##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:miaViz.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings miaViz_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/miaViz.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* 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 for sufficient/correct file permissions ... 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 loading without being on the library search path ... 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       91.047  0.647  91.913
plotDMN        29.301  0.080  29.436
plotAbundance  16.684  0.375  17.577
plotPrevalence 10.976  0.060  11.088
plotCCA         7.007  0.076   6.930
plotLoadings    5.963  0.183   6.160
* 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
  ‘/home/biocbuild/bbs-3.20-bioc/meat/miaViz.Rcheck/00check.log’
for details.