===============================
BiocCheckGitClone('VISTA')
===============================
Registered S3 method overwritten by 'bit64':
method from
print.bitstring tools
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4144/e0b8a1a4367f0ff1b6f57797e292cd95b333d69e/VISTA
→ BiocVersion: 3.23
→ Package: VISTA
→ PackageVersion: 0.99.5
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4144/e0b8a1a4367f0ff1b6f57797e292cd95b333d69e/VISTA.BiocCheck
→ BiocCheckVersion: 1.47.23
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4144/e0b8a1a4367f0ff1b6f57797e292cd95b333d69e/VISTA
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
* Checking individual file sizes...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking NAMESPACE...
* Checking for valid maintainer...
* Checking CITATION...
i NOTE: (Optional) CITATION file not found. Only include a CITATION file if
there is a preprint or publication for this Bioconductor package. Note that
Bioconductor packages are not required to have a CITATION file but it is useful
both for users and for tracking Bioconductor project-wide metrics. When
including a CITATION file, add the publication using the 'doi' argument of
'bibentry()'.
── BiocCheck v1.47.23 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/4144/e0b8a1a4367f0ff1b6f57797e292cd95b333d69e/VISTA.Rcheck’
* using R version 4.6.0 alpha (2026-04-05 r89794)
* 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: 2026-04-07 05:43:47 UTC
* using option ‘--no-vignettes’
* checking for file ‘VISTA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘VISTA’ version ‘0.99.5’
* 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 for future file timestamps ... 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 ... [12s/12s] OK
* checking whether the package can be loaded with stated dependencies ... [12s/12s] OK
* checking whether the package can be unloaded cleanly ... [12s/12s] OK
* checking whether the namespace can be loaded with stated dependencies ... [11s/11s] OK
* checking whether the namespace can be unloaded cleanly ... [12s/12s] OK
* checking loading without being on the library search path ... [12s/12s] OK
* checking use of S3 registration ... 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 ... [57s/57s] 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
‘display_gene’
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 ‘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
‘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
‘gene_id’
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 ... [1s/1s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'enrichMsigDB.Rd':
\examples lines wider than 100 characters:
out <- try(enrichMsigDB(v, gene_list = genes, from_type = 'ENSEMBL', msigdb_category = 'H'), silent = TRUE)
Rd file 'get_enrichment_plot.Rd':
\examples lines wider than 100 characters:
ms <- try(get_msigdb_enrichment(v, sample_comparison = com, regulation = 'Up', from_type = 'ENSEMBL'), silent = TRUE)
Rd file 'get_foldchange_chromosome_plot.Rd':
\examples lines wider than 100 characters:
p <- try(get_foldchange_chromosome_plot(v, sample_comparison = names(comparisons(v))[1]), silent = TRUE)
Rd file 'get_foldchange_scatter.Rd':
\examples lines wider than 100 characters:
v <- create_vista(count_data[seq_len(150), ], sample_metadata, column_geneid = 'gene_id', group_column = 'cell',
Rd file 'get_gsea.Rd':
\examples lines wider than 100 characters:
out <- try(get_gsea(v, sample_comparison = comp, set_type = 'msigdb', from_type = 'ENSEMBL', species = 'Homo sapiens'), silent = TRUE ... [TRUNCATED]
Rd file 'get_kegg_enrichment.Rd':
\examples lines wider than 100 characters:
out <- try(get_kegg_enrichment(v, sample_comparison = comp, from_type = 'ENSEMBL', orgdb = org.Mm.eg.db::org.Mm.eg.db), silent = TRUE ... [TRUNCATED]
These lines will be truncated in the PDF manual.
* 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 ... [0s/0s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [146s/146s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
get_pairwise_corr_plot 5.619 0.057 5.676
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [91s/91s]
[91s/91s] 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 ... [6s/6s] OK
* DONE
Status: 2 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/4144/e0b8a1a4367f0ff1b6f57797e292cd95b333d69e/VISTA.Rcheck/00check.log’
for details.
===============================
BiocCheck('VISTA_0.99.5.tar.gz')
===============================
Registered S3 method overwritten by 'bit64':
method from
print.bitstring tools
── Installing VISTA ────────────────────────────────────────────────────────────
✔ Package installed successfully
── VISTA session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpIaFhXl/file37d25950c24a68/VISTA
→ BiocVersion: 3.23
→ Package: VISTA
→ PackageVersion: 0.99.5
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4144/e0b8a1a4367f0ff1b6f57797e292cd95b333d69e/VISTA.BiocCheck
→ BiocCheckVersion: 1.47.23
→ sourceDir: /tmp/RtmpIaFhXl/file37d25950c24a68/VISTA
→ installDir: /tmp/RtmpIaFhXl/file37d2593dac66da
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on VISTA ──────────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
i NOTE: Update R version dependency from 4.3 to 4.6.0
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
→ Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* Checking build system compatibility...
* Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
i NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with
'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (26%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
i NOTE: No 'fnd' role found in Authors@R. If the work is supported by a grant,
consider adding the 'fnd' role to the list of authors.
* Checking NAMESPACE...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of VISTA...
* Checking coding practice...
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
• R/utils-internal.R (line 1341, column 10)
* Checking parsed R code in R directory, examples, vignettes...
i Found @ in vignettes/VISTA-airway.Rmd
i NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 24 times)
• suppressWarnings() in R/benchmarking.R (line 979, column 19)
• ...
• suppressWarnings() in R/viz_related.R (line 5374, column 57)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 72
functions greater than 50 lines.
The longest 5 functions are:
• run_vista_report() (R/reporting.R): 816 lines
• ...
• get_foldchange_lollipop() (R/viz_related.R): 329 lines
* Checking man page documentation...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
• get_enrichment_plot.Rd
• ...
• run_vista_report.Rd
i NOTE: Usage of dontrun / donttest tags found in man page examples. 18% of man
pages use at least one of these tags.
Found in files:
• benchmark_vista_equivalence.Rd
• ...
• VISTA-accessors.Rd
i NOTE: Use donttest instead of dontrun.
Found in files:
• get_enrichment_plot.Rd
• ...
• run_vista_report.Rd
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
i NOTE: Consider shorter lines; 1316 lines (8%) are > 80 characters long.
First few lines:
• R/accessors.R#L2 #' @description These accessor functions ...
• ...
• vignettes/VISTA-airway.Rmd#L1538 - Yu G et al. (2012). clusterProfiler: ...
i NOTE: Consider multiples of 4 spaces for line indents; 6441 lines (37%) are
not.
First few lines:
• R/accessors.R#L97 source <- match.arg(source) ...
• ...
• vignettes/VISTA-airway.Rmd#L1435 row.names = FALSE ...
i See https://contributions.bioconductor.org/r-code.html
i See styler package: https://cran.r-project.org/package=styler as described in
the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
i Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
i Maintainer is registered at support site.
i Package is in the Support Site Watched Tags.
── BiocCheck v1.47.23 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 12 NOTES
i See the VISTA.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.