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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:broadSeq.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings broadSeq_1.3.3.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/broadSeq.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘broadSeq/DESCRIPTION’ ... OK
* this is package ‘broadSeq’ version ‘1.3.3’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ‘broadSeq’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘BiocStyle’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
genes_plot: warning in facet(facet.by, scale = "fixed"): partial
  argument match of 'scale' to 'scales'
volcanoPlot: warning in ggscatter(x = lFCName, y = "padj", color =
  color, palette = palette, title = "Volcano plot", label = labelName,
  repel = TRUE, label.rectangle = TRUE, show.legend = FALSE,
  label.select = selectedLabel): partial argument match of
  'show.legend' to 'show.legend.text'
assay_plot: no visible global function definition for ‘ggarrange’
assay_plot: no visible global function definition for ‘text_grob’
biplotAnyPC: no visible binding for global variable ‘PC’
biplotAnyPC: no visible binding for global variable ‘var_pct’
biplotAnyPC: no visible global function definition for ‘pull’
biplotAnyPC: no visible binding for global variable ‘gene’
biplotAnyPC: no visible global function definition for ‘aes’
biplotAnyPC: no visible global function definition for ‘arrow’
biplotAnyPC: no visible global function definition for ‘unit’
combinedEnrichment: no visible global function definition for
  ‘keytypes’
extract_topGeneLoadings: no visible global function definition for
  ‘desc’
extract_topGeneLoadings: no visible global function definition for
  ‘all_of’
genes_plot: no visible global function definition for ‘rowData’
normalizeEdgerCPM: no visible global function definition for ‘is’
plotAnyPC: no visible binding for global variable ‘PC’
plotAnyPC: no visible binding for global variable ‘var_pct’
plotHeatmapCluster: no visible global function definition for ‘is’
plotHeatmapCluster: no visible global function definition for ‘colData’
plotHeatmapCluster: no visible global function definition for ‘rowData’
plotHeatmapCluster: no visible global function definition for ‘all_of’
plot_MDS: no visible global function definition for ‘is’
plot_MDS: no visible global function definition for ‘dist’
plot_MDS: no visible global function definition for ‘cmdscale’
plot_MDS: no visible global function definition for ‘colData’
prcompTidy: no visible global function definition for ‘is’
prcompTidy: no visible global function definition for ‘prcomp’
prcompTidy: no visible binding for global variable ‘stdev’
prcompTidy: no visible binding for global variable ‘var’
prcompTidy: no visible binding for global variable ‘var_pct’
prcompTidy: no visible binding for global variable ‘PC’
prcompTidy: no visible binding for global variable ‘.’
prcompTidy: no visible binding for global variable ‘gene’
transformDESeq2: no visible global function definition for ‘is’
transformDESeq2: no visible global function definition for ‘assays<-’
transformDESeq2: no visible global function definition for ‘assay’
use_DELocal: no visible global function definition for ‘desc’
use_DELocal: no visible binding for global variable ‘relative.logFC’
use_EBSeq: no visible binding for global variable ‘RealFC’
use_EBSeq: no visible binding for global variable ‘Status’
use_EBSeq: no visible global function definition for ‘desc’
use_EBSeq: no visible binding for global variable ‘PPDE’
use_NOIseq: no visible global function definition for ‘desc’
use_NOIseq: no visible binding for global variable ‘prob’
use_SAMseq: no visible binding for global variable ‘q-value(%)’
use_deseq2: no visible binding for global variable ‘padj’
use_edgeR: no visible binding for global variable ‘logFC’
use_edgeR: no visible binding for global variable ‘FDR’
use_edgeR: no visible global function definition for ‘:=’
use_limma: no visible global function definition for ‘par’
use_limma: no visible binding for global variable ‘logFC’
use_limma: no visible binding for global variable ‘B’
use_limma: no visible global function definition for ‘:=’
volcanoPlot: no visible global function definition for ‘labs’
volcanoPlot: no visible global function definition for ‘geom_abline’
Undefined global functions or variables:
  . := B FDR PC PPDE RealFC Status aes all_of arrow assay assays<-
  cmdscale colData desc dist gene geom_abline ggarrange is keytypes
  labs logFC padj par prcomp prob pull q-value(%) relative.logFC
  rowData stdev text_grob unit var var_pct
Consider adding
  importFrom("graphics", "par")
  importFrom("methods", "is")
  importFrom("stats", "cmdscale", "dist", "prcomp", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  genes_plot.Rd: SummarizedExperiment, ggboxplot
  normalizeEdgerCPM.Rd: SummarizedExperiment, normLibSizes, cpm
  plotHeatmapCluster.Rd: SummarizedExperiment, pheatmap
  plot_MDS.Rd: SummarizedExperiment, ggscatter
  prcompTidy.Rd: SummarizedExperiment, ggscatter
  sampleAssay_plot.Rd: SummarizedExperiment, ggboxplot
  transformDESeq2.Rd: SummarizedExperiment,
    varianceStabilizingTransformation, normTransform, rlog
  use_DELocal.Rd: SummarizedExperiment, DELocal
  use_EBSeq.Rd: SummarizedExperiment, GetDEResults
  use_NOIseq.Rd: noiseqbio, SummarizedExperiment
  use_SAMseq.Rd: SummarizedExperiment
  use_deseq2.Rd: SummarizedExperiment, results, DESeqResults
  use_edgeR.Rd: SummarizedExperiment, glmLRT, exactTest, topTags
  use_limma.Rd: SummarizedExperiment
  use_multDE.Rd: SummarizedExperiment
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from Rd file 'volcanoPlot.Rd':
volcanoPlot
  Code: function(df, pValName, lFCName, color = NULL, sigThreshold =
                 0.05, logFCThreshold = 1, labelName = NULL,
                 selectedLabel = NULL, palette = "nejm")
  Docs: function(df, pValName, lFCName, sigThreshold = 0.05,
                 logFCThreshold = 1, labelName = NULL, selectedLabel =
                 NULL, palette = "nejm")
  Argument names in code not in docs:
    color
  Mismatches in argument names (first 3):
    Position: 4 Code: color Docs: sigThreshold
    Position: 5 Code: sigThreshold Docs: logFCThreshold
    Position: 6 Code: logFCThreshold Docs: labelName

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
sampleAssay_plot 8.791  0.147   8.939
use_multDE       7.960  0.092   8.044
transformDESeq2  5.112  0.030   5.143
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/broadSeq.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL broadSeq
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘broadSeq’ ...
** this is package ‘broadSeq’ version ‘1.3.3’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (broadSeq)