##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:VISTA.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings VISTA_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/VISTA.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-04-30 10:09:38 UTC
* checking for file ‘VISTA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘VISTA’ version ‘1.0.0’
* 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 loading without being on the library search path ... 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
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
get_pairwise_corr_plot 5.643      0   5.643
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

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

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL VISTA
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘VISTA’ ...
** this is package ‘VISTA’ version ‘1.0.0’
** 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)

R version 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 
 93.044   2.336  95.402