##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings FlowSOM_2.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/FlowSOM.Rcheck’
* using R Under development (unstable) (2025-03-02 r87868)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FlowSOM/DESCRIPTION’ ... OK
* this is package ‘FlowSOM’ version ‘2.15.0’
* 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 ‘FlowSOM’ can be installed ... OK
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 whether startup messages can be suppressed ... 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 ... OK
* checking Rd files ... NOTE
checkRd: (-1) PlotDimRed.Rd:55: Lost braces
    55 | of the dimred default = function(dimred){dimred$Y}.}
       |                                         ^
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Non-topic package-anchored link(s) in Rd file 'pipe.Rd':
  ‘[magrittr:pipe]{%>%}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
FlowSOMmary        48.641  2.130  51.045
PlotDimRed         42.765  2.658  46.077
PlotOutliers       21.369  0.966  22.732
UpdateMetaclusters 17.037  1.400  18.705
PlotMarker         16.822  1.112  18.083
PlotStars          14.934  1.018  16.143
PlotGroups         12.579  1.053  13.836
GroupStats         12.103  0.830  13.027
FlowSOM            11.523  0.936  12.570
Plot2DScatters      9.193  0.675  10.003
query_multiple      9.255  0.448   9.819
AddAnnotation       9.097  0.588   9.772
QueryMultiple       9.178  0.414   9.716
PlotManualBars      7.790  0.780   8.659
PlotNumbers         7.740  0.813   8.713
PlotNode            7.546  0.758   8.410
GetFlowJoLabels     7.361  0.586   8.027
PlotVariable        6.693  0.713   7.497
QueryStarPlot       6.937  0.375   7.419
PlotPies            6.278  0.766   7.166
PlotFlowSOM         6.223  0.701   7.025
NClusters           5.748  0.799   6.644
UpdateNodeSize      6.177  0.248   6.491
NMetaclusters       5.706  0.682   6.486
PlotLabels          5.708  0.669   6.488
CountGroups         5.734  0.595   6.420
TestOutliers        5.347  0.724   6.184
SaveClustersToFCS   5.129  0.765   5.994
MetaclusterMFIs     5.022  0.773   5.873
GetMetaclusterCVs   4.960  0.633   5.692
PlotOverview2D      4.581  0.572   5.230
GetFeatures         4.757  0.385   5.180
GetPercentages      4.351  0.696   5.101
print.FlowSOM       4.397  0.617   5.081
MetaclusterCVs      4.393  0.616   5.060
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/FlowSOM.Rcheck/00check.log’
for details.