Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-10-15 15:06:25 -0400 (Fri, 15 Oct 2021).

CHECK results for tidybulk on tokay2

To the developers/maintainers of the tidybulk package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/tidybulk.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1912/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
tidybulk 1.4.0  (landing page)
Stefano Mangiola
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/tidybulk
git_branch: RELEASE_3_13
git_last_commit: 945a727
git_last_commit_date: 2021-05-19 12:50:13 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: tidybulk
Version: 1.4.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:tidybulk.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings tidybulk_1.4.0.tar.gz
StartedAt: 2021-10-15 06:35:58 -0400 (Fri, 15 Oct 2021)
EndedAt: 2021-10-15 06:51:50 -0400 (Fri, 15 Oct 2021)
EllapsedTime: 952.0 seconds
RetCode: 0
Status:   OK  
CheckDir: tidybulk.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:tidybulk.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings tidybulk_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/tidybulk.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.4.0'
* 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 whether package 'tidybulk' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.2Mb
    help   1.3Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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'
.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_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'
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'
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 '.element'
get_reduced_dimensions_TSNE_bulk_SE: no visible binding for global
  variable 'Y'
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'
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 .element
  .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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                         user system elapsed
test_gene_overrepresentation-methods    22.48   0.92   23.43
test_gene_rank-methods                  16.82   1.53   30.03
test_differential_abundance-methods     15.10   0.53   15.63
test_differential_cellularity-methods   13.31   0.02   13.32
test_stratification_cellularity-methods  7.25   0.90    8.17
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                         user system elapsed
test_gene_overrepresentation-methods    24.37   1.11   25.49
test_gene_rank-methods                  17.11   1.50   30.09
test_differential_cellularity-methods   13.35   0.03   13.37
test_differential_abundance-methods     13.28   0.02   13.30
test_stratification_cellularity-methods  7.74   0.05    7.78
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/tidybulk.Rcheck/00check.log'
for details.



Installation output

tidybulk.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/tidybulk_1.4.0.tar.gz && rm -rf tidybulk.buildbin-libdir && mkdir tidybulk.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=tidybulk.buildbin-libdir tidybulk_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL tidybulk_1.4.0.zip && rm tidybulk_1.4.0.tar.gz tidybulk_1.4.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 21 3549k   21  769k    0     0  1870k      0  0:00:01 --:--:--  0:00:01 1868k
100 3549k  100 3549k    0     0  3532k      0  0:00:01  0:00:01 --:--:-- 3535k

install for i386

* 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  
    add_attr                                html  
    add_class                               html  
    add_scaled_counts_bulk.calcNormFactor   html  
    add_scaled_counts_bulk.get_low_expressed
                                            html  
    adjust_abundance-methods                html  
    aggregate_duplicated_transcripts_bulk   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  
    create_tt_from_bam_sam_bulk             html  
    create_tt_from_tibble_bulk              html  
    deconvolve_cellularity-methods          html  
    describe_transcript-methods             html  
    distinct-methods                        html  
    dplyr-methods                           html  
    drop_attr                               html  
    drop_class                              html  
    ensembl_symbol_mapping                  html  
    ensembl_to_symbol-methods               html  
    error_if_counts_is_na                   html  
    error_if_duplicated_genes               html  
    error_if_log_transformed                html  
    error_if_wrong_input                    html  
    fill_NA_using_formula                   html  
    fill_NA_using_value                     html  
    fill_NA_with_row_median                 html  
    fill_missing_abundance-methods          html  
    filter-methods                          html  
    flybaseIDs                              html  
    get_abundance_norm_if_exists            html  
    get_adjusted_counts_for_unwanted_variation_bulk
                                            html  
    get_bibliography-methods                html  
    get_cell_type_proportions               html  
    get_clusters_SNN_bulk                   html  
    get_clusters_SNN_bulk_SE                html  
    get_clusters_kmeans_bulk                html  
    get_clusters_kmeans_bulk_SE             html  
    get_differential_transcript_abundance_bulk
                                            html  
    get_differential_transcript_abundance_bulk_SE
                                            html  
    get_differential_transcript_abundance_bulk_voom
                                            html  
    get_differential_transcript_abundance_bulk_voom_SE
                                            html  
    get_differential_transcript_abundance_deseq2
                                            html  
    get_differential_transcript_abundance_deseq2_SE
                                            html  
    get_elements                            html  
    get_elements_features                   html  
    get_elements_features_abundance         html  
    get_reduced_dimensions_MDS_bulk         html  
    get_reduced_dimensions_MDS_bulk_SE      html  
    get_reduced_dimensions_PCA_bulk         html  
    get_reduced_dimensions_PCA_bulk_SE      html  
    get_reduced_dimensions_TSNE_bulk        html  
    get_reduced_dimensions_TSNE_bulk_SE     html  
    get_rotated_dimensions                  html  
    get_sample                              html  
    get_sample_counts                       html  
    get_sample_transcript                   html  
    get_sample_transcript_counts            html  
    get_scaled_counts_bulk                  html  
    get_symbol_from_ensembl                 html  
    get_transcript                          html  
    get_x_y_annotation_columns              html  
    group_by-methods                        html  
    identify_abundant-methods               html  
    ifelse2_pipe                            html  
    ifelse_pipe                             html  
    impute_missing_abundance-methods        html  
    join-methods                            html  
    keep_abundant-methods                   html  
    keep_variable-methods                   html  
    keep_variable_transcripts               html  
    keep_variable_transcripts_SE            html  
    log10_reverse_trans                     html  
    logit_trans                             html  
    mutate-methods                          html  
    nest-methods                            html  
    parse_formula                           html  
    parse_formula_survival                  html  
    pipe                                    html  
    pivot_sample-methods                    html  
    pivot_transcript-methods                html  
    prepend                                 html  
    quo_names                               html  
    reduce_dimensions-methods               html  
    reexports                               html  
    remove_redundancy-methods               html  
    remove_redundancy_elements_though_reduced_dimensions
                                            html  
    remove_redundancy_elements_though_reduced_dimensions_SE
                                            html  
    remove_redundancy_elements_through_correlation
                                            html  
    remove_redundancy_elements_through_correlation_SE
                                            html  
    rename-methods                          html  
    rotate_dimensions-methods               html  
    rowwise-methods                         html  
    run_epic                                html  
    run_llsr                                html  
    scale_abundance-methods                 html  
    scale_design                            html  
    se                                      html  
    se_mini                                 html  
    select_closest_pairs                    html  
    summarise-methods                       html  
    symbol_to_entrez                        html  
    test_deseq2_df                          html  
    test_differential_abundance-methods     html  
    test_differential_cellularity-methods   html  
    test_differential_cellularity_          html  
    test_gene_enrichment-methods            html  
    test_gene_enrichment_bulk_EGSEA         html  
    test_gene_overrepresentation-methods    html  
    test_gene_rank-methods                  html  
    test_stratification_cellularity-methods
                                            html  
    test_stratification_cellularity_        html  
    tidybulk-methods                        html  
    tidybulk_SAM_BAM-methods                html  
    tidybulk_to_SummarizedExperiment        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

install for x64

* installing *source* package 'tidybulk' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'tidybulk' as tidybulk_1.4.0.zip
* DONE (tidybulk)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'tidybulk' successfully unpacked and MD5 sums checked

Tests output

tidybulk.Rcheck/tests_i386/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 1.4.0
If you use TIDYBULK in published research, please cite:

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

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


Attaching package: 'tidybulk'

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

    filter

> 
> test_check("tidybulk")
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 = 0.492881)!
Learning embedding...
Iteration 50: error is 54.494755 (50 iterations in 0.05 seconds)
Iteration 100: error is 54.020061 (50 iterations in 0.05 seconds)
Iteration 150: error is 54.354710 (50 iterations in 0.05 seconds)
Iteration 200: error is 57.588348 (50 iterations in 0.05 seconds)
Iteration 250: error is 57.407652 (50 iterations in 0.05 seconds)
Iteration 300: error is 1.280524 (50 iterations in 0.05 seconds)
Iteration 350: error is 0.886771 (50 iterations in 0.03 seconds)
Iteration 400: error is 0.831105 (50 iterations in 0.03 seconds)
Iteration 450: error is 0.814734 (50 iterations in 0.03 seconds)
Iteration 500: error is 0.773757 (50 iterations in 0.03 seconds)
Iteration 550: error is 0.763011 (50 iterations in 0.03 seconds)
Iteration 600: error is 0.759704 (50 iterations in 0.03 seconds)
Iteration 650: error is 0.758247 (50 iterations in 0.03 seconds)
Iteration 700: error is 0.756961 (50 iterations in 0.03 seconds)
Iteration 750: error is 0.755739 (50 iterations in 0.03 seconds)
Iteration 800: error is 0.756957 (50 iterations in 0.03 seconds)
Iteration 850: error is 0.756588 (50 iterations in 0.03 seconds)
Iteration 900: error is 0.756439 (50 iterations in 0.03 seconds)
Iteration 950: error is 0.755246 (50 iterations in 0.03 seconds)
Iteration 1000: error is 0.753370 (50 iterations in 0.03 seconds)
Fitting performed in 0.72 seconds.
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 = 0.492881)!
Learning embedding...
Iteration 50: error is 54.494755 (50 iterations in 0.05 seconds)
Iteration 100: error is 54.020061 (50 iterations in 0.03 seconds)
Iteration 150: error is 54.354710 (50 iterations in 0.03 seconds)
Iteration 200: error is 57.588348 (50 iterations in 0.05 seconds)
Iteration 250: error is 57.407652 (50 iterations in 0.05 seconds)
Iteration 300: error is 1.280524 (50 iterations in 0.05 seconds)
Iteration 350: error is 0.886771 (50 iterations in 0.05 seconds)
Iteration 400: error is 0.831105 (50 iterations in 0.03 seconds)
Iteration 450: error is 0.814734 (50 iterations in 0.03 seconds)
Iteration 500: error is 0.773757 (50 iterations in 0.03 seconds)
Iteration 550: error is 0.763011 (50 iterations in 0.03 seconds)
Iteration 600: error is 0.759704 (50 iterations in 0.03 seconds)
Iteration 650: error is 0.758247 (50 iterations in 0.03 seconds)
Iteration 700: error is 0.756961 (50 iterations in 0.03 seconds)
Iteration 750: error is 0.755739 (50 iterations in 0.03 seconds)
Iteration 800: error is 0.756957 (50 iterations in 0.03 seconds)
Iteration 850: error is 0.756588 (50 iterations in 0.03 seconds)
Iteration 900: error is 0.756439 (50 iterations in 0.03 seconds)
Iteration 950: error is 0.755246 (50 iterations in 0.03 seconds)
Iteration 1000: error is 0.753370 (50 iterations in 0.03 seconds)
Fitting performed in 0.70 seconds.
 @Article{tidybulk,
  title = {tidybulk: an R tidy framework for modular transcriptomic data analysis},
  author = {Stefano Mangiola and Ramyar Molania and Ruining Dong and Maria A. Doyle & Anthony T. Papenfuss},
  journal = {Genome Biology},
  year = {2021},
  volume = {22},
  number = {42},
  url = {https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02233-7},
  }
@article{wickham2019welcome,
  title={Welcome to the Tidyverse},
  author={Wickham, Hadley and Averick, Mara and Bryan, Jennifer and Chang, Winston and McGowan, Lucy D'Agostino and Francois, Romain and Grolemund, Garrett and Hayes, Alex and Henry, Lionel and Hester, Jim and others},
  journal={Journal of Open Source Software},
  volume={4},
  number={43},
  pages={1686},
  year={2019}
	}
@article{robinson2010edger,
  title={edgeR: a Bioconductor package for differential expression analysis of digital gene expression data},
  author={Robinson, Mark D and McCarthy, Davis J and Smyth, Gordon K},
  journal={Bioinformatics},
  volume={26},
  number={1},
  pages={139--140},
  year={2010},
  publisher={Oxford University Press}
	}
@article{robinson2010scaling,
  title={A scaling normalization method for differential expression analysis of RNA-seq data},
  author={Robinson, Mark D and Oshlack, Alicia},
  journal={Genome biology},
  volume={11},
  number={3},
  pages={1--9},
  year={2010},
  publisher={BioMed Central}
	}
== Skipped tests ===============================================================
* empty test (2)

[ FAIL 0 | WARN 22 | SKIP 2 | PASS 206 ]
> 
> proc.time()
   user  system elapsed 
 227.01   14.03  241.03 

tidybulk.Rcheck/tests_x64/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
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 1.4.0
If you use TIDYBULK in published research, please cite:

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

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


Attaching package: 'tidybulk'

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

    filter

> 
> test_check("tidybulk")
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 = 0.492881)!
Learning embedding...
Iteration 50: error is 54.494755 (50 iterations in 0.05 seconds)
Iteration 100: error is 54.020061 (50 iterations in 0.03 seconds)
Iteration 150: error is 54.354710 (50 iterations in 0.03 seconds)
Iteration 200: error is 57.588348 (50 iterations in 0.05 seconds)
Iteration 250: error is 57.407652 (50 iterations in 0.05 seconds)
Iteration 300: error is 1.280524 (50 iterations in 0.05 seconds)
Iteration 350: error is 0.886771 (50 iterations in 0.03 seconds)
Iteration 400: error is 0.831105 (50 iterations in 0.01 seconds)
Iteration 450: error is 0.814734 (50 iterations in 0.03 seconds)
Iteration 500: error is 0.773757 (50 iterations in 0.03 seconds)
Iteration 550: error is 0.763011 (50 iterations in 0.03 seconds)
Iteration 600: error is 0.759704 (50 iterations in 0.03 seconds)
Iteration 650: error is 0.758247 (50 iterations in 0.03 seconds)
Iteration 700: error is 0.756961 (50 iterations in 0.03 seconds)
Iteration 750: error is 0.755739 (50 iterations in 0.03 seconds)
Iteration 800: error is 0.756957 (50 iterations in 0.03 seconds)
Iteration 850: error is 0.756588 (50 iterations in 0.03 seconds)
Iteration 900: error is 0.756439 (50 iterations in 0.03 seconds)
Iteration 950: error is 0.755246 (50 iterations in 0.03 seconds)
Iteration 1000: error is 0.753370 (50 iterations in 0.02 seconds)
Fitting performed in 0.66 seconds.
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 = 0.492881)!
Learning embedding...
Iteration 50: error is 54.494755 (50 iterations in 0.05 seconds)
Iteration 100: error is 54.020061 (50 iterations in 0.03 seconds)
Iteration 150: error is 54.354710 (50 iterations in 0.05 seconds)
Iteration 200: error is 57.588348 (50 iterations in 0.05 seconds)
Iteration 250: error is 57.407652 (50 iterations in 0.05 seconds)
Iteration 300: error is 1.280524 (50 iterations in 0.03 seconds)
Iteration 350: error is 0.886771 (50 iterations in 0.05 seconds)
Iteration 400: error is 0.831105 (50 iterations in 0.03 seconds)
Iteration 450: error is 0.814734 (50 iterations in 0.03 seconds)
Iteration 500: error is 0.773757 (50 iterations in 0.03 seconds)
Iteration 550: error is 0.763011 (50 iterations in 0.01 seconds)
Iteration 600: error is 0.759704 (50 iterations in 0.02 seconds)
Iteration 650: error is 0.758247 (50 iterations in 0.03 seconds)
Iteration 700: error is 0.756961 (50 iterations in 0.03 seconds)
Iteration 750: error is 0.755739 (50 iterations in 0.03 seconds)
Iteration 800: error is 0.756957 (50 iterations in 0.03 seconds)
Iteration 850: error is 0.756588 (50 iterations in 0.03 seconds)
Iteration 900: error is 0.756439 (50 iterations in 0.03 seconds)
Iteration 950: error is 0.755246 (50 iterations in 0.03 seconds)
Iteration 1000: error is 0.753370 (50 iterations in 0.03 seconds)
Fitting performed in 0.67 seconds.
 @Article{tidybulk,
  title = {tidybulk: an R tidy framework for modular transcriptomic data analysis},
  author = {Stefano Mangiola and Ramyar Molania and Ruining Dong and Maria A. Doyle & Anthony T. Papenfuss},
  journal = {Genome Biology},
  year = {2021},
  volume = {22},
  number = {42},
  url = {https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02233-7},
  }
@article{wickham2019welcome,
  title={Welcome to the Tidyverse},
  author={Wickham, Hadley and Averick, Mara and Bryan, Jennifer and Chang, Winston and McGowan, Lucy D'Agostino and Francois, Romain and Grolemund, Garrett and Hayes, Alex and Henry, Lionel and Hester, Jim and others},
  journal={Journal of Open Source Software},
  volume={4},
  number={43},
  pages={1686},
  year={2019}
	}
@article{robinson2010edger,
  title={edgeR: a Bioconductor package for differential expression analysis of digital gene expression data},
  author={Robinson, Mark D and McCarthy, Davis J and Smyth, Gordon K},
  journal={Bioinformatics},
  volume={26},
  number={1},
  pages={139--140},
  year={2010},
  publisher={Oxford University Press}
	}
@article{robinson2010scaling,
  title={A scaling normalization method for differential expression analysis of RNA-seq data},
  author={Robinson, Mark D and Oshlack, Alicia},
  journal={Genome biology},
  volume={11},
  number={3},
  pages={1--9},
  year={2010},
  publisher={BioMed Central}
	}
== Skipped tests ===============================================================
* empty test (2)

[ FAIL 0 | WARN 22 | SKIP 2 | PASS 206 ]
> 
> proc.time()
   user  system elapsed 
 219.64    4.21  223.87 

Example timings

tidybulk.Rcheck/examples_i386/tidybulk-Ex.timings

nameusersystemelapsed
adjust_abundance-methods2.710.102.80
aggregate_duplicates-methods0.340.000.34
arrange-methods000
as_matrix0.080.010.09
bind-methods000
cluster_elements-methods0.090.020.11
deconvolve_cellularity-methods2.190.192.37
describe_transcript-methods0.980.021.00
distinct-methods0.090.000.10
dplyr-methods1.860.061.92
ensembl_to_symbol-methods1.500.091.59
fill_missing_abundance-methods0.130.000.13
filter-methods000
get_bibliography-methods0.060.000.06
group_by-methods000
identify_abundant-methods0.020.000.02
impute_missing_abundance-methods0.040.000.04
join-methods3.020.273.28
keep_abundant-methods0.050.000.05
keep_variable-methods0.040.000.05
log10_reverse_trans0.250.010.26
logit_trans0.130.020.14
mutate-methods0.050.000.05
nest-methods1.780.412.19
pivot_sample-methods0.010.000.01
pivot_transcript-methods0.020.000.02
reduce_dimensions-methods0.170.000.17
remove_redundancy-methods0.550.060.70
rename-methods0.030.000.04
rotate_dimensions-methods0.150.000.15
rowwise-methods0.080.000.08
scale_abundance-methods0.140.000.14
summarise-methods0.020.000.02
symbol_to_entrez0.480.000.48
test_differential_abundance-methods15.10 0.5315.63
test_differential_cellularity-methods13.31 0.0213.32
test_gene_enrichment-methods000
test_gene_overrepresentation-methods22.48 0.9223.43
test_gene_rank-methods16.82 1.5330.03
test_stratification_cellularity-methods7.250.908.17
tidybulk-methods0.100.020.11

tidybulk.Rcheck/examples_x64/tidybulk-Ex.timings

nameusersystemelapsed
adjust_abundance-methods4.030.164.18
aggregate_duplicates-methods0.410.000.41
arrange-methods0.010.000.02
as_matrix0.070.030.09
bind-methods000
cluster_elements-methods0.070.010.09
deconvolve_cellularity-methods1.440.041.47
describe_transcript-methods0.780.010.80
distinct-methods0.100.000.09
dplyr-methods2.360.062.42
ensembl_to_symbol-methods1.730.131.86
fill_missing_abundance-methods0.120.000.12
filter-methods000
get_bibliography-methods0.050.000.05
group_by-methods0.010.000.01
identify_abundant-methods0.040.000.03
impute_missing_abundance-methods0.040.000.05
join-methods3.060.333.39
keep_abundant-methods0.10.00.1
keep_variable-methods0.080.000.07
log10_reverse_trans0.260.030.30
logit_trans0.170.000.17
mutate-methods0.050.000.05
nest-methods1.80.01.8
pivot_sample-methods0.030.000.03
pivot_transcript-methods0.010.000.01
reduce_dimensions-methods0.210.000.21
remove_redundancy-methods0.370.000.37
rename-methods0.030.000.03
rotate_dimensions-methods0.140.000.14
rowwise-methods0.050.000.05
scale_abundance-methods0.110.000.11
summarise-methods000
symbol_to_entrez0.390.000.39
test_differential_abundance-methods13.28 0.0213.30
test_differential_cellularity-methods13.35 0.0313.37
test_gene_enrichment-methods000
test_gene_overrepresentation-methods24.37 1.1125.49
test_gene_rank-methods17.11 1.5030.09
test_stratification_cellularity-methods7.740.057.78
tidybulk-methods0.060.000.06