binding for
  global variable 'data_base'
test_gene_enrichment,RangedSummarizedExperiment: no visible binding for
  global variable 'web_page'
test_gene_enrichment,SummarizedExperiment: no visible global function
  definition for 'buildCustomIdx'
test_gene_enrichment,SummarizedExperiment: no visible global function
  definition for 'buildIdx'
test_gene_enrichment,SummarizedExperiment: no visible global function
  definition for 'egsea'
test_gene_enrichment,SummarizedExperiment: no visible binding for
  global variable 'pathway'
test_gene_enrichment,SummarizedExperiment: no visible binding for
  global variable 'data_base'
test_gene_enrichment,SummarizedExperiment: no visible binding for
  global variable 'web_page'
test_stratification_cellularity,RangedSummarizedExperiment: no visible
  binding for global variable 'X_cibersort'
test_stratification_cellularity,RangedSummarizedExperiment: no visible
  binding for global variable '.'
test_stratification_cellularity,RangedSummarizedExperiment: no visible
  binding for global variable '.cell_type'
test_stratification_cellularity,SummarizedExperiment: no visible
  binding for global variable 'X_cibersort'
test_stratification_cellularity,SummarizedExperiment: no visible
  binding for global variable '.'
test_stratification_cellularity,SummarizedExperiment: no visible
  binding for global variable '.cell_type'
test_stratification_cellularity,spec_tbl_df: no visible binding for
  global variable 'X_cibersort'
test_stratification_cellularity,spec_tbl_df: no visible binding for
  global variable '.'
test_stratification_cellularity,tbl_df: no visible binding for global
  variable 'X_cibersort'
test_stratification_cellularity,tbl_df: no visible binding for global
  variable '.'
test_stratification_cellularity,tidybulk: no visible binding for global
  variable 'X_cibersort'
test_stratification_cellularity,tidybulk: no visible binding for global
  variable '.'
tidybulk,RangedSummarizedExperiment: no visible binding for global
  variable '.'
tidybulk,RangedSummarizedExperiment: no visible binding for global
  variable 'feature'
tidybulk,SummarizedExperiment: no visible binding for global variable
  '.'
tidybulk,SummarizedExperiment: no visible binding for global variable
  'feature'
Undefined global functions or variables:
  (Intercept) . .abundance_scaled .abundant .cell_type .feature
  .proportion Component Component value EPIC GeneID Status X_cibersort
  Y abundance buildCustomIdx buildIdx cell_type cell_type_proportions
  cluster cluster kmeans correlation counts cov_data ct_data data_base
  description egsea element ensembl_id entrez feature fit geneID genes
  gs_cat item1 m med multiplier my_n n_aggr name nf pathway prop rc
  read count ref_genome rotated dimensions sample 1 sample 2 sample a
  sample b sample_idx samples sdev seurat_clusters surv_test temp term
  test tot tot_filt transcript transcript_upper tt_columns value
  variable web_page x
Consider adding
  importFrom("base", "sample")
  importFrom("stats", "kmeans")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: remove_redundancy-methods.Rd:136-138: Dropping empty section \details
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                        user system elapsed
test_differential_cellularity-methods   9.30   0.01    9.32
test_stratification_cellularity-methods 5.97   0.03    6.00
test_differential_abundance-methods     5.59   0.22    5.81
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/tidybulk.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL tidybulk
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-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
  converting help for package 'tidybulk'
    finding HTML links ... done
    X_cibersort                             html  
    adjust_abundance-methods                html  
    aggregate_duplicates-methods            html  
    arrange-methods                         html  
    as_SummarizedExperiment-methods         html  
    as_matrix                               html  
    bind-methods                            html  
    breast_tcga_mini_SE                     html  
    check_if_counts_is_na                   html  
    check_if_duplicated_genes               html  
    check_if_wrong_input                    html  
    cluster_elements-methods                html  
    counts_SE                               html  
    counts_ensembl                          html  
    deconvolve_cellularity-methods          html  
    describe_transcript-methods             html  
    distinct-methods                        html  
    dplyr-methods                           html  
    ensembl_symbol_mapping                  html  
    ensembl_to_symbol-methods               html  
    fill_missing_abundance-methods          html  
    filter-methods                          html  
    flybaseIDs                              html  
    get_bibliography-methods                html  
    get_reduced_dimensions_UMAP_bulk        html  
    get_reduced_dimensions_UMAP_bulk_SE     html  
    group_by-methods                        html  
    identify_abundant-methods               html  
    impute_missing_abundance-methods        html  
    join-methods                            html  
    keep_abundant-methods                   html  
    keep_variable-methods                   html  
    log10_reverse_trans                     html  
    logit_trans                             html  
    mutate-methods                          html  
    nest-methods                            html  
    pipe                                    html  
    pivot_sample-methods                    html  
    pivot_transcript-methods                html  
    reduce_dimensions-methods               html  
    reexports                               html  
    remove_redundancy-methods               html  
    rename-methods                          html  
    rotate_dimensions-methods               html  
    rowwise-methods                         html  
    scale_abundance-methods                 html  
    se                                      html  
    se_mini                                 html  
    summarise-methods                       html  
    symbol_to_entrez                        html  
    test_deseq2_df                          html  
    test_differential_abundance-methods     html  
    test_differential_cellularity-methods   html  
    test_gene_enrichment-methods            html  
    test_gene_overrepresentation-methods    html  
    test_gene_rank-methods                  html  
    test_stratification_cellularity-methods
                                            html  
    tidybulk-methods                        html  
    tidybulk_SAM_BAM-methods                html  
    vignette_manuscript_signature_boxplot   html  
    vignette_manuscript_signature_tsne      html  
    vignette_manuscript_signature_tsne2     html  
*** 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)
Making 'packages.html' ... done

R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 1.7.1
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 
Performing PCA
Read the 251 x 50 data matrix successfully!
OpenMP is working. 1 threads.
Using no_dims = 2, perplexity = 30.000000, and theta = 0.500000
Computing input similarities...
Building tree...
Done in 0.05 seconds (sparsity = 0.490437)!
Learning embedding...
Iteration 50: error is 55.923458 (50 iterations in 0.05 seconds)
Iteration 100: error is 53.433488 (50 iterations in 0.06 seconds)
Iteration 150: error is 55.281806 (50 iterations in 0.06 seconds)
Iteration 200: error is 54.967648 (50 iterations in 0.06 seconds)
Iteration 250: error is 55.971976 (50 iterations in 0.05 seconds)
Iteration 300: error is 1.012080 (50 iterations in 0.06 seconds)
Iteration 350: error is 0.842669 (50 iterations in 0.03 seconds)
Iteration 400: error is 0.806371 (50 iterations in 0.03 seconds)
Iteration 450: error is 0.801135 (50 iterations in 0.03 seconds)
Iteration 500: error is 0.786040 (50 iterations in 0.03 seconds)
Iteration 550: error is 0.781440 (50 iterations in 0.03 seconds)
Iteration 600: error is 0.780893 (50 iterations in 0.05 seconds)
Iteration 650: error is 0.780526 (50 iterations in 0.03 seconds)
Iteration 700: error is 0.779401 (50 iterations in 0.03 seconds)
Iteration 750: error is 0.779206 (50 iterations in 0.05 seconds)
Iteration 800: error is 0.778141 (50 iterations in 0.03 seconds)
Iteration 850: error is 0.777425 (50 iterations in 0.05 seconds)
Iteration 900: error is 0.777316 (50 iterations in 0.03 seconds)
Iteration 950: error is 0.777144 (50 iterations in 0.05 seconds)
Iteration 1000: error is 0.776572 (50 iterations in 0.03 seconds)
Fitting performed in 0.84 seconds.
[ FAIL 0 | WARN 24 | SKIP 0 | PASS 212 ]

[ FAIL 0 | WARN 24 | SKIP 0 | PASS 212 ]
> 
> proc.time()
   user  system elapsed 
 176.18   12.50  201.31