##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:miaViz.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings miaViz_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/miaViz.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'miaViz/DESCRIPTION' ... OK
* this is package 'miaViz' version '1.14.0'
* 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 whether package 'miaViz' 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 dependencies in R code ... NOTE
Namespace in Imports field not imported from: 'purrr'
  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
.add_signif_to_vector_labels : <anonymous>: no visible global function
  definition for 'italic'
.calculate_max_and_min_for_loadings: no visible binding for global
  variable 'PC'
.calculate_max_and_min_for_loadings: no visible binding for global
  variable 'Value'
.get_prevalence_plot_matrix: no visible binding for global variable
  'ID'
.get_series_data: no visible global function definition for 'rowData<-'
.get_series_data: no visible binding for global variable 'Y'
.incorporate_rda_vis: no visible global function definition for
  'scores'
.plot_bar_or_lollipop: no visible binding for global variable 'Sign'
.plot_bar_or_lollipop: no visible binding for global variable
  'max_scale_abs'
.plot_bar_or_lollipop: no visible binding for global variable
  'max_scale'
.plot_loadings: no visible binding for global variable 'PC'
.plot_loadings: no visible binding for global variable 'Feature'
.plot_loadings: no visible binding for global variable 'Value'
.rda_plotter: no visible binding for global variable 'color'
.rda_plotter: no visible binding for global variable 'x'
.rda_plotter: no visible binding for global variable 'y'
.remove_taxonomic_level_from_labels: no visible binding for global
  variable 'TAXONOMY_RANKS'
plotLoadings,SingleCellExperiment: no visible global function
  definition for 'reducedDims'
plotLoadings,TreeSummarizedExperiment: no visible global function
  definition for 'reducedDims'
Undefined global functions or variables:
  Feature ID PC Sign TAXONOMY_RANKS Value Y color italic max_scale
  max_scale_abs reducedDims rowData<- scores x y
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
plotTree       72.43   2.63   75.14
plotDMN        23.59   0.00   24.15
plotAbundance  14.12   1.02   14.12
plotPrevalence 10.42   0.22   10.67
plotLoadings    5.06   0.45    5.50
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  'F:/biocbuild/bbs-3.20-bioc/meat/miaViz.Rcheck/00check.log'
for details.