Multiple platform build/check report for BioC 3.23 - CHECK results for VISTA on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.4 LTS)	x86_64	4.6.0 alpha (2026-04-05 r89794)	4957
kjohnson3	macOS 13.7.7 Ventura	arm64	4.6.0 alpha (2026-04-08 r89818)	4686
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4627
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

CHECK results for VISTA on kjohnson3

To the developers/maintainers of the VISTA package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/VISTA.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: VISTA

Version: 0.99.8

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:VISTA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings VISTA_0.99.8.tar.gz

StartedAt: 2026-04-17 22:53:01 -0400 (Fri, 17 Apr 2026)

EndedAt: 2026-04-17 22:55:57 -0400 (Fri, 17 Apr 2026)

EllapsedTime: 176.0 seconds

RetCode: 0

Status: OK

CheckDir: VISTA.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:VISTA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings VISTA_0.99.8.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/VISTA.Rcheck’
* using R version 4.6.0 alpha (2026-04-08 r89818)
* using platform: aarch64-apple-darwin23
* R was compiled by
    Apple clang version 17.0.0 (clang-1700.3.19.1)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-04-18 02:53:02 UTC
* using option ‘--no-vignettes’
* checking for file ‘VISTA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘VISTA’ version ‘0.99.8’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 25 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ‘VISTA’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking 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
.build_example_vista: no visible global function definition for ‘data’
.build_example_vista: no visible binding for global variable
  ‘sample_metadata’
.build_example_vista: no visible binding for global variable
  ‘count_data’
.choose_celltypes: no visible binding for global variable ‘cell_type’
.choose_celltypes: no visible binding for global variable ‘score’
.choose_celltypes: no visible binding for global variable ‘mean_score’
.cluster_log2fc_matrix: no visible binding for global variable ‘.data’
.cluster_log2fc_matrix: no visible binding for global variable
  ‘comparison’
.cluster_log2fc_matrix: no visible binding for global variable ‘log2fc’
.cluster_log2fc_matrix: no visible global function definition for ‘:=’
.collapse_ensembl_symbol_ids: no visible binding for global variable
  ‘gene’
.collapse_ensembl_symbol_ids: no visible binding for global variable
  ‘gene_symbol’
.collapse_rowdata_symbols: no visible binding for global variable
  ‘gene_id’
.collapse_rowdata_symbols: no visible binding for global variable
  ‘symbol’
.collect_deg_count_data : .std_deg_sum: no visible binding for global
  variable ‘.data’
.collect_deg_count_data: no visible binding for global variable ‘.data’
.deg_count_payload_from_reference : <anonymous>: no visible binding for
  global variable ‘.data’
.ma_payload_from_reference: no visible binding for global variable
  ‘.data’
.ma_payload_from_vista: no visible binding for global variable ‘.data’
.order_expression_plot_samples: no visible binding for global variable
  ‘.data’
.pca_payload_from_reference: no visible binding for global variable
  ‘.data’
.pca_payload_from_vista: no visible binding for global variable ‘.data’
.plot_deg_count_circular: no visible binding for global variable
  ‘.data’
.plot_mds: no visible binding for global variable ‘Dim1’
.plot_mds: no visible binding for global variable ‘Dim2’
.plot_mds: no visible global function definition for ‘aes_string’
.plot_pca: no visible binding for global variable ‘PC1’
.plot_pca: no visible binding for global variable ‘PC2’
.plot_pca: no visible global function definition for ‘aes_string’
.plot_pca: no visible global function definition for ‘stat_ellipse’
.plot_reference_deg_count: no visible binding for global variable
  ‘.data’
.plot_reference_ma: no visible binding for global variable ‘.data’
.plot_reference_pca: no visible binding for global variable ‘.data’
.plot_reference_volcano: no visible binding for global variable ‘.data’
.prepare_sample_metadata: no visible binding for global variable
  ‘.data’
.run_deseq_comparisons: no visible binding for global variable
  ‘regulation’
.run_reference_deseq2: no visible binding for global variable ‘.data’
.run_reference_edger: no visible binding for global variable ‘.data’
.run_reference_limma: no visible binding for global variable ‘.data’
.standardize_deg_count_payload: no visible binding for global variable
  ‘.data’
.standardize_deg_count_payload: no visible binding for global variable
  ‘sample_comparisons’
.standardize_deg_count_payload: no visible binding for global variable
  ‘regulation’
.validate_vista_self_consistency: no visible binding for global
  variable ‘.data’
.vista_expression_long: no visible binding for global variable ‘gene’
.vista_expression_long: no visible binding for global variable ‘.data’
.volcano_payload_from_table: no visible binding for global variable
  ‘.data’
benchmark_vista_equivalence: no visible binding for global variable
  ‘.data’
export_vista_assets: no visible global function definition for ‘head’
get_celltype_barplot: no visible binding for global variable
  ‘cell_type’
get_celltype_barplot: no visible binding for global variable ‘group’
get_celltype_barplot: no visible binding for global variable ‘score’
get_celltype_barplot: no visible binding for global variable
  ‘mean_score’
get_celltype_group_dotplot: no visible binding for global variable
  ‘cell_type’
get_celltype_group_dotplot: no visible binding for global variable
  ‘group’
get_celltype_group_dotplot: no visible binding for global variable
  ‘score’
get_celltype_group_dotplot: no visible binding for global variable
  ‘sd_score’
get_celltype_group_dotplot: no visible binding for global variable
  ‘value’
get_celltype_group_dotplot: no visible binding for global variable ‘m’
get_celltype_group_dotplot: no visible binding for global variable
  ‘err’
get_celltype_heatmap: no visible binding for global variable
  ‘cell_type’
get_celltype_heatmap: no visible binding for global variable ‘score’
get_celltype_heatmap: no visible global function definition for
  ‘hclust’
get_celltype_heatmap: no visible binding for global variable ‘.data’
get_celltype_heatmap: no visible binding for global variable ‘group’
get_celltype_heatmap: no visible binding for global variable ‘value’
get_chromosome_plot: no visible binding for global variable ‘.data’
get_chromosome_plot: no visible binding for global variable ‘chr’
get_chromosome_plot: no visible binding for global variable ‘pos_mb’
get_chromosome_plot: no visible binding for global variable
  ‘value_clipped’
get_chromosome_plot: no visible binding for global variable
  ‘gene_label’
get_corr_heatmap: no visible binding for global variable ‘Var1’
get_corr_heatmap: no visible binding for global variable ‘Var2’
get_corr_heatmap: no visible global function definition for ‘hclust’
get_corr_heatmap: no visible global function definition for ‘as.dist’
get_corr_heatmap: no visible binding for global variable ‘.data’
get_corr_heatmap: no visible binding for global variable ‘value’
get_deg_alluvial : <anonymous>: no visible binding for global variable
  ‘.data’
get_deg_alluvial: no visible binding for global variable ‘gene_id’
get_deg_alluvial: no visible binding for global variable ‘comparison’
get_deg_alluvial: no visible binding for global variable ‘regulation’
get_deg_alluvial: no visible binding for global variable ‘value’
get_deg_alluvial: no visible binding for global variable ‘name’
get_deg_alluvial: no visible binding for global variable ‘..stratum..’
get_deg_alluvial: no visible binding for global variable ‘..count..’
get_deg_count_barplot: no visible binding for global variable ‘.data’
get_enrichment_plot: no visible binding for global variable ‘.data’
get_enrichment_plot: no visible binding for global variable ‘logFDR’
get_enrichment_plot: no visible binding for global variable
  ‘Description’
get_expression_barplot: no visible binding for global variable ‘gene’
get_expression_barplot: no visible binding for global variable ‘.data’
get_expression_boxplot: no visible global function definition for
  ‘head’
get_expression_boxplot: no visible binding for global variable ‘gene’
get_expression_boxplot: no visible binding for global variable ‘.data’
get_expression_chromosome_plot: no visible binding for global variable
  ‘.data’
get_expression_density: no visible binding for global variable ‘gene’
get_expression_heatmap: no visible binding for global variable
  ‘gene_id’
get_expression_joyplot: no visible binding for global variable ‘gene’
get_expression_joyplot: no visible binding for global variable ‘.data’
get_expression_lineplot: no visible global function definition for
  ‘head’
get_expression_lineplot: no visible binding for global variable ‘.data’
get_expression_lineplot: no visible binding for global variable ‘gene’
get_expression_lollipop: no visible binding for global variable ‘gene’
get_expression_lollipop: no visible binding for global variable ‘.data’
get_expression_raincloud: no visible binding for global variable
  ‘.data’
get_expression_scatter: no visible binding for global variable ‘expr_x’
get_expression_scatter: no visible binding for global variable ‘expr_y’
get_expression_scatter: no visible binding for global variable ‘gene’
get_expression_violinplot: no visible global function definition for
  ‘head’
get_expression_violinplot: no visible binding for global variable
  ‘gene’
get_expression_violinplot: no visible binding for global variable
  ‘.data’
get_foldchange_barplot: no visible binding for global variable ‘log2fc’
get_foldchange_barplot: no visible binding for global variable ‘.data’
get_foldchange_barplot: no visible binding for global variable
  ‘gene_id’
get_foldchange_barplot: no visible binding for global variable
  ‘comparison’
get_foldchange_boxplot: no visible binding for global variable
  ‘gene_id’
get_foldchange_boxplot: no visible binding for global variable
  ‘log2FoldChange’
get_foldchange_boxplot: no visible binding for global variable
  ‘comparison’
get_foldchange_lineplot: no visible binding for global variable ‘.data’
get_foldchange_lineplot: no visible binding for global variable
  ‘comparison’
get_foldchange_lineplot: no visible binding for global variable
  ‘log2fc’
get_foldchange_lineplot: no visible binding for global variable
  ‘cluster’
get_foldchange_lineplot: no visible binding for global variable
  ‘avg_log2FC’
get_foldchange_lineplot: no visible binding for global variable
  ‘display_gene’
get_foldchange_lineplot: no visible binding for global variable ‘n’
get_foldchange_lineplot: no visible binding for global variable ‘label’
get_foldchange_lollipop : <anonymous>: no visible binding for global
  variable ‘.data’
get_foldchange_lollipop: no visible binding for global variable ‘.data’
get_foldchange_lollipop: no visible binding for global variable
  ‘comparison’
get_foldchange_lollipop: no visible binding for global variable
  ‘log2fc’
get_foldchange_lollipop: no visible binding for global variable
  ‘gene_id’
get_foldchange_lollipop: no visible binding for global variable
  ‘fc_dir’
get_foldchange_lollipop: no visible binding for global variable
  ‘x_dodge’
get_foldchange_raincloud: no visible binding for global variable
  ‘gene_id’
get_foldchange_raincloud: no visible binding for global variable
  ‘log2FoldChange’
get_foldchange_raincloud: no visible binding for global variable
  ‘comparison’
get_foldchange_raincloud: no visible binding for global variable
  ‘.data’
get_foldchange_scatter: no visible binding for global variable ‘.data’
get_foldchange_scatter: no visible binding for global variable
  ‘log2fc1’
get_foldchange_scatter: no visible binding for global variable
  ‘log2fc2’
get_foldchange_scatter: no visible binding for global variable ‘status’
get_foldchange_scatter: no visible binding for global variable
  ‘display_gene’
get_ma_plot: no visible binding for global variable ‘.data’
get_ma_plot: no visible binding for global variable ‘display_gene’
get_ma_plot: no visible binding for global variable ‘regulation’
get_ma_plot: no visible binding for global variable ‘log2fc’
get_ma_plot: no visible binding for global variable ‘log10_baseMean’
get_ma_plot: no visible binding for global variable ‘label’
get_mds_plot: no visible binding for global variable ‘Dim1’
get_mds_plot: no visible binding for global variable ‘Dim2’
get_mds_plot: no visible binding for global variable ‘.data’
get_pairwise_corr_plot: no visible binding for global variable ‘.data’
get_pathway_genes: no visible binding for global variable ‘.data’
get_pca_plot: no visible binding for global variable ‘PC1’
get_pca_plot: no visible binding for global variable ‘PC2’
get_pca_plot: no visible binding for global variable ‘.data’
get_umap_plot: no visible binding for global variable ‘UMAP1’
get_umap_plot: no visible binding for global variable ‘UMAP2’
get_umap_plot: no visible binding for global variable ‘.data’
print.VISTA: no visible global function definition for ‘as’
run_cell_deconvolution: no visible global function definition for
  ‘getFromNamespace’
run_edger_analysis: no visible binding for global variable ‘regulation’
run_limma_analysis: no visible binding for global variable ‘regulation’
run_vista_report: no visible global function definition for ‘head’
run_vista_report : <anonymous>: no visible global function definition
  for ‘head’
enrichMsigDB,VISTA : convert_ids: no visible global function definition
  for ‘na.omit’
Undefined global functions or variables:
  ..count.. ..stratum.. .data := Description Dim1 Dim2 PC1 PC2 UMAP1
  UMAP2 Var1 Var2 aes_string as as.dist avg_log2FC cell_type chr
  cluster comparison count_data data display_gene err expr_x expr_y
  fc_dir gene gene_id gene_label gene_symbol getFromNamespace group
  hclust head label log10_baseMean log2FoldChange log2fc log2fc1
  log2fc2 logFDR m mean_score n na.omit name pos_mb regulation
  sample_comparisons sample_metadata score sd_score stat_ellipse status
  symbol value value_clipped x_dodge
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "as.dist", "hclust", "na.omit")
  importFrom("utils", "data", "getFromNamespace", "head")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* 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 data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/VISTA.Rcheck/00check.log’
for details.

Installation output

VISTA.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’
* installing *source* package ‘VISTA’ ...
** this is package ‘VISTA’ version ‘0.99.8’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** 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 (VISTA)

Tests output

VISTA.Rcheck/tests/testthat.Rout


R version 4.6.0 alpha (2026-04-08 r89818)
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23

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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(VISTA)

> 
> test_check("VISTA")
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
calcNormFactors has been renamed to normLibSizes
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
calcNormFactors has been renamed to normLibSizes
calcNormFactors has been renamed to normLibSizes
calcNormFactors has been renamed to normLibSizes
calcNormFactors has been renamed to normLibSizes
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
estimating size factors
estimating dispersions
calcNormFactors has been renamed to normLibSizes
calcNormFactors has been renamed to normLibSizes
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
calcNormFactors has been renamed to normLibSizes
calcNormFactors has been renamed to normLibSizes
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
calcNormFactors has been renamed to normLibSizes
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
Starting xCell2 Analysis...

Using human MSigDB with ortholog mapping to mouse. Use `db_species = "MM"` for mouse-native gene sets.
This message is displayed once per session.
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
calcNormFactors has been renamed to normLibSizes
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
[ FAIL 0 | WARN 3 | SKIP 1 | PASS 427 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• xCell2 runtime failed in this environment: xCell2 scoring failed with
  `xCell2Analysis()`. (1): 'test-deconvolution.R:21:5'

[ FAIL 0 | WARN 3 | SKIP 1 | PASS 427 ]
> 
> proc.time()
   user  system elapsed 
 36.654   1.161  38.849

Example timings

VISTA.Rcheck/VISTA-Ex.timings

name	user	system	elapsed
VISTA-accessors	1.269	0.028	1.312
VISTA-class	0.001	0.000	0.001
as_vista	0.025	0.002	0.026
benchmark_vista_equivalence	0.248	0.008	0.261
create_vista	0.713	0.007	0.734
derive_vista_metadata	0.085	0.004	0.091
enrichMsigDB	0.001	0.000	0.001
example_vista	0.001	0.000	0.001
export_vista_assets	0.256	0.008	0.265
get_cell_fractions	1.122	0.095	1.241
get_celltype_barplot	0.313	0.003	0.320
get_celltype_group_dotplot	0.548	0.004	0.557
get_celltype_heatmap	0.108	0.002	0.111
get_corr_heatmap	0.100	0.001	0.102
get_deg_alluvial	1.129	0.027	1.164
get_deg_count_barplot	0.101	0.001	0.102
get_deg_count_donutplot	0.087	0.001	0.089
get_deg_count_pieplot	0.081	0.001	0.082
get_deg_venn_diagram	0.000	0.001	0.000
get_enrichment_chord	1.843	0.020	1.872
get_enrichment_plot	0	0	0
get_expression_barplot	1.390	0.026	1.454
get_expression_boxplot	0.187	0.002	0.191
get_expression_chromosome_plot	0.007	0.001	0.008
get_expression_density	0.153	0.003	0.160
get_expression_heatmap	1.240	0.032	1.285
get_expression_joyplot	0.127	0.003	0.131
get_expression_lineplot	0.182	0.004	0.189
get_expression_lollipop	1.356	0.015	1.398
get_expression_matrix	0.006	0.000	0.006
get_expression_raincloud	0.427	0.010	0.443
get_expression_scatter	0.204	0.003	0.208
get_expression_violinplot	0.328	0.009	0.345
get_foldchange_barplot	1.308	0.006	1.318
get_foldchange_boxplot	0.084	0.001	0.085
get_foldchange_chromosome_plot	0.001	0.000	0.000
get_foldchange_heatmap	0.081	0.003	0.085
get_foldchange_lineplot	0.123	0.001	0.123
get_foldchange_lollipop	0.544	0.003	0.549
get_foldchange_matrix	0.001	0.000	0.001
get_foldchange_raincloud	0.118	0.002	0.122
get_foldchange_scatter	0	0	0
get_genes_by_regulation	0.003	0.000	0.003
get_go_enrichment	0	0	0
get_gsea	0.000	0.001	0.000
get_kegg_enrichment	0.066	0.004	0.074
get_ma_plot	0.105	0.000	0.105
get_mds_plot	0.084	0.000	0.084
get_msigdb_enrichment	0.033	0.002	0.035
get_pairwise_corr_plot	1.881	0.011	1.904
get_pathway_genes	0.036	0.002	0.038
get_pathway_heatmap	0.033	0.002	0.035
get_pca_plot	1.143	0.008	1.158
get_umap_plot	2.162	0.016	2.197
get_volcano_plot	0.179	0.004	0.187
match_vista_inputs	0.073	0.001	0.074
print.VISTA	0.001	0.000	0.002
read_vista_counts	0.076	0.001	0.077
read_vista_metadata	0.007	0.000	0.007
run_cell_deconvolution	0.464	0.005	0.485
run_deseq_analysis	0.084	0.001	0.085
run_vista_report	0	0	0
save_vista_data	0.001	0.001	0.001
save_vista_plot	0.113	0.001	0.114
set_de_source	0.735	0.007	0.748
set_rowdata	0.019	0.000	0.019
set_vista_comparison_colors	0.014	0.000	0.014
set_vista_group_colors	0.014	0.000	0.015
validate_vista	0.058	0.003	0.065
validate_vista_deep	0.195	0.002	0.197