##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:MetaNeighbor.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings MetaNeighbor_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/MetaNeighbor.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    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 ‘MetaNeighbor/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MetaNeighbor’ version ‘1.22.0’
* 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 ‘MetaNeighbor’ 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 R 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
MetaNeighbor : <anonymous>: no visible binding for global variable
  ‘cell_type’
ggPlotHeatmap: no visible binding for global variable ‘target_ct’
ggPlotHeatmap: no visible binding for global variable ‘ref_ct’
ggPlotHeatmap: no visible binding for global variable ‘auroc’
is_reciprocal_top_hit: no visible binding for global variable ‘auroc’
is_reciprocal_top_hit: no visible binding for global variable
  ‘ref_cell_type’
is_reciprocal_top_hit: no visible binding for global variable
  ‘target_cell_type’
is_reciprocal_top_hit: no visible binding for global variable
  ‘reciprocal_cell_type’
is_reciprocal_top_hit: no visible binding for global variable
  ‘is_reciprocal’
plotDotPlot: no visible binding for global variable ‘cluster’
plotDotPlot: no visible binding for global variable ‘gene’
plotDotPlot: no visible binding for global variable ‘cell_type’
plotDotPlot: no visible binding for global variable
  ‘average_expression’
plotDotPlot: no visible binding for global variable
  ‘percent_expressing’
plotMetaClusters: no visible global function definition for
  ‘order_sym_matrix’
topHitsByStudy: no visible binding for global variable ‘ref_cell_type’
topHitsByStudy: no visible binding for global variable
  ‘target_cell_type’
topHitsByStudy: no visible binding for global variable ‘ref_study’
topHitsByStudy: no visible binding for global variable ‘target_study’
topHitsByStudy: no visible binding for global variable ‘.’
topHitsByStudy: no visible binding for global variable ‘pair_id’
topHitsByStudy: no visible binding for global variable ‘is_reciprocal’
topHitsByStudy: no visible global function definition for ‘desc’
topHitsByStudy: no visible binding for global variable ‘Match_type’
variableGenes: no visible binding for global variable ‘gene’
variableGenes: no visible binding for global variable ‘is_hvg’
variableGenes: no visible binding for global variable ‘var_quant’
variableGenes: no visible binding for global variable ‘recurrence’
variableGenes: no visible global function definition for ‘desc’
variableGenes: no visible binding for global variable ‘score’
variable_genes_single_exp: no visible binding for global variable
  ‘bin_med’
variable_genes_single_exp: no visible binding for global variable
  ‘variance’
variable_genes_single_exp: no visible binding for global variable
  ‘var_quant’
Undefined global functions or variables:
  . Match_type auroc average_expression bin_med cell_type cluster desc
  gene is_hvg is_reciprocal order_sym_matrix pair_id percent_expressing
  reciprocal_cell_type recurrence ref_cell_type ref_ct ref_study score
  target_cell_type target_ct target_study var_quant variance
* 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 LazyData ... 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
MetaNeighbor          223.470  1.270 227.137
neighborVoting        213.694  0.436 214.399
plotBPlot             211.329  1.730 212.893
plotHeatmap            21.263  0.100  21.408
MetaNeighborUS         21.267  0.071  21.385
topHitsByStudy         20.897  0.060  21.002
topHits                20.568  0.004  20.608
plotHeatmapPretrained  20.354  0.047  20.440
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/MetaNeighbor.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL MetaNeighbor
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’
* installing *source* package ‘MetaNeighbor’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (MetaNeighbor)

R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(MetaNeighbor)
> 
> test_check("MetaNeighbor")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
> 
> proc.time()
   user  system elapsed 
  0.578   0.076   0.648