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### 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_2.18.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/FlowSOM.Rcheck’
* using R version 4.5.2 (2025-10-31)
* 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 ‘2.18.0’
* 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: ‘MacOSX11.3.1.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                       97.508  2.519 103.593
PlotDimRed                        73.953  3.015  79.461
PlotOutliers                      69.309  1.077  74.264
PlotMarker                        37.429  1.384  40.605
UpdateMetaclusters                34.958  1.318  38.228
PlotStars                         29.789  1.151  32.065
GroupStats                        27.198  1.140  29.660
PlotGroups                        23.350  1.435  25.376
FlowSOM                           23.233  1.489  25.591
Plot2DScatters                    20.729  1.125  22.391
QueryMultiple                     20.478  0.597  21.541
query_multiple                    20.091  0.573  21.121
PlotManualBars                    17.992  1.094  19.988
AddAnnotation                     17.850  0.987  19.079
QueryStarPlot                     14.895  0.457  15.918
GetFlowJoLabels                   14.054  0.835  15.430
PlotNode                          13.664  1.034  14.860
PlotNumbers                       13.438  0.983  14.654
UpdateNodeSize                    13.448  0.283  14.422
PlotPies                          12.754  0.973  13.891
PlotVariable                      12.552  0.988  13.714
GetFeatures                       11.698  0.764  12.610
CountGroups                       11.418  0.726  12.534
PlotFlowSOM                       10.744  0.961  11.855
SaveClustersToFCS                 10.177  0.950  12.179
PlotLabels                         9.838  0.755  11.015
MetaclusterMFIs                    9.570  0.994  10.844
NClusters                          9.456  0.921  10.776
NMetaclusters                      9.250  1.099  10.699
TestOutliers                       8.869  0.732  10.598
PlotOverview2D                     8.425  0.782   9.306
GetMetaclusters                    8.370  0.706   9.356
FlowSOMSubset                      8.348  0.722   9.260
GetMetaclusterPercentagesPositive  8.107  0.863   9.358
GetMetaclusterCVs                  8.043  0.892   9.047
MetaclusterCVs                     8.041  0.892   9.328
GetMetaclusterMFIs                 8.087  0.827   9.287
print.FlowSOM                      8.061  0.825   9.736
GetPercentages                     7.959  0.783   9.237
GetMFIs                            7.862  0.786   8.778
GetClusterPercentagesPositive      7.786  0.695   8.683
GetCounts                          7.722  0.686   8.472
NewData                            7.714  0.639   8.665
GetClusterMFIs                     7.731  0.572   9.010
GetClusters                        7.741  0.553   8.726
MetaClustering                     6.420  0.702   7.284
ReadInput                          6.521  0.489   7.420
metaClustering_consensus           5.222  0.452   6.129
* 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-3.22-bioc/meat/FlowSOM.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL FlowSOM
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘FlowSOM’ ...
** this is package ‘FlowSOM’ version ‘2.18.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.1.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c som.c -o som.o
clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o FlowSOM.so som.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-FlowSOM/00new/FlowSOM/libs
** R
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (FlowSOM)