===============================
BiocCheckGitClone('GExPipe')
===============================
── Running Git clone checks on GExPipe ─────────────────────────────────────────
* Checking valid files...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
i (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()'.
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/4162/a590e6c82ce30ee5ed44f2aea3c5d481f0eb416b/GExPipe.Rcheck’
* using R version 4.6.1 (2026-06-24)
* 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: 2026-07-07 16:08:02 UTC
* using option ‘--no-vignettes’
* checking for file ‘GExPipe/DESCRIPTION’ ... OK
* this is package ‘GExPipe’ version ‘0.99.21’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 63 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 ‘GExPipe’ 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 ... WARNING
Found the following files with non-ASCII characters:
R/server_common_genes.R
R/server_results.R
R/server_results_summary.R
R/server_roc.R
R/server_wgcna.R
R/ui_common_genes.R
R/ui_nomogram.R
R/ui_results.R
R/ui_results_summary.R
R/ui_wgcna.R
Portable packages must use only ASCII characters in their R code and
NAMESPACE directives, except perhaps in comments.
Use \uxxxx escapes for other characters.
Function ‘tools::showNonASCIIfile’ can help in finding non-ASCII
characters in files.
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [0s/0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [0s/0s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... WARNING
'::' or ':::' imports not declared from:
‘bslib’ ‘crosstalk’ ‘fontawesome’ ‘htmltools’ ‘htmlwidgets’
'loadNamespace' or 'requireNamespace' call not declared from: ‘rmda’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [37s/37s] NOTE
gexp_stringdb_get_ppi_data_safe : <anonymous>: no visible binding for
'<<-' assignment to ‘timeout_seen’
server_batch : .batch_pvca_ggplot: no visible global function
definition for ‘geom_bar’
server_batch : .batch_pvca_ggplot: no visible global function
definition for ‘scale_fill_manual’
server_batch : .batch_pvca_ggplot: no visible global function
definition for ‘ylim’
server_batch : .batch_pvca_render: no visible global function
definition for ‘plot.new’
server_batch : .batch_pvca_render: no visible global function
definition for ‘text’
server_batch : .batch_pca_polar_plot: no visible binding for global
variable ‘theta’
server_batch : .batch_pca_polar_plot: no visible binding for global
variable ‘r’
server_batch : .batch_pca_polar_plot: no visible global function
definition for ‘coord_polar’
server_batch : .batch_pca_polar_plot: no visible global function
definition for ‘scale_x_continuous’
server_batch : .batch_pca_polar_plot: no visible global function
definition for ‘scale_y_continuous’
server_batch : .batch_pca_polar_plot: no visible global function
definition for ‘geom_point’
server_batch : .batch_pca_polar_plot: no visible binding for global
variable ‘Condition’
server_batch : .batch_pca_polar_plot: no visible global function
definition for ‘scale_color_manual’
server_batch : .batch_pca_platform_plot: no visible binding for global
variable ‘theta’
server_batch : .batch_pca_platform_plot: no visible binding for global
variable ‘r’
server_batch : .batch_pca_platform_plot: no visible binding for global
variable ‘Platform’
server_batch : .batch_pca_platform_plot: no visible global function
definition for ‘geom_point’
server_batch : .batch_pca_platform_plot: no visible global function
definition for ‘scale_color_manual’
server_batch : .batch_pca_platform_plot: no visible global function
definition for ‘coord_polar’
server_batch : .batch_pca_platform_plot: no visible global function
definition for ‘scale_x_continuous’
server_batch : .batch_pca_platform_plot: no visible global function
definition for ‘scale_y_continuous’
server_batch: no visible global function definition for ‘cor’
server_batch: no visible global function definition for ‘as.dist’
server_batch: no visible global function definition for ‘hclust’
server_batch: no visible global function definition for
‘colorRampPalette’
server_batch : <anonymous>: no visible global function definition for
‘plot.new’
server_batch : <anonymous>: no visible global function definition for
‘text’
server_batch : batch_hclust_to_file: no visible global function
definition for ‘cor’
server_batch : batch_hclust_to_file: no visible global function
definition for ‘as.dist’
server_batch : batch_hclust_to_file: no visible global function
definition for ‘hclust’
server_batch : batch_hclust_to_file : <anonymous>: no visible global
function definition for ‘plot.new’
server_batch : batch_hclust_to_file : <anonymous>: no visible global
function definition for ‘text’
server_batch : batch_hclust_to_file: no visible global function
definition for ‘dev.off’
server_batch : <anonymous> : <anonymous>: no visible global function
definition for ‘png’
server_batch : <anonymous> : <anonymous>: no visible global function
definition for ‘jpeg’
server_batch : <anonymous> : <anonymous>: no visible global function
definition for ‘pdf’
server_common_genes: no visible global function definition for
‘plot.new’
server_common_genes: no visible global function definition for ‘text’
server_common_genes : <anonymous>: no visible global function
definition for ‘png’
server_common_genes : <anonymous>: no visible global function
definition for ‘dev.off’
server_common_genes : <anonymous>: no visible global function
definition for ‘jpeg’
server_common_genes : <anonymous>: no visible global function
definition for ‘pdf’
server_common_genes : <anonymous>: no visible global function
definition for ‘plot.new’
server_common_genes : <anonymous>: no visible global function
definition for ‘text’
server_common_genes : make_kegg_barplot: no visible binding for global
variable ‘Description’
server_common_genes : make_kegg_barplot: no visible binding for global
variable ‘Count’
server_common_genes : make_kegg_barplot: no visible binding for global
variable ‘p.adjust’
server_common_genes: no visible global function definition for
‘setNames’
server_common_genes : kegg_chord_to_file: no visible global function
definition for ‘plot.new’
server_common_genes : kegg_chord_to_file: no visible global function
definition for ‘text’
server_common_genes : kegg_chord_to_file: no visible global function
definition for ‘setNames’
server_common_genes : <anonymous> : <anonymous>: no visible global
function definition for ‘jpeg’
server_common_genes : <anonymous> : <anonymous>: no visible global
function definition for ‘pdf’
server_groups: no visible global function definition for ‘reactiveVal’
server_gsea: no visible global function definition for ‘%>%’
server_gsea : <local>: no visible global function definition for ‘%>%’
server_gsea : <local>: no visible global function definition for
‘plot.new’
server_gsea : <local>: no visible global function definition for ‘text’
server_gsea : <local> : <anonymous>: no visible global function
definition for ‘plot.new’
server_gsea : <local> : <anonymous>: no visible global function
definition for ‘text’
server_gsea : <local> : <anonymous>: no visible global function
definition for ‘jpeg’
server_gsea : <local> : <anonymous>: no visible global function
definition for ‘dev.off’
server_gsea : <local> : <anonymous>: no visible global function
definition for ‘pdf’
server_ml: no visible global function definition for ‘coef’
server_ml: no visible global function definition for ‘setNames’
server_ml: no visible global function definition for ‘plot.new’
server_ml: no visible global function definition for ‘text’
server_ml: no visible global function definition for ‘cor’
server_ml : <anonymous>: no visible global function definition for
‘plot.new’
server_ml : <anonymous>: no visible global function definition for
‘text’
server_ml : <anonymous>: no visible global function definition for
‘setNames’
server_ml : plot_rf_error: no visible global function definition for
‘predict’
server_ml : plot_rf_error: no visible global function definition for
‘par’
server_ml : plot_rf_error: no visible global function definition for
‘legend’
server_ml : plot_rf_importance: no visible global function definition
for ‘par’
server_ml : plot_rf_importance: no visible global function definition
for ‘barplot’
server_ml : plot_lasso_path: no visible global function definition for
‘par’
server_ml : plot_lasso_path: no visible global function definition for
‘title’
server_ml : plot_lasso_dev: no visible global function definition for
‘par’
server_ml : plot_lasso_dev: no visible global function definition for
‘title’
server_ml : plot_elastic_path: no visible global function definition
for ‘par’
server_ml : plot_elastic_path: no visible global function definition
for ‘title’
server_ml : plot_elastic_dev: no visible global function definition for
‘par’
server_ml : plot_elastic_dev: no visible global function definition for
‘title’
server_ml : plot_ridge_path: no visible global function definition for
‘par’
server_ml : plot_ridge_path: no visible global function definition for
‘title’
server_ml : plot_ridge_dev: no visible global function definition for
‘par’
server_ml : plot_ridge_dev: no visible global function definition for
‘title’
server_ml : download_plot: no visible global function definition for
‘png’
server_ml : download_plot: no visible global function definition for
‘jpeg’
server_ml : download_plot: no visible global function definition for
‘pdf’
server_ml : download_plot: no visible global function definition for
‘dev.off’
server_ml : plot_ml_biomarker_cor_heatmap: no visible global function
definition for ‘plot.new’
server_ml : plot_ml_biomarker_cor_heatmap: no visible global function
definition for ‘text’
server_ml : plot_ml_biomarker_cor_heatmap: no visible global function
definition for ‘cor’
server_ml : plot_ml_biomarker_coexp_network: no visible global function
definition for ‘plot.new’
server_ml : plot_ml_biomarker_coexp_network: no visible global function
definition for ‘text’
server_ml : plot_ml_biomarker_coexp_network: no visible global function
definition for ‘cor’
server_ml : ml_biomarker_to_file: no visible global function definition
for ‘pdf’
server_ml : ml_biomarker_to_file: no visible global function definition
for ‘jpeg’
server_ml : ml_biomarker_to_file: no visible global function definition
for ‘png’
server_ml : ml_biomarker_to_file: no visible global function definition
for ‘dev.off’
server_nomogram: no visible global function definition for ‘as.formula’
server_nomogram: no visible global function definition for ‘predict’
server_nomogram : <anonymous>: no visible global function definition
for ‘glm’
server_nomogram : <anonymous>: no visible global function definition
for ‘binomial’
server_nomogram : <anonymous>: no visible global function definition
for ‘predict’
server_nomogram: no visible global function definition for ‘glm’
server_nomogram: no visible global function definition for ‘binomial’
server_nomogram : <anonymous>: no visible global function definition
for ‘setNames’
server_nomogram: no visible global function definition for ‘setNames’
server_nomogram: no visible global function definition for ‘coef’
server_nomogram: no visible global function definition for ‘vcov’
server_nomogram: no visible global function definition for ‘%>%’
server_nomogram: no visible binding for global variable ‘plogis’
server_nomogram: no visible global function definition for ‘title’
server_nomogram: no visible global function definition for ‘text’
server_nomogram: no visible global function definition for ‘legend’
server_nomogram : nomogram_plot_to_file : <anonymous>: no visible
global function definition for ‘dev.off’
server_nomogram : nomogram_plot_to_file: no visible binding for global
variable ‘plogis’
server_nomogram : nomogram_plot_to_file: no visible global function
definition for ‘title’
server_nomogram : <anonymous> : <anonymous>: no visible global function
definition for ‘png’
server_nomogram : <anonymous> : <anonymous>: no visible global function
definition for ‘jpeg’
server_nomogram : <anonymous> : <anonymous>: no visible global function
definition for ‘pdf’
server_nomogram : nomogram_panel_to_file: no visible global function
definition for ‘pdf’
server_nomogram : nomogram_panel_to_file: no visible global function
definition for ‘jpeg’
server_nomogram : nomogram_panel_to_file: no visible global function
definition for ‘png’
server_nomogram : nomogram_panel_to_file: no visible global function
definition for ‘dev.off’
server_nomogram : plot_nomogram_roc_train: no visible global function
definition for ‘text’
server_nomogram : plot_nomogram_roc_val: no visible global function
definition for ‘text’
server_nomogram : plot_nomogram_impact_train: no visible global
function definition for ‘legend’
server_nomogram : plot_nomogram_impact_val: no visible global function
definition for ‘legend’
server_normalize: no visible global function definition for
‘reactiveValues’
server_normalize: no visible binding for global variable ‘Stage’
server_normalize: no visible binding for global variable ‘Expression’
server_normalize: no visible global function definition for
‘geom_boxplot’
server_normalize: no visible global function definition for
‘scale_fill_manual’
server_normalize: no visible global function definition for
‘facet_wrap’
server_normalize: no visible global function definition for ‘margin’
server_normalize: no visible global function definition for
‘element_rect’
server_normalize : <anonymous>: no visible binding for global variable
‘Expression’
server_normalize : <anonymous>: no visible binding for global variable
‘Stage’
server_normalize : <anonymous>: no visible global function definition
for ‘geom_density’
server_normalize : <anonymous>: no visible global function definition
for ‘scale_fill_manual’
server_normalize : <anonymous>: no visible global function definition
for ‘scale_color_manual’
server_normalize : <anonymous> : <anonymous>: no visible global
function definition for ‘plot.new’
server_normalize : <anonymous> : <anonymous>: no visible global
function definition for ‘text’
server_normalize: no visible global function definition for ‘plot.new’
server_normalize: no visible global function definition for ‘text’
server_normalize: no visible global function definition for
‘geom_density’
server_normalize: no visible global function definition for
‘scale_color_manual’
server_normalize : <anonymous>: no visible global function definition
for ‘plot.new’
server_normalize : <anonymous>: no visible global function definition
for ‘text’
server_normalize: no visible global function definition for ‘cor’
server_normalize: no visible binding for global variable ‘Sample1’
server_normalize: no visible binding for global variable ‘Sample2’
server_normalize: no visible binding for global variable ‘Correlation’
server_normalize: no visible global function definition for ‘geom_tile’
server_normalize: no visible global function definition for
‘scale_fill_gradient2’
server_normalize: no visible binding for global variable ‘Before’
server_normalize: no visible binding for global variable ‘After’
server_normalize: no visible global function definition for
‘geom_abline’
server_normalize: no visible global function definition for
‘geom_point’
server_normalize: no visible binding for global variable ‘median’
server_normalize: no visible binding for global variable ‘Sample’
server_normalize: no visible binding for global variable ‘Dataset’
server_normalize: no visible global function definition for ‘density’
server_normalize: no visible binding for global variable ‘x’
server_normalize: no visible binding for global variable ‘y’
server_normalize: no visible global function definition for ‘geom_line’
server_normalize: no visible global function definition for
‘geom_hline’
server_normalize: no visible global function definition for
‘geom_smooth’
server_normalize: no visible binding for global variable ‘Mean’
server_normalize: no visible global function definition for
‘scale_y_log10’
server_normalize: no visible global function definition for
‘scale_x_log10’
server_ppi: no visible global function definition for ‘reactiveValues’
server_ppi: no visible global function definition for ‘keys’
server_ppi: no visible global function definition for
‘updateNumericInput’
server_ppi: no visible global function definition for ‘selectizeInput’
server_ppi : draw_ppi_traditional: no visible global function
definition for ‘par’
server_ppi : draw_ppi_traditional: no visible global function
definition for ‘legend’
server_ppi : draw_ppi_circular: no visible global function definition
for ‘par’
server_ppi : draw_ppi_circular: no visible global function definition
for ‘legend’
server_ppi : make_ppi_ggraph_plot: no visible global function
definition for ‘%>%’
server_ppi : make_ppi_ggraph_plot: no visible binding for global
variable ‘nodes’
server_ppi : make_ppi_ggraph_plot: no visible binding for global
variable ‘degree’
server_ppi : make_ppi_ggraph_plot: no visible binding for global
variable ‘hub_status’
server_ppi : make_ppi_ggraph_plot: no visible binding for global
variable ‘SYMBOL’
server_ppi : draw_ppi_kamada: no visible global function definition for
‘par’
server_ppi : draw_ppi_kamada: no visible global function definition for
‘legend’
server_ppi : draw_ppi_hub_or_other: no visible global function
definition for ‘par’
server_ppi: no visible global function definition for ‘plot.new’
server_ppi: no visible global function definition for ‘text’
server_ppi: no visible global function definition for ‘par’
server_ppi: no visible global function definition for ‘legend’
server_ppi : <anonymous>: no visible global function definition for
‘plot.new’
server_ppi : <anonymous>: no visible global function definition for
‘text’
server_ppi: no visible global function definition for ‘%>%’
server_ppi: no visible binding for global variable ‘nodes’
server_ppi: no visible binding for global variable ‘degree’
server_ppi: no visible binding for global variable ‘hub_status’
server_ppi: no visible binding for global variable ‘SYMBOL’
server_ppi : <anonymous>: no visible global function definition for
‘png’
server_ppi : <anonymous>: no visible global function definition for
‘dev.off’
server_ppi : <anonymous>: no visible global function definition for
‘jpeg’
server_ppi : <anonymous>: no visible global function definition for
‘pdf’
server_ppi : ppi_network_plot_to_file: no visible global function
definition for ‘par’
server_ppi : ppi_network_plot_to_file: no visible global function
definition for ‘legend’
server_ppi : ppi_network_plot_to_file: no visible global function
definition for ‘dev.off’
server_ppi : <anonymous> : <anonymous>: no visible global function
definition for ‘png’
server_ppi : <anonymous> : <anonymous>: no visible global function
definition for ‘jpeg’
server_ppi : <anonymous> : <anonymous>: no visible global function
definition for ‘pdf’
server_ppi: no visible global function definition for ‘setNames’
server_qc : draw_qc_venn_to_dev: no visible global function definition
for ‘plot.new’
server_qc : draw_qc_venn_to_dev: no visible global function definition
for ‘text’
server_qc : draw_qc_venn_to_dev : <anonymous>: no visible global
function definition for ‘plot.new’
server_qc : draw_qc_venn_to_dev : <anonymous>: no visible global
function definition for ‘text’
server_qc : draw_qc_venn_to_dev: no visible global function definition
for ‘venn.diagram’
server_qc : draw_qc_venn_to_dev: no visible global function definition
for ‘grid.draw’
server_qc : draw_qc_upset_to_dev: no visible global function definition
for ‘plot.new’
server_qc : draw_qc_upset_to_dev: no visible global function definition
for ‘text’
server_qc : draw_qc_upset_to_dev : <anonymous>: no visible global
function definition for ‘plot.new’
server_qc : draw_qc_upset_to_dev : <anonymous>: no visible global
function definition for ‘text’
server_qc: no visible binding for global variable ‘Sample’
server_qc: no visible binding for global variable ‘Expression’
server_qc: no visible binding for global variable ‘Platform’
server_qc: no visible global function definition for ‘geom_boxplot’
server_qc : make_qc_pca_plot: no visible binding for global variable
‘PC1’
server_qc : make_qc_pca_plot: no visible binding for global variable
‘PC2’
server_qc : make_qc_pca_plot: no visible binding for global variable
‘Dataset’
server_qc : make_qc_pca_plot: no visible binding for global variable
‘IsOutlier’
server_qc : make_qc_pca_plot: no visible binding for global variable
‘Sample’
server_qc : make_qc_conn_plot: no visible binding for global variable
‘Sample’
server_qc : make_qc_conn_plot: no visible binding for global variable
‘Connectivity’
server_qc : make_qc_conn_plot: no visible binding for global variable
‘IsOutlier’
server_qc : <anonymous>: no visible global function definition for
‘png’
server_qc : <anonymous>: no visible global function definition for
‘dev.off’
server_qc : <anonymous>: no visible global function definition for
‘jpeg’
server_qc : <anonymous>: no visible global function definition for
‘pdf’
server_qc: no visible global function definition for ‘setNames’
server_qc: no visible global function definition for
‘updateCheckboxGroupInput’
server_results: no visible global function definition for
‘model.matrix’
server_results: no visible binding for global variable ‘Disease’
server_results: no visible binding for global variable ‘Normal’
server_results: no visible binding for global variable ‘logFC’
server_results: no visible binding for global variable ‘neg_log10_padj’
server_results: no visible binding for global variable ‘Significance’
server_results: no visible binding for global variable ‘Label’
server_results : <anonymous>: no visible global function definition for
‘plot.new’
server_results : <anonymous>: no visible global function definition for
‘text’
server_results: no visible global function definition for ‘plot.new’
server_results: no visible global function definition for ‘text’
server_results: no visible global function definition for
‘colorRampPalette’
server_results : <anonymous>: no visible binding for global variable
‘logFC’
server_results : <anonymous>: no visible binding for global variable
‘neg_log10_padj’
server_results : <anonymous>: no visible binding for global variable
‘Significance’
server_results : <anonymous>: no visible binding for global variable
‘Label’
server_results : <anonymous>: no visible global function definition for
‘png’
server_results : <anonymous>: no visible global function definition for
‘colorRampPalette’
server_results : <anonymous>: no visible global function definition for
‘dev.off’
server_results : <anonymous>: no visible global function definition for
‘jpeg’
server_results : <anonymous>: no visible global function definition for
‘pdf’
server_results: no visible global function definition for ‘renderDT’
server_results: no visible global function definition for ‘%>%’
server_results: no visible global function definition for ‘datatable’
server_results: no visible global function definition for ‘formatRound’
server_results: no visible global function definition for ‘reactiveVal’
server_results: no visible global function definition for
‘updateActionButton’
server_results_summary: no visible global function definition for
‘plot.new’
server_results_summary: no visible global function definition for
‘text’
server_results_summary: no visible global function definition for ‘par’
server_results_summary: no visible global function definition for
‘prcomp’
server_results_summary: no visible binding for global variable ‘plogis’
server_results_summary: no visible global function definition for
‘title’
server_results_summary : <anonymous>: no visible global function
definition for ‘plot.new’
server_results_summary : <anonymous>: no visible global function
definition for ‘text’
server_results_summary: no visible binding for global variable ‘logFC’
server_results_summary: no visible binding for global variable
‘neg_log10_padj’
server_results_summary: no visible binding for global variable
‘Significance’
server_results_summary: no visible global function definition for
‘colorRampPalette’
server_results_summary: no visible global function definition for
‘as.dendrogram’
server_results_summary : set_edge_par: no visible global function
definition for ‘is.leaf’
server_results_summary: no visible global function definition for
‘dendrapply’
server_results_summary: no visible global function definition for
‘axis’
server_results_summary: no visible binding for global variable
‘Description’
server_results_summary: no visible binding for global variable ‘Count’
server_results_summary: no visible binding for global variable
‘p.adjust’
server_results_summary: no visible global function definition for ‘cor’
server_results_summary : rs_plot_to_file: no visible global function
definition for ‘pdf’
server_results_summary : rs_plot_to_file: no visible global function
definition for ‘jpeg’
server_results_summary : rs_plot_to_file: no visible global function
definition for ‘png’
server_results_summary : rs_plot_to_file: no visible global function
definition for ‘dev.off’
server_results_summary : draw_rs_batch_before_after: no visible global
function definition for ‘plot.new’
server_results_summary : draw_rs_batch_before_after: no visible global
function definition for ‘text’
server_results_summary : draw_rs_batch_before_after: no visible global
function definition for ‘par’
server_results_summary : draw_rs_batch_before_after: no visible global
function definition for ‘prcomp’
server_results_summary : draw_rs_volcano: no visible binding for global
variable ‘logFC’
server_results_summary : draw_rs_volcano: no visible binding for global
variable ‘neg_log10_padj’
server_results_summary : draw_rs_volcano: no visible binding for global
variable ‘Significance’
server_results_summary : draw_rs_de_heatmap: no visible global function
definition for ‘plot.new’
server_results_summary : draw_rs_de_heatmap: no visible global function
definition for ‘text’
server_results_summary : draw_rs_de_heatmap: no visible global function
definition for ‘colorRampPalette’
server_results_summary : draw_rs_soft_threshold: no visible global
function definition for ‘plot.new’
server_results_summary : draw_rs_soft_threshold: no visible global
function definition for ‘text’
server_results_summary : draw_rs_soft_threshold: no visible global
function definition for ‘par’
server_results_summary : draw_rs_sample_tree: no visible global
function definition for ‘plot.new’
server_results_summary : draw_rs_sample_tree: no visible global
function definition for ‘text’
server_results_summary : draw_rs_sample_tree: no visible global
function definition for ‘as.dendrogram’
server_results_summary : draw_rs_sample_tree : set_edge_par: no visible
global function definition for ‘is.leaf’
server_results_summary : draw_rs_sample_tree: no visible global
function definition for ‘dendrapply’
server_results_summary : draw_rs_sample_tree: no visible global
function definition for ‘par’
server_results_summary : draw_rs_sample_tree: no visible global
function definition for ‘axis’
server_results_summary : draw_rs_wgcna_dendro: no visible global
function definition for ‘plot.new’
server_results_summary : draw_rs_wgcna_dendro: no visible global
function definition for ‘text’
server_results_summary : draw_rs_wgcna_dendro: no visible global
function definition for ‘par’
server_results_summary : draw_rs_module_trait: no visible global
function definition for ‘plot.new’
server_results_summary : draw_rs_module_trait: no visible global
function definition for ‘text’
server_results_summary : draw_rs_module_trait: no visible global
function definition for ‘par’
server_results_summary : draw_rs_kegg_plot: no visible binding for
global variable ‘Description’
server_results_summary : draw_rs_kegg_plot: no visible binding for
global variable ‘Count’
server_results_summary : draw_rs_kegg_plot: no visible binding for
global variable ‘p.adjust’
server_results_summary : draw_rs_ppi_plot: no visible global function
definition for ‘plot.new’
server_results_summary : draw_rs_ppi_plot: no visible global function
definition for ‘text’
server_results_summary : draw_rs_ppi_plot: no visible global function
definition for ‘par’
server_results_summary : draw_rs_ml_venn: no visible global function
definition for ‘plot.new’
server_results_summary : draw_rs_ml_venn: no visible global function
definition for ‘text’
server_results_summary : draw_rs_roc_plot: no visible global function
definition for ‘plot.new’
server_results_summary : draw_rs_roc_plot: no visible global function
definition for ‘text’
server_results_summary : draw_rs_nomogram_plot: no visible global
function definition for ‘plot.new’
server_results_summary : draw_rs_nomogram_plot: no visible global
function definition for ‘text’
server_results_summary : draw_rs_nomogram_plot: no visible binding for
global variable ‘plogis’
server_results_summary : draw_rs_nomogram_plot: no visible global
function definition for ‘title’
server_results_summary : draw_rs_gsea_plot: no visible global function
definition for ‘plot.new’
server_results_summary : draw_rs_gsea_plot: no visible global function
definition for ‘text’
server_roc: no visible global function definition for ‘setNames’
server_roc: no visible global function definition for ‘plot.new’
server_roc: no visible global function definition for ‘text’
server_roc: no visible global function definition for ‘par’
server_roc: no visible global function definition for ‘barplot’
server_roc : <anonymous>: no visible global function definition for
‘jpeg’
server_roc : <anonymous>: no visible global function definition for
‘par’
server_roc : <anonymous>: no visible global function definition for
‘barplot’
server_roc : <anonymous>: no visible global function definition for
‘dev.off’
server_roc : <anonymous>: no visible global function definition for
‘pdf’
server_roc: no visible global function definition for ‘glm’
server_roc: no visible global function definition for ‘legend’
server_roc : roc_combined_panel_plot_to_dev: no visible global function
definition for ‘par’
server_roc : roc_combined_panel_plot_to_dev: no visible global function
definition for ‘legend’
server_roc : <anonymous>: no visible global function definition for
‘plot.new’
server_roc : <anonymous>: no visible global function definition for
‘text’
server_roc : <anonymous>: no visible global function definition for
‘legend’
server_roc: no visible binding for global variable ‘Group’
server_roc: no visible binding for global variable ‘Expression’
server_roc : <anonymous>: no visible global function definition for
‘setNames’
server_roc : <anonymous>: no visible binding for global variable
‘Group’
server_roc : <anonymous>: no visible binding for global variable
‘Expression’
server_roc : roc_comparison_plot_fn: no visible binding for global
variable ‘Gene’
server_roc : roc_comparison_plot_fn: no visible binding for global
variable ‘AUC’
server_roc : roc_comparison_plot_fn: no visible binding for global
variable ‘Source’
server_roc : roc_validation_boxplot_fn: no visible global function
definition for ‘setNames’
server_roc : roc_validation_boxplot_fn: no visible binding for global
variable ‘Group’
server_roc : roc_validation_boxplot_fn: no visible binding for global
variable ‘Expression’
server_roc: no visible global function definition for
‘updateCheckboxGroupInput’
server_validation: no visible global function definition for ‘untar’
server_validation : <anonymous>: no visible global function definition
for ‘fetch_geo_series_matrix_metadata’
server_validation: no visible global function definition for
‘model.matrix’
server_validation: no visible binding for global variable ‘Disease’
server_validation: no visible binding for global variable ‘Normal’
server_validation: no visible binding for global variable ‘logFC’
server_validation: no visible binding for global variable
‘neg_log10_padj’
server_validation: no visible binding for global variable
‘Significance’
server_validation: no visible binding for global variable ‘Label’
server_validation : <anonymous>: no visible global function definition
for ‘plot.new’
server_validation : <anonymous>: no visible global function definition
for ‘text’
server_validation : make_volcano_plot: no visible binding for global
variable ‘logFC’
server_validation : make_volcano_plot: no visible binding for global
variable ‘neg_log10_padj’
server_validation : make_volcano_plot: no visible binding for global
variable ‘Significance’
server_validation : make_volcano_plot: no visible binding for global
variable ‘Label’
server_validation: no visible global function definition for
‘updateTabItems’
server_wgcna: no visible global function definition for ‘hclust’
server_wgcna: no visible global function definition for ‘dist’
server_wgcna : get_sample_merge_heights: no visible global function
definition for ‘setNames’
server_wgcna: no visible global function definition for ‘median’
server_wgcna: no visible global function definition for ‘mad’
server_wgcna: no visible global function definition for ‘sd’
server_wgcna : draw_wgcna_sample_tree: no visible global function
definition for ‘as.dendrogram’
server_wgcna : draw_wgcna_sample_tree : set_edge_par: no visible global
function definition for ‘is.leaf’
server_wgcna : draw_wgcna_sample_tree: no visible global function
definition for ‘dendrapply’
server_wgcna : draw_wgcna_sample_tree : set_leaf_par: no visible global
function definition for ‘is.leaf’
server_wgcna : draw_wgcna_sample_tree: no visible global function
definition for ‘par’
server_wgcna : draw_wgcna_sample_tree: no visible global function
definition for ‘title’
server_wgcna : draw_wgcna_sample_tree: no visible global function
definition for ‘mtext’
server_wgcna : draw_wgcna_sample_tree: no visible global function
definition for ‘axis’
server_wgcna: no visible global function definition for
‘updateNumericInput’
server_wgcna : draw_soft_threshold_plot: no visible global function
definition for ‘par’
server_wgcna : draw_soft_threshold_plot: no visible global function
definition for ‘text’
server_wgcna: no visible global function definition for ‘as.dist’
server_wgcna: no visible global function definition for ‘cor’
server_wgcna : draw_wgcna_dendrogram: no visible global function
definition for ‘par’
server_wgcna : draw_wgcna_dendrogram: no visible global function
definition for ‘plot.new’
server_wgcna : draw_wgcna_dendrogram: no visible global function
definition for ‘text’
server_wgcna: no visible global function definition for ‘rnorm’
server_wgcna: no visible global function definition for ‘par’
server_wgcna: no visible global function definition for ‘plot.new’
server_wgcna: no visible global function definition for ‘text’
server_wgcna : wgcna_module_trait_to_file: no visible global function
definition for ‘par’
server_wgcna : wgcna_module_trait_to_file: no visible global function
definition for ‘dev.off’
server_wgcna : <anonymous> : <anonymous>: no visible global function
definition for ‘png’
server_wgcna : <anonymous> : <anonymous>: no visible global function
definition for ‘jpeg’
server_wgcna : <anonymous> : <anonymous>: no visible global function
definition for ‘pdf’
server_wgcna : <anonymous>: no visible global function definition for
‘png’
server_wgcna : <anonymous>: no visible global function definition for
‘dev.off’
server_wgcna : <anonymous>: no visible global function definition for
‘jpeg’
server_wgcna : <anonymous>: no visible global function definition for
‘pdf’
server_wgcna : make_me_correlation_plot: no visible global function
definition for ‘par’
server_wgcna : make_me_correlation_plot: no visible global function
definition for ‘plot.new’
server_wgcna : make_me_correlation_plot: no visible global function
definition for ‘text’
server_wgcna: no visible global function definition for ‘as.dendrogram’
server_wgcna : set_edge_par: no visible global function definition for
‘is.leaf’
server_wgcna: no visible global function definition for ‘dendrapply’
server_wgcna: no visible global function definition for ‘axis’
server_wgcna: no visible global function definition for
‘colorRampPalette’
server_wgcna : draw_me_dendrogram: no visible global function
definition for ‘as.dendrogram’
server_wgcna : draw_me_dendrogram : set_edge_par: no visible global
function definition for ‘is.leaf’
server_wgcna : draw_me_dendrogram: no visible global function
definition for ‘dendrapply’
server_wgcna : draw_me_dendrogram: no visible global function
definition for ‘par’
server_wgcna : draw_me_dendrogram: no visible global function
definition for ‘axis’
server_wgcna : make_me_scatter_plot: no visible binding for global
variable ‘ME1’
server_wgcna : make_me_scatter_plot: no visible binding for global
variable ‘ME2’
server_wgcna : make_me_scatter_plot: no visible global function
definition for ‘geom_point’
server_wgcna : make_me_scatter_plot: no visible global function
definition for ‘element_rect’
server_wgcna : make_eigengene_distance_heatmap: no visible global
function definition for ‘as.dist’
server_wgcna : make_eigengene_distance_heatmap: no visible global
function definition for ‘colorRampPalette’
server_wgcna : make_module_significance_barplot : <anonymous>: no
visible global function definition for ‘colors’
server_wgcna : make_module_significance_barplot: no visible binding for
global variable ‘Module’
server_wgcna : make_module_significance_barplot: no visible global
function definition for ‘geom_rect’
server_wgcna : make_module_significance_barplot: no visible binding for
global variable ‘ymin’
server_wgcna : make_module_significance_barplot: no visible binding for
global variable ‘ymax’
server_wgcna : make_module_significance_barplot: no visible binding for
global variable ‘fill_val’
server_wgcna : make_module_significance_barplot: no visible global
function definition for ‘scale_fill_identity’
server_wgcna : make_module_significance_barplot: no visible global
function definition for ‘geom_hline’
server_wgcna : make_module_significance_barplot: no visible global
function definition for ‘element_rect’
server_wgcna : make_module_size_correlation_plot: no visible binding
for global variable ‘Size’
server_wgcna : make_module_size_correlation_plot: no visible binding
for global variable ‘Correlation’
server_wgcna : make_module_size_correlation_plot: no visible binding
for global variable ‘Direction’
server_wgcna : make_module_size_correlation_plot: no visible global
function definition for ‘geom_point’
server_wgcna : make_module_size_correlation_plot: no visible global
function definition for ‘scale_color_manual’
server_wgcna : make_module_size_correlation_plot: no visible global
function definition for ‘element_rect’
server_wgcna : make_gs_mm_plot: no visible global function definition
for ‘cor’
server_wgcna : make_gs_mm_plot: no visible binding for global variable
‘MM’
server_wgcna : make_gs_mm_plot: no visible binding for global variable
‘GS_trait’
server_wgcna : make_gs_mm_plot: no visible binding for global variable
‘Significant’
server_wgcna: no visible global function definition for ‘title’
server_wgcna : <anonymous>: no visible global function definition for
‘zip’
server_wgcna : <anonymous>: no visible global function definition for
‘par’
server_wgcna: no visible global function definition for ‘tail’
Undefined global functions or variables:
%>% AUC After Before Condition Connectivity Correlation Count Dataset
Description Direction Disease Expression GS_trait Gene Group
IsOutlier Label ME1 ME2 MM Mean Module Normal PC1 PC2 Platform SYMBOL
Sample Sample1 Sample2 Significance Significant Size Source Stage
as.dendrogram as.dist as.formula axis barplot binomial coef
colorRampPalette colors coord_polar cor datatable degree dendrapply
density dev.off dist element_rect facet_wrap
fetch_geo_series_matrix_metadata fill_val formatRound geom_abline
geom_bar geom_boxplot geom_density geom_hline geom_line geom_point
geom_rect geom_smooth geom_tile glm grid.draw hclust hub_status
is.leaf jpeg keys legend logFC mad margin median model.matrix mtext
neg_log10_padj nodes p.adjust par pdf plogis plot.new png prcomp
predict r reactiveVal reactiveValues renderDT rnorm
scale_color_manual scale_fill_gradient2 scale_fill_identity
scale_fill_manual scale_x_continuous scale_x_log10 scale_y_continuous
scale_y_log10 sd selectizeInput setNames tail text theta title untar
updateActionButton updateCheckboxGroupInput updateNumericInput
updateTabItems vcov venn.diagram x y ylim ymax ymin zip
Consider adding
importFrom("grDevices", "colorRampPalette", "colors", "dev.off",
"jpeg", "pdf", "png")
importFrom("graphics", "axis", "barplot", "legend", "mtext", "par",
"plot.new", "text", "title")
importFrom("stats", "as.dendrogram", "as.dist", "as.formula",
"binomial", "coef", "cor", "dendrapply", "density", "dist",
"glm", "hclust", "is.leaf", "mad", "median", "model.matrix",
"p.adjust", "plogis", "prcomp", "predict", "rnorm", "sd",
"setNames", "vcov")
importFrom("utils", "tail", "untar", "zip")
to your NAMESPACE file.
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 files in ‘vignettes’ ... OK
* checking examples ... [7s/7s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [18s/18s]
[18s/18s] 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 ... [5s/5s] OK
* DONE
Status: 2 WARNINGs, 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/4162/a590e6c82ce30ee5ed44f2aea3c5d481f0eb416b/GExPipe.Rcheck/00check.log’
for details.
===============================
BiocCheck('GExPipe_0.99.21.tar.gz')
===============================
── Installing GExPipe ──────────────────────────────────────────────────────────
✔ Package installed successfully
── GExPipe session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp4S89qu/file18ef3f7268a3ab/GExPipe
→ BiocVersion: 3.23
→ Package: GExPipe
→ PackageVersion: 0.99.21
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4162/a590e6c82ce30ee5ed44f2aea3c5d481f0eb416b/GExPipe.BiocCheck
→ BiocCheckVersion: 1.49.21
→ sourceDir: /tmp/Rtmp4S89qu/file18ef3f7268a3ab/GExPipe
→ installDir: /tmp/Rtmp4S89qu/file18ef3f445f55f/lib
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on GExPipe ────────────────────────────────────────────────
* 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...
* 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 for whitespace in DESCRIPTION field names...
* Checking if 'Package:' field matches directory / tarball...
* 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 (22%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
i 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 GExPipe...
* Checking coding practice...
i NOTE: Avoid sapply(); use vapply()
Found in files:
• R/server_groups.R (line 118, column 19)
• ...
• R/server_wgcna.R (line 1588, column 28)
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• server_gsea.R (line 245, column 26)
• ...
• server_wgcna.R (line 536, column 19)
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
• print() in R/server_batch.R (line 482, column 22)
• ...
• print() in R/server_wgcna.R (line 1922, column 26)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
• R/server_wgcna.R (line 890, column 16)
! WARNING: Remove set.seed usage (found 28 times)
• set.seed() in R/server_batch.R (line 866, column 9)
• ...
• set.seed() in R/server_ppi.R (line 1091, column 5)
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid '<<-' if possible (found 8 times)
• <<- in R/server_ppi.R (line 23, column 16)
• ...
• <<- in R/server_results.R (line 12, column 23)
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 38 times)
• suppressWarnings() in R/gexp_download_pipeline.R (line 741, column 69)
• ...
• suppressMessages() in R/server_validation.R (line 238, column 27)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 57
functions greater than 50 lines.
The longest 5 functions are:
• server_wgcna() (R/server_wgcna.R): 2084 lines
• ...
• server_roc() (R/server_roc.R): 1138 lines
* Checking man page documentation...
* 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; 3997 lines (14%) are > 80 characters long.
First few lines:
• R/gexp_batch_pipeline.R#L19 #' @param expr Combined expression matri ...
• ...
• vignettes/GExPipe.Rmd#L538 | **Corporate proxy** | `Sys.setenv(http ...
i NOTE: Consider multiples of 4 spaces for line indents; 13010 lines (45%) are
not.
First few lines:
• R/dummy_imports.R#L6 affy::ReadAffy ...
• ...
• vignettes/GExPipe.Rmd#L515 decreasing = TRUE), ...
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 'gexpipe' is already in your 'Watched Tags' on the Support Site.
── BiocCheck v1.49.21 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 1 WARNINGS | i 10 NOTES
i See the GExPipe.BiocCheck folder and run
`browseVignettes(package = 'BiocCheck')`
for details.