##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MetaNeighbor.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings MetaNeighbor_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/MetaNeighbor.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MetaNeighbor/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MetaNeighbor' version '1.12.0'
* 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 whether package 'MetaNeighbor' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   7.1Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... 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 ... WARNING
  LazyData DB of 7.1 MB without LazyDataCompression set
  See §1.1.6 of 'Writing R Extensions'
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
MetaNeighbor   24.24   1.32   25.56
plotBPlot      15.70   0.65   16.36
neighborVoting 15.25   0.52   15.77
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
MetaNeighbor   17.88   0.47   18.34
neighborVoting 11.27   0.50   11.77
plotBPlot      10.67   0.44   11.11
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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 WARNING, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/MetaNeighbor.Rcheck/00check.log'
for details.