===============================
BiocCheckGitClone('VISTA')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4144/be96afc7e6154a051f9c4f653cb0d2661cedeb2d/VISTA
BiocVersion: 3.23
Package: VISTA
PackageVersion: 0.99.1
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4144/be96afc7e6154a051f9c4f653cb0d2661cedeb2d/VISTA.BiocCheck
BiocCheckVersion: 1.47.20
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4144/be96afc7e6154a051f9c4f653cb0d2661cedeb2d/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 v1.47.20 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/be96afc7e6154a051f9c4f653cb0d2661cedeb2d/VISTA.Rcheck
* using R Under development (unstable) (2026-03-05 r89546)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-03-24 02:18:54 UTC
* using option --no-vignettes
* checking for file VISTA/DESCRIPTION ... OK
* checking extension type ... Package
* this is package VISTA version 0.99.1
* 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 ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
ggplot2 dplyr
A package should be listed in only one of these fields.
* 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 ... [11s/11s] OK
* checking whether the package can be loaded with stated dependencies ... [11s/11s] OK
* checking whether the package can be unloaded cleanly ... [14s/14s] OK
* checking whether the namespace can be loaded with stated dependencies ... [12s/12s] OK
* checking whether the namespace can be unloaded cleanly ... [11s/11s] OK
* checking loading without being on the library search path ... [11s/11s] 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 ... [52s/52s] NOTE
.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
.deg_count_payload_from_reference: no visible binding for global
variable sample_comparisons
.deg_count_payload_from_reference: no visible binding for global
variable regulation
.deg_count_payload_from_reference: no visible binding for global
variable .data
.deg_count_payload_from_vista: 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
.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
example_vista: no visible global function definition for data
example_vista: no visible binding for global variable sample_metadata
example_vista: no visible binding for global variable count_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 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 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
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.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("stats", "as.dist", "hclust", "na.omit")
importFrom("utils", "data", "getFromNamespace", "head")
to your NAMESPACE file.
* 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[1:150, ], 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 files in vignettes ... OK
* checking examples ... [257s/256s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
run_vista_report 17.888 1.100 17.276
get_umap_plot 11.371 0.041 11.412
get_pairwise_corr_plot 8.737 0.065 8.802
get_expression_heatmap 7.521 0.061 7.587
get_foldchange_lollipop 6.478 0.005 6.482
get_foldchange_barplot 5.968 0.017 6.009
get_expression_lollipop 5.921 0.046 5.967
get_enrichment_plot 4.865 0.134 5.002
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [345s/345s]
[345s/345s] 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: 3 NOTEs
See
/home/pkgbuild/packagebuilder/workers/jobs/4144/be96afc7e6154a051f9c4f653cb0d2661cedeb2d/VISTA.Rcheck/00check.log
for details.
WARNING: R CMD check exceeded 10 min requirement
===============================
BiocCheck('VISTA_0.99.1.tar.gz')
===============================
Installing VISTA
Package installed successfully
VISTA session metadata
sourceDir: /tmp/RtmptX8dvH/file3e9018b39d9fa/VISTA
BiocVersion: 3.23
Package: VISTA
PackageVersion: 0.99.1
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4144/be96afc7e6154a051f9c4f653cb0d2661cedeb2d/VISTA.BiocCheck
BiocCheckVersion: 1.47.20
sourceDir: /tmp/RtmptX8dvH/file3e9018b39d9fa/VISTA
installDir: /tmp/RtmptX8dvH/file3e9018371e0f0d
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...
i NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* 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 sapply(); use vapply()
Found in files:
R/functional_analysis.R (line 130, column 9)
R/functional_analysis.R (line 132, column 9)
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
utils-internal.R (line 913, column 49)
...
viz_related.R (line 553, column 10)
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
R/utils-internal.R (line 1347, column 10)
* Checking parsed R code in R directory, examples, vignettes...
i Found @ in vignettes/VISTA-airway.Rmd
i Found @ in vignettes/VISTA-chord.Rmd
i Found @ in vignettes/VISTA-code-economy.Rmd
i NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
i NOTE: Avoid '<<-' if possible (found 19 times)
<<- in R/exporting.R (line 382, column 17)
...
<<- in R/viz_related.R (line 5722, column 33)
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 23 times)
suppressWarnings() in R/benchmarking.R (line 940, column 19)
...
suppressWarnings() in R/viz_related.R (line 5164, 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): 815 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.
benchmark_vista_equivalence.Rd
...
validate_vista_deep.Rd
i NOTE: Usage of dontrun / donttest tags found in man page examples. 17% of man
pages use at least one of these tags.
Found in files:
benchmark_vista_equivalence.Rd
...
VISTA-accessors.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; 1399 lines (7%) are > 80 characters long.
First few lines:
R/accessors.R#L2 #' @description These accessor functions ...
...
vignettes/VISTA-reference.Rmd#L238 - `get_genes_by_regulation(...)`: extrac
...
i NOTE: Consider multiples of 4 spaces for line indents; 7047 lines (35%) are
not.
First few lines:
R/accessors.R#L97 source <- match.arg(source) ...
...
vignettes/VISTA-raincloud.Rmd#L270 ggplot2::coord_flip() ...
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 v1.47.20 results
0 ERRORS | 0 WARNINGS | i 15 NOTES
i See the VISTA.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.